Infectious Diseases

Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Biomedicines biomedicines	3.9	5.2	2013	15.3 Days	CHF 2600
Viruses viruses	3.8	7.3	2009	16.1 Days	CHF 2600
Journal of Fungi jof	4.2	6.7	2015	17.1 Days	CHF 2600
Microorganisms microorganisms	4.1	7.4	2013	13.4 Days	CHF 2700
Journal of Clinical Medicine jcm	3.0	5.7	2012	17.3 Days	CHF 2600

2 pages, 189 KiB

Open AccessReply

Reply to Daitch et al. Comment on “Huang et al. Colistin Monotherapy versus Colistin plus Meropenem Combination Therapy for the Treatment of Multidrug-Resistant Acinetobacter baumannii Infection: A Meta-Analysis. J. Clin. Med. 2022, 11, 3239”

by Chienhsiu Huang, Ihung Chen and Tiju Tang

J. Clin. Med. 2022, 11(24), 7508; https://doi.org/10.3390/jcm11247508 - 19 Dec 2022

Viewed by 883

Abstract

This is an Author Reply to the Letter to the Editor entitled “Colistin Monotherapy versus Colistin plus Meropenem Combination Therapy for the Treatment of Multidrug-Resistant Acinetobacter baumannii Infection: A Meta-Analysis” by Daitch V. et al. [...] Full article

(This article belongs to the Topic Infectious Diseases)

2 pages, 187 KiB

Open AccessComment

Comment on Huang et al. Colistin Monotherapy versus Colistin plus Meropenem Combination Therapy for the Treatment of Multidrug-Resistant Acinetobacter baumannii Infection: A Meta-Analysis. J. Clin. Med. 2022, 11, 3239

by Vered Daitch, Mical Paul and Leonard Leibovici

J. Clin. Med. 2022, 11(23), 7029; https://doi.org/10.3390/jcm11237029 - 28 Nov 2022

Cited by 1 | Viewed by 1097

Abstract

In the recently published meta-analysis titled “Colistin Monotherapy versus Colistin plus Meropenem Combination Therapy for the Treatment of Multidrug-Resistant Acinetobacter baumannii Infection: A Meta-Analysis”, Huang et al. compared the efficacy and safety of treatment with colistin monotherapy versus colistin plus meropenem combination therapy [...] Read more.

In the recently published meta-analysis titled “Colistin Monotherapy versus Colistin plus Meropenem Combination Therapy for the Treatment of Multidrug-Resistant Acinetobacter baumannii Infection: A Meta-Analysis”, Huang et al. compared the efficacy and safety of treatment with colistin monotherapy versus colistin plus meropenem combination therapy in patients with drug-resistant Acinetobacter baumannii infection [...] Full article

(This article belongs to the Topic Infectious Diseases)

8 pages, 544 KiB

Open AccessArticle

Remdesivir Treatment in Moderately Ill COVID-19 Patients: A Retrospective Single Center Study

by Vedrana Terkes, Karla Lisica, Martina Marusic, Nikola Verunica, Anela Tolic and Miro Morovic

J. Clin. Med. 2022, 11(17), 5066; https://doi.org/10.3390/jcm11175066 - 29 Aug 2022

Cited by 5 | Viewed by 1482

Abstract

Almost two years after remdesivir was approved and extensively used in numerous clinical studies for the treatment of COVID-19 patients, there is still no clear recommendation for the time and phase of the disease of remdesivir administration. This retrospective observational study included adults [...] Read more.

Almost two years after remdesivir was approved and extensively used in numerous clinical studies for the treatment of COVID-19 patients, there is still no clear recommendation for the time and phase of the disease of remdesivir administration. This retrospective observational study included adults (≥18 years) with severe COVID-19, radiologically confirmed pneumonia, a need for supplemental oxygen and an interval from symptom onset to enrolment of 10 days or less. All patients were treated with remdesivir for 5 to 10 days, or with clinical improvement within that period. The primary goal was the outcome in patients treated with remdesivir during the early stage of the disease considering the different disease severity. The median time from symptom onset to treatment was 8.4 days (3–10). Clinical improvements and good outcomes were observed in 104 of 137 patients (75.9%); 33 (24.1%) of 137 patients died. Subgroup analyses showed that the mortality rate was significantly lower in moderately ill patients (3 out of 51 patients; 5.9%) than in the group of severely/critically ill patients (30 out of 86 patients; 34.8%; p < 0.005). Older age, rise of CRP and CT score were shown to be significant predictors of disease outcome. Overall, remdesivir was well tolerated, and the treatment was discontinued in only four patients. The results of this observational study in 137 patients with different disease severity contribute to the attitude concerning remdesivir administration in the early stage of COVID-19, at least in moderately ill patients with a high risk of progression, before the transition to a more severe stage. Full article

(This article belongs to the Topic Infectious Diseases)

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17 pages, 668 KiB

Open AccessReview

Pitfalls in the Serological Evaluation of Maternal Cytomegalovirus Infection as a Potential Cause of Fetal and Neonatal Involvements: A Narrative Literature Review

by Shigeo Iijima

J. Clin. Med. 2022, 11(17), 5006; https://doi.org/10.3390/jcm11175006 - 26 Aug 2022

Cited by 6 | Viewed by 10062

Abstract

Cytomegalovirus (CMV) is the most common cause of intrauterine infection and serological assays are the primary tools for assessing CMV infections during pregnancy. CMV-specific immunoglobulin M (IgM) antibodies have been used as a diagnostic marker for primary CMV infection in pregnant women, although [...] Read more.

Cytomegalovirus (CMV) is the most common cause of intrauterine infection and serological assays are the primary tools for assessing CMV infections during pregnancy. CMV-specific immunoglobulin M (IgM) antibodies have been used as a diagnostic marker for primary CMV infection in pregnant women, although CMV-IgM has been detected in non-primary CMV infections. IgG avidity testing may aid the distinguishing of primary from non-primary CMV infection; however, there is no standardized assay for detecting this difference. Moreover, when maternal serology shows positive CMV-IgG with negative CMV-IgM findings, vertical transmission probability following primary CMV infection is often excluded. However, symptomatic congenital CMV infections in the context of negative findings for maternal CMV-IgM have been reported recently. The absence of CMV-IgM is recognized in both primary and non-primary CMV infections. Furthermore, maternal non-primary CMV infections during pregnancy may yield a greater proportion of symptomatic congenital CMV infections than previously thought. If universal prenatal screening is performed, ultrasonography for abnormal fetal findings should be conducted regardless of CMV-IgM antibody status. If not universally screened, CMV antibody screening should be performed whenever routine fetal ultrasound reveals abnormal findings. For suspected fetal CMV infection, amniotic fluid or postnatal infant urine CMV-DNA testing is required. Full article

(This article belongs to the Topic Infectious Diseases)

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1 pages, 180 KiB

Open AccessReply

Reply to Fabbris et al. A Viable Alternative. Comment on “Kohmer et al. Self-Collected Samples to Detect SARS-CoV-2: Direct Comparison of Saliva, Tongue Swab, Nasal Swab, Chewed Cotton Pads and Gargle Lavage. J. Clin. Med. 2021, 10, 5751”

by Sebastian Hoehl, Niko Kohmer, Lisa Eckermann, Rene Gottschalk and Sandra Ciesek

J. Clin. Med. 2022, 11(16), 4920; https://doi.org/10.3390/jcm11164920 - 22 Aug 2022

Viewed by 997

Abstract

We thank Fabbris et al. for their remarks [...] Full article

(This article belongs to the Topic Infectious Diseases)

15 pages, 4048 KiB

Open AccessArticle

Persisting Smell and Taste Disorders in Patients Who Recovered from SARS-CoV-2 Virus Infection—Data from the Polish PoLoCOV-CVD Study

by Michał Chudzik, Mateusz Babicki, Agnieszka Mastalerz-Migas and Joanna Kapusta

Viruses 2022, 14(8), 1763; https://doi.org/10.3390/v14081763 - 12 Aug 2022

Cited by 9 | Viewed by 2152

Abstract

In the majority of cases, patients infected with the SARS-CoV-2 virus experience a complete resolution of symptoms within six weeks of acquiring the infection, but an increasing number of patients report persistent symptoms. This study aimed to analyse the prevalence of self-reported smell [...] Read more.

In the majority of cases, patients infected with the SARS-CoV-2 virus experience a complete resolution of symptoms within six weeks of acquiring the infection, but an increasing number of patients report persistent symptoms. This study aimed to analyse the prevalence of self-reported smell and/or taste disorders (STDs) in a group of convalescent patients after infection with the SARS-CoV-2 virus and to identify risk factors for the disease. The study included 2218 COVID-19 convalescents after both inpatient and outpatient treatment. The sample group was analysed with regard to chronic diseases, place of isolation and clinical symptoms occurring during COVID-19 along with their duration. The assessment also included the most common symptoms of COVID-19 and the severity of the disease course. A total of 98 patients reported persistent smell and taste disorders up to three months after the end of isolation (67.4% of men and 32.6% of women). The mean age of the participants was 53.8 ± 13.5 years (49.19 ± 14.68 in patients with an STD vs. 54.01 ± 13.44 in patients without an STD). The patients treated for COVID-19 at home (p < 0.001) constituted almost the entire group of patients with persistent smell and taste disorders (97%). Among the patients with persistent smell and taste disorders, 57.1% suffered from at least one chronic condition (vs. 71.4% of patients without an STD). In patients with an STD, the number of symptoms per patient was higher than in the other group at 8.87 ± 3.65 (p = 0.018), while the most common clinical symptoms during the acute phase of COVID-19 were smell and taste disorders (84%) (p < 0.001), significant weakness (70%), headache (60%), cough (55%), arthralgia (51%) (p = 0.034) and back muscle pain (51%). Based on the results obtained, the following conclusions were drawn: the risk of developing persistent smell and taste disorders after COVID-19 is greater in younger people with less comorbidities and a higher number of symptoms during the acute phase of COVID-19. The risk is associated with clinical symptoms occurring during the acute phase of COVID-19, i.e., smell and taste disorders and arthralgia. In addition, this risk is higher in patients receiving outpatient treatment for COVID-19. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 1568 KiB

Open AccessReview

What Is Currently Known about Intramedullary Spinal Cord Abscess among Children? A Concise Review

by Bartosz Szmyd, Redwan Jabbar, Weronika Lusa, Filip Franciszek Karuga, Agnieszka Pawełczyk, Maciej Błaszczyk, Jakub Jankowski, Julia Sołek, Grzegorz Wysiadecki, R. Shane Tubbs, Joe Iwanaga and Maciej Radek

J. Clin. Med. 2022, 11(15), 4549; https://doi.org/10.3390/jcm11154549 - 4 Aug 2022

Cited by 3 | Viewed by 2697

Abstract

Intramedullary spinal cord abscesses (ISCA) are rare. Typical symptoms include signs of infection and neurological deficits. Symptoms among (younger) children can be highly uncharacteristic. Therefore, prompt and proper diagnoses may be difficult. Typical therapeutic options include antibiotics and neurosurgical exploration and drainage. In [...] Read more.

Intramedullary spinal cord abscesses (ISCA) are rare. Typical symptoms include signs of infection and neurological deficits. Symptoms among (younger) children can be highly uncharacteristic. Therefore, prompt and proper diagnoses may be difficult. Typical therapeutic options include antibiotics and neurosurgical exploration and drainage. In this review, we analyze published cases of ISCA among children. Most pediatric cases were found to be under the age of 6 years. The typical symptoms included motor deficits in 89.06%, infection signs in 85.94%, and sensory deficits in 39.06%. Urinary dysfunction was observed in 43.75%, and bowel dysfunction in 17.19%. The predisposing factors included dermal sinuses, (epi)dermoid cysts, prior infection, iatrogenic disorder, and trauma. The most common pathogens were: Staphylococcus aureus, Mycobacterium tuberculosis, Escherichia coli, and Proteus mirabilis. The pediatric population has good outcomes as 45.93% of patients had complete neurological recovery and only 26.56% had residual neurological deficits. Fifteen (23.44%) had persistent neurological deficits. Only one (1.56%) patient died with an ISCA. In two (3.13%) cases, there were no details about follow-up examinations. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 1227 KiB

Open AccessArticle

Correlating IgG Levels with Neutralising Antibody Levels to Indicate Clinical Protection in Healthcare Workers at Risk during a Measles Outbreak

by Siyuan Hu, Nicola Logan, Sarah Coleman, Cariad Evans, Brian J. Willett and Margaret J. Hosie

Viruses 2022, 14(8), 1716; https://doi.org/10.3390/v14081716 - 4 Aug 2022

Cited by 3 | Viewed by 2118

Abstract

The rapid transmission of measles poses a great challenge for measles elimination. Thus, rapid testing is required to screen the health status in the population during measles outbreaks. A pseudotype-based virus neutralisation assay was used to measure neutralising antibody titres in serum samples [...] Read more.

The rapid transmission of measles poses a great challenge for measles elimination. Thus, rapid testing is required to screen the health status in the population during measles outbreaks. A pseudotype-based virus neutralisation assay was used to measure neutralising antibody titres in serum samples collected from healthcare workers in Sheffield during the measles outbreak in 2016. Vesicular stomatitis virus (VSV) pseudotypes bearing the haemagglutinin and fusion glycoproteins of measles virus (MeV) and carrying a luciferase marker gene were prepared; the neutralising antibody titre was defined as the dilution resulting in 90% reduction in luciferase activity. Spearman’s correlation coefficients between IgG titres and neutralising antibody levels ranged from 0.40 to 0.55 (p < 0.05) or from 0.71 to 0.79 (p < 0.0001) when the IgG titres were obtained using different testing kits. In addition, the currently used vaccine was observed to cross-neutralise most circulating MeV genotypes. However, the percentage of individuals being “well-protected” was lower than 95%, the target rate of vaccination coverage to eliminate measles. These results demonstrate that the level of clinical protection against measles in individuals could be inferred by IgG titre, as long as a precise correlation has been established between IgG testing and neutralisation assay; moreover, maintaining a high vaccination coverage rate is still necessary for measles elimination. Full article

(This article belongs to the Topic Infectious Diseases)

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2 pages, 190 KiB

Open AccessComment

A Viable Alternative. Comment on Kohmer et al. Self-Collected Samples to Detect SARS-CoV-2: Direct Comparison of Saliva, Tongue Swab, Nasal Swab, Chewed Cotton Pads and Gargle Lavage. J. Clin. Med. 2021, 10, 5751

by Cristoforo Fabbris, Riccardo Camerotto, Veronica Battistuzzi and Giacomo Spinato

J. Clin. Med. 2022, 11(15), 4501; https://doi.org/10.3390/jcm11154501 - 2 Aug 2022

Cited by 1 | Viewed by 1092

Abstract

We read with great interest and would like to comment on the article “Self-Collected Samples to Detect SARS-CoV-2: Direct Comparison of Saliva, Tongue Swab, Nasal Swab, Chewed Cotton Pads and Gargle Lavage” [...] Full article

(This article belongs to the Topic Infectious Diseases)

8 pages, 1195 KiB

Open AccessArticle

Characteristics of Computed Tomography for Identifying Patients at High Risk of Endogenous Endophthalmitis Due to Klebsiella pneumoniae-Related Pyogenic Liver Abscess

by Jae Jung Lee, Seung Baek Hong, Nam Kyung Lee, Young Joo Park, So Hee Kim, Sung Who Park, Iksoo Byon and Suk Kim

J. Clin. Med. 2022, 11(15), 4376; https://doi.org/10.3390/jcm11154376 - 28 Jul 2022

Cited by 4 | Viewed by 1693

Abstract

Endogenous endophthalmitis (EE) associated with Klebsiella pneumoniae (K. pneumoniae)-related pyogenic liver abscess (PLA) is one of the fatal complications of PLA and leads to loss of vision. Early diagnosis and treatment are important to save the patient’s vision. We investigated the [...] Read more.

Endogenous endophthalmitis (EE) associated with Klebsiella pneumoniae (K. pneumoniae)-related pyogenic liver abscess (PLA) is one of the fatal complications of PLA and leads to loss of vision. Early diagnosis and treatment are important to save the patient’s vision. We investigated the characteristics of computed tomography (CT) in EE associated with K. pneumoniae-related PLA for the identification of the predictors of EE, in order to facilitate early diagnosis. A total of 274 patients diagnosed with K. pneumoniae-related PLA, including 15 patients with EE, were identified between January 2005 and December 2019. The clinical (age, gender, and underlying disease) and radiologic (the location, size, and number of abscesses) features were reviewed. In addition, the involvement of the adjacent vessels, such as the hepatic vein and portal vein, was carefully reviewed. A comparative analysis was performed between the EE and non-EE groups. Uni- and multivariate logistic regression analyses were used to identify the predictors of EE. Diabetes mellitus (DM), the involvement of the left or both hepatic lobes, and the adjacent vessels on the CT were significantly more frequent than those in the non-EE group (p < 0.05 in all), and they were the significant predictors of EE in the logistic regression analyses. In patients with K. pneumoniae-related PLA, the CT findings, such as the locations of the abscess (i.e., left or both lobes) and the involvement of the adjacent vessels, should be considered in addition to the ocular symptoms for an early diagnosis of EE. Full article

(This article belongs to the Topic Infectious Diseases)

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Flow diagram of the inclusion and exclusion criteria. Full article ">Figure 2
Representative images of a 59-year-old woman with diabetes mellitus who presented with endogenous endophthalmitis due to Klebsiella pneumoniae-related pyogenic liver abscess. (A) A contrast-enhanced computed tomography (CT) image showed a 7.5 cm septated cystic lesion, representing a Klebsiella hepatic abscess, at liver segment IV. The CT image also showed thrombophlebitis on the adjacent hepatic vein due to direct invasion from the hepatic abscess (arrow). (B) Hyperemia and a 2 mm hypopyon in the anterior chamber were observed in the slit-lamp examination. (C) A whitish mass-like lesion, a suspected subretinal abscess, was noticed on wide fundus photograph. Both the slit-lamp examination and the fundus photograph indicated signs of endophthalmitis. Full article ">Figure 3
Representative images of an 87-year-old man with diabetes mellitus who presented endogenous endophthalmitis due to Klebsiella pneumoniae-related pyogenic liver abscess. (A) This patient had biliary cirrhosis due to recurrent pyogenic cholangitis and underwent contrast computed tomography (CT) examination. The CT image showed a 6.8 cm septated cystic lesion, representing a Klebsiella hepatic abscess, at liver segments II and IV. The CT image also showed the hepatic abscess with invasion from the adjacent hepatic vein (arrow). (B) Severe corneal edema and anterior chamber haziness were noted during an initial slit-lamp examination without history of previous ocular surgery. (C) Despite aggressive treatment, his eye developed phthisis. Full article ">

14 pages, 4145 KiB

Open AccessReview

Doripenem in the Treatment of Patients with Nosocomial Pneumonia: A Meta-Analysis

by Chienhsiu Huang, Ihung Chen and Yalun Yang

J. Clin. Med. 2022, 11(14), 4014; https://doi.org/10.3390/jcm11144014 - 11 Jul 2022

Cited by 3 | Viewed by 2230

Abstract

Introduction: Clinically, doripenem therapy for nosocomial pneumonia remains a serious concern. The purpose of this meta-analysis was to explore the efficacy and the safety of doripenem therapy for nosocomial pneumonia in comparison with other antimicrobial agents. Methods: Studies were eligible for inclusion only [...] Read more.

Introduction: Clinically, doripenem therapy for nosocomial pneumonia remains a serious concern. The purpose of this meta-analysis was to explore the efficacy and the safety of doripenem therapy for nosocomial pneumonia in comparison with other antimicrobial agents. Methods: Studies were eligible for inclusion only if they directly compared the clinical effectiveness of doripenem and other antimicrobial agent therapies for nosocomial pneumonia in adult patients between 1 January 2000 and 30 April 2022. All studies were included if they reported one or more of the following outcomes: clinical cure rate, microbiological cure rate, all-cause mortality, and adverse events. Results: Six randomized controlled trials and three retrospective studies were included in the meta-analysis. There were 952 patients in the doripenem group and 1183 patients in the comparator group. The comparator antimicrobial agents included imipenem/cilastatin, meropenem, and piperacillin/tazobactam. Seven studies had a high risk of bias. Doripenem therapy for nosocomial pneumonia had a microbiological cure rate, a clinical cure rate, an all-cause mortality, and adverse events similar to those of comparators. Conclusions: The efficacy and the safety of doripenem therapy for nosocomial pneumonia were comparable with those of comparators. Randomized controlled trials are needed to confirm the role of doripenem in nosocomial pneumonia therapy. Full article

(This article belongs to the Topic Infectious Diseases)

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13 pages, 610 KiB

Open AccessArticle

Impact of Chronic Bronchial Infection by Staphylococcus aureus on Bronchiectasis

by Marta García Clemente, Casilda Olveira, Rosa Girón, Luis Máiz, Oriol Sibila, Rafael Golpe, Rosario Menéndez, Juan Rodríguez, Esther Barreiro, Juan Luis Rodríguez Hermosa, Concepción Prados, David De la Rosa, Claudia Madrid Carbajal, Marta Solís and Miguel Ángel Martínez-García

J. Clin. Med. 2022, 11(14), 3960; https://doi.org/10.3390/jcm11143960 - 7 Jul 2022

Cited by 8 | Viewed by 1756

Abstract

The objective of the study was to analyze the factors associated with chronic bronchial infection (CBI) due to methicillin-susceptible Staphylococcus aureus (SA) and assess the clinical impact on severity, exacerbations, hospitalizations, and loss of lung function compared to patients with no isolation of [...] Read more.

The objective of the study was to analyze the factors associated with chronic bronchial infection (CBI) due to methicillin-susceptible Staphylococcus aureus (SA) and assess the clinical impact on severity, exacerbations, hospitalizations, and loss of lung function compared to patients with no isolation of PPMs in a large longitudinal series of patients from the Spanish bronchiectasis registry (RIBRON). Material and methods: A prospective, longitudinal, multicenter study was conducted with patients included in the RIBRON registry between January 2015 and October 2020. The inclusion criteria were an age of 18 years or older and an initial diagnosis of bronchiectasis. Patients recorded in the registry had a situation of clinical stability in the absence of an exacerbation in the four weeks before their inclusion. All patients were encouraged to provide a sputum sample at each visit for microbiological culture. Annual pulmonary function tests were performed according to the national spirometry guidelines. Results: A total of 426 patients were ultimately included in the study: 77 patients (18%) with CBI due to SA and 349 (82%) who did not present any isolation of PPMs in sputum. The mean age was 66.9 years (16.2), and patients 297 (69.7%) were female, with an average BMI of 25.1 (4.7) kg/m² and an average Charlson index of 1.74 (1.33). The mean baseline value of FEV1 2 L was 0.76, with a mean FEV1% of 78.8% (23.1). One hundred and seventy-two patients (40.4%) had airflow obstruction with FEV1/FVC < 0.7. The mean predictive FACED score was 1.62 (1.41), with a mean value of 2.62 (2.07) for the EFACED score and 7.3 (4.5) for the BSI score. Patients with CBI caused by SA were younger (p < 0.0001), and they had a lower BMI (p = 0.024) and more exacerbations in the previous year (p = 0.019), as well as in the first, second, and third years of follow-up (p = 0.020, p = 0.001, and p = 0.018, respectively). As regards lung function, patients with CBI due to SA had lower levels of FEV1% at the time of inclusion in the registry (p = 0.021), and they presented more frequently with bronchial obstruction (p = 0.042). A lower age (OR: 0.97; 95% CI: 0.94–0.99; p < 0.001), lower FEV1 value% (OR: 0.98; 95% CI: 0.97–0.99; p = 0.035), higher number of affected lobes (OR: 1.53; 95% CI: 1.2–1.95; p < 0.001), and the presence of two or more exacerbations in the previous year (OR: 2.33; 95% CI: 1.15–4.69; p = 0.018) were observed as independent factors associated with CBI due to SA. The reduction in FEv1% in all patients included in the study was −0.31%/year (95% CI: −0.7; −0.07) (p = 0.110). When the reduction in FEv1% is analyzed in the group of patients with CBI due to SA and the group without pathogens, we observed that the reduction in FEV1% was −1.19% (95% CI: −2.09, −0.69) (p < 0.001) in the first group and −0.02% (95% CI: −0.07, −0.01) (p = 0.918) in the second group. According to a linear regression model (mixed effects) applied to determine which factors were associated with a more pronounced reduction in FEv1% in the overall group (including those with CBI due to SA and those with no PPM isolation), age (p = 0.0019), use of inhaled corticosteroids (p = 0.004), presence of CBI due to SA (p = 0.007), female gender (p < 0.001), and the initial value of FEV1 (p < 0.001) were significantly related. Conclusions: Patients with non-CF bronchiectasis with CBI due to SA were younger, with lower FEV1% values, more significant extension of bronchiectasis, and a higher number of exacerbations of mild to moderate symptoms than those with no PPM isolation in respiratory secretions. The reduction in FEV1% was −1.19% (95% CI: −2.09, −0.69) (p < 0.001) in patients with CBI caused by SA. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 572 KiB

Open AccessArticle

Evaluation of Four Fully Integrated Molecular Assays for the Detection of Respiratory Viruses during the Co-Circulation of SARS-CoV-2, Influenza and RSV

by Eric Farfour, Thomas Yung, Robin Baudoin and Marc Vasse

J. Clin. Med. 2022, 11(14), 3942; https://doi.org/10.3390/jcm11143942 - 6 Jul 2022

Cited by 3 | Viewed by 1917

Abstract

Background: The clinical presentation of viral respiratory infections is unspecific. We assessed the performances of two new RT-PCR, the Idylla™ SARS-CoV-2 and the Idylla™ SARS-CoV2/Flu/RSV, and two isothermal amplification assays, the ID NOW COVID and the ID NOW influenza A & B [...] Read more.

Background: The clinical presentation of viral respiratory infections is unspecific. We assessed the performances of two new RT-PCR, the Idylla™ SARS-CoV-2 and the Idylla™ SARS-CoV2/Flu/RSV, and two isothermal amplification assays, the ID NOW COVID and the ID NOW influenza A & B 2. Methods: The study was conducted in two parts: (i) the Idylla™ assays were assessed using a collection of nasopharyngeal swabs which were positive for various respiratory viruses. (ii) The performances of the four assays were assessed prospectively: all of the symptomatic patients admitted to the emergency department from 10 to 21 December were enrolled. Results: (i) All of the SARS-CoV-2 false negatives with the Idylla™ assays had a Ct value greater than 30 with the reference RT-PCR. No cross-reactivity was identified. (ii) Overall, 218 patients were enrolled. The respective prevalences of SARS-CoV-2, influenza A, and RSV were 19.8%, 4.8%, and 3.2%. All of the assays were 100% specific. The sensitivity of SARS-CoV-2 detection was 97.7%, 82.5%, and 86.3% for the Idylla™ SARS-CoV2, the Idylla™ SARS-CoV2/Flu/RSV, and the ID NOW COVID-19, respectively. For influenza A, it was 90.0% for the Idylla™ SARS-CoV2/Flu/RSV and 80.0% for the ID NOW Influenza. Discussion. All of the assays are suitable for testing patients with respiratory symptoms. False negatives should be considered, and the test should be repeated regarding the context. Full article

(This article belongs to the Topic Infectious Diseases)

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17 pages, 1343 KiB

Open AccessArticle

Early, Delayed and Late Cardiac Implantable Electronic Device Infections: Do the Timing of Onset and Pathogens Matter?

by Anna Polewczyk, Wojciech Jacheć, Maciej Polewczyk, Dorota Szczęśniak-Stańczyk and Andrzej Kutarski

J. Clin. Med. 2022, 11(14), 3929; https://doi.org/10.3390/jcm11143929 - 6 Jul 2022

Cited by 6 | Viewed by 1539

Abstract

Infections involving cardiac implantable electronic devices (CIEDs) occur at different times after device-related procedures. The aim of this study was to investigate the timing of onset and factors influencing the occurrence of all types of CIED infections to identify the type of pathogen [...] Read more.

Infections involving cardiac implantable electronic devices (CIEDs) occur at different times after device-related procedures. The aim of this study was to investigate the timing of onset and factors influencing the occurrence of all types of CIED infections to identify the type of pathogen and to examine the long-term survival of patients with all types of CIED infections. We performed a post hoc analysis of the clinical data from 3344 patients who underwent transvenous lead extraction (TLE) at a single high-volume center between 2006 and 2020, including a group of 890 patients with CIED infections. The occurrence of pocket infection (PI), lead-related infective endocarditis (LRIE) and PI coexisting with LRIE (PI + LRIE) was assessed at the following time intervals: 0–12 months, 13–36 months and > 36 months since last CIED-related procedure. In the study group, there were 274 (30.79%) early infections, 266 (29.89%) delayed infections and 350 (39.32%) late infections. Pocket infection was the most common early complication (97; 39.43%), while LRIE was predominant over 36 months from the last CIED procedure (172; 54.09%). The most common early infections were PIs that were associated with the preceding CIED-related procedure. Late LRIE was most likely to occur in patients with intracardiac lead abrasion. The probability of early versus late LRIE was higher in patients with CoNS cultures. The timing of infection onset irrespective of its type does not affect long-term survival after transvenous lead extraction. The majority of infectious complications (69%) occur more than 12 months after the last CIED-related procedure. Early infections are probably associated with pocket contamination during CIED-related procedure, while delayed and late systemic infections are related to other lead-dependent factors (especially to intracardiac lead abrasion). Time to LRIE onset is associated with pathogen type. The timing of symptom onset does not affect long-term survival after TLE. Full article

(This article belongs to the Topic Infectious Diseases)

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Prevalence of CIED infections at each time interval after a CIED-related procedure for noninfectious indications. Full article ">Figure 2
Probability of survival depending on onset of infection: (A) All cardiac implantable device infections. (B) Isolated pocket infections. (C) Pocket infection coexisting with systemic infections. (D) Lead-related infective endocarditis. (A): Probability of survival after TLE depending on infection type p < 0.001. (B): Probability of survival after TLE due to pocket infection depending on temporal onset related to last CIED procedure p = 0.680. (C): Probability of survival after TLE due to pocket and systemic infection depending on temporal onset related to last CIED procedure p = 0.993. (D): Probability of survival after TLE due to systemic infection depending on temporal onset related to last CIED procedure p = 0.751. Full article ">Figure 2 Cont.
Probability of survival depending on onset of infection: (A) All cardiac implantable device infections. (B) Isolated pocket infections. (C) Pocket infection coexisting with systemic infections. (D) Lead-related infective endocarditis. (A): Probability of survival after TLE depending on infection type p < 0.001. (B): Probability of survival after TLE due to pocket infection depending on temporal onset related to last CIED procedure p = 0.680. (C): Probability of survival after TLE due to pocket and systemic infection depending on temporal onset related to last CIED procedure p = 0.993. (D): Probability of survival after TLE due to systemic infection depending on temporal onset related to last CIED procedure p = 0.751. Full article ">

2 pages, 191 KiB

Open AccessCorrection

Correction: Yang et al. A Kinesin Vdkin2 Required for Vacuole Formation, Mycelium Growth, and Penetration Structure Formation of Verticillium dahliae. J. Fungi 2022, 8, 391

by Xing Yang, Cuimei Guo, Chi Chen, Zhijuan Hu, Xinyao Zheng, Shan Xu, Xingyong Yang and Chengjian Xie

J. Fungi 2022, 8(7), 707; https://doi.org/10.3390/jof8070707 - 4 Jul 2022

Cited by 1 | Viewed by 989

Abstract

In the original publication [...] Full article

(This article belongs to the Topic Infectious Diseases)

12 pages, 831 KiB

Open AccessArticle

Tocilizumab Use among Patients Who Developed Pulmonary Embolism in the Course of Cytokine Release Storm and COVID-19 Pneumonia—A Retrospective Study

by Daniel Chober, Bogusz Aksak-Wąs, Jolanta Niścigorska-Olsen, Małgorzata Niekrasz and Miłosz Parczewski

Biomedicines 2022, 10(7), 1581; https://doi.org/10.3390/biomedicines10071581 - 2 Jul 2022

Cited by 2 | Viewed by 1764

Abstract

Introduction: Thromboembolic events, including mainly pulmonary embolisms and ischemic strokes, occur in up to one-third of COVID-19 patients. As efficacy of tocilizumab (TCZ) among patients with acute pulmonary embolism (PE) was not previously investigated, this study aimed to provide such data. Objectives: The [...] Read more.

Introduction: Thromboembolic events, including mainly pulmonary embolisms and ischemic strokes, occur in up to one-third of COVID-19 patients. As efficacy of tocilizumab (TCZ) among patients with acute pulmonary embolism (PE) was not previously investigated, this study aimed to provide such data. Objectives: The aim of the study was to investigate the effect of TCZ on mortality in patients with confirmed acute pulmonary embolism, cytokine release storm and COVID-19 pneumonia. Patients and methods: Longitudinal data of 4287 patients with confirmed SARS-CoV-2 infection were collected between 4 March 2020 and 16 January 2022. In this study, we retrospectively analyzed the samples and dataset of cases with confirmed acute pulmonary embolism associated with at least moderate lung involvement due to COVID-19 pneumonia. Results: In the analyzed dataset, 64 adult patients were diagnosed with PE, and of these, 28 (44%) cases were treated with two 8 mg/kg doses of TCZ, and 36 (56%) did not receive this agent. The groups were balanced regarding demographics, comorbidities and the biochemical markers. Overall mortality in our study was 29.6% (n = 17). Mortality in the group treated with TCZ was 43% (n = 12) compared to 19% (n = 7) in the group without TCZ. In multivariate proportional Cox hazards models, intravenous administration of TCZ was independently associated with higher mortality (HR: 3.342 (CI: 1.077–10.370), p = 0.036). Conclusions: In patients with COVID-19 pneumonia with at least moderate lung involvement, CRS and acute pulmonary embolism, administration of TCZ is associated with increased mortality. Therefore, TCZ should be used with caution in SARS-CoV-2 cases with pulmonary embolism. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 689 KiB

Open AccessArticle

Frequency, Etiology, Mortality, Cost, and Prevention of Respiratory Tract Infections—Prospective, One Center Study

by Wieslawa Duszynska, Marta Idziak, Klaudia Smardz, Anna Burkot, Malgorzata Grotowska and Stanislaw Rojek

J. Clin. Med. 2022, 11(13), 3764; https://doi.org/10.3390/jcm11133764 - 29 Jun 2022

Cited by 8 | Viewed by 2297

Abstract

Background: Ventilator-associated pneumonia (VAP) is the most monitored form of respiratory tract infections (RTIs). A small number of epidemiological studies have monitored community-acquired pneumonia (CAP), non-ventilator hospital-acquired pneumonia (NV-HAP) and ventilator-associated tracheobronchitis (VAT) in intensive care units (ICUs). The objective of this study [...] Read more.

Background: Ventilator-associated pneumonia (VAP) is the most monitored form of respiratory tract infections (RTIs). A small number of epidemiological studies have monitored community-acquired pneumonia (CAP), non-ventilator hospital-acquired pneumonia (NV-HAP) and ventilator-associated tracheobronchitis (VAT) in intensive care units (ICUs). The objective of this study was to assess the frequency, etiology, mortality, and additional costs of RTIs. Methods: One-year prospective RTI surveillance at a 30-bed ICU. The study assessed the rates and microbiological profiles of CAP, VAP, NV-HAP, VAT, and VAP prevention factors, the impact of VAP and NV-HAP on the length of ICU stays, and the additional costs of RTI treatment and mortality. Results: Among 578 patients, RTIs were found in 30%. The CAP, NV-HAP, VAP, and VAT rates/100 admissions were 5.9, 9.0, 8.65, and 6.05, respectively. The VAP incidence density/1000 MV-days was 10.8. The most common pathogen of RTI was Acinetobacter baumannii MDR. ICU stays were extended by VAP and NV-HAP for 17.8 and 3.7 days, respectively, and these RTIs increased the cost of therapy by 13,029 and 2708 EUR per patient, respectively. The mortality rate was higher by 11.55% in patients with VAP than those without device-associated and healthcare-associated infections (p = 0.0861). Conclusions: RTIs are a serious epidemiological problem in patients who are admitted and treated in ICU, as they may affect one-third of patients. Hospital-acquired RTIs extend hospitalization time, increase the cost of treatment, and worsen outcomes. Full article

(This article belongs to the Topic Infectious Diseases)

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17 pages, 2965 KiB

Open AccessArticle

Novel ABC Transporter Associated with Fluconazole Resistance in Aging of Cryptococcus neoformans

by Natalia Kronbauer Oliveira, Somanon Bhattacharya, Rina Gambhir, Manav Joshi and Bettina C. Fries

J. Fungi 2022, 8(7), 677; https://doi.org/10.3390/jof8070677 - 28 Jun 2022

Cited by 5 | Viewed by 2486

Abstract

Cryptococcus neoformans causes meningoencephalitis in immunocompromised individuals, which is treated with fluconazole (FLC) monotherapy when resources are limited. This can lead to azole resistance, which can be mediated by overexpression of ABC transporters, a class of efflux pumps. ABC pump-mediated efflux of FLC [...] Read more.

Cryptococcus neoformans causes meningoencephalitis in immunocompromised individuals, which is treated with fluconazole (FLC) monotherapy when resources are limited. This can lead to azole resistance, which can be mediated by overexpression of ABC transporters, a class of efflux pumps. ABC pump-mediated efflux of FLC is also augmented in 10-generation old C. neoformans cells. Here, we describe a new ABC transporter Afr3 (CNAG_06909), which is overexpressed in C. neoformans cells of advanced generational age that accumulate during chronic infection. The Δafr3 mutant strain showed higher FLC susceptibility by FLC E-Test strip testing and also by a killing test that measured survival after 3 h FLC exposure. Furthermore, Δafr3 cells exhibited lower Rhodamine 6G efflux compared to the H99 wild-type cells. Afr3 was expressed in the Saccharomyces cerevisiae ADΔ strain, which lacks several drug transporters, thus reducing background transport. The ADΔ + Afr3 strain demonstrated a higher efflux with both Rhodamine 6G and Nile red, and a higher FLC resistance. Afr3-GFP localized in the plasma membrane of the ADΔ + Afr3 strain, further highlighting its importance as an efflux pump. Characterization of the Δafr3 mutant revealed unattenuated growth but a prolongation (29%) of the replicative life span. In addition, Δafr3 exhibited decreased resistance to macrophage killing and attenuated virulence in the Galleria mellonella infection model. In summary, our data indicate that a novel ABC pump Afr3, which is upregulated in C. neoformans cells of advanced age, may contribute to their enhanced FLC tolerance, by promoting drug efflux. Lastly, its role in macrophage resistance may also contribute to the selection of older C. neoformans cells during chronic infection. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Afr3 (CNAG_06909) Has Similar Motifs to Afr1 (CNAG_00730). (A) Afr3 possesses one ATP-binding cassette (ABC) domain, an ATPase domain that utilizes ATP binding and hydrolysis to fuel the transport of different molecules across membranes, while Afr1 has two. The search was conducted using Prosite (<a href="https://prosite.expasy.org/scanprosite/" target="_blank">https://prosite.expasy.org/scanprosite/</a>; accessed on 3 December 2021); (B) alignment analysis between the ABC transporter domain of Afr3 (CnAFR3) and the two domains of Afr1 (CnAFR1.1 and CnAFR1.2) was performed with ClustalW, in the BioEdit program. The figure was generated using GeneDoc. Sequences in black are highly conserved. Full article ">Figure 2
Afr3 is an Important Pump for Drug Resistance. (A) C. neoformans Δafr3 is more sensitive to FLC than H99 in an FLC E-Test in a YPD plate; (B) H99 cells that underwent FLC treatment with 32 μg/mL for 2 h (checkered blue/white bar) do not increase expression of AFR3 and AFR1 compared to H99 wild-type (blue bar); (C) Δafr3 (red line) decreases efflux compared to H99 (blue line) in a Rhodamine 6G assay. Statistical analysis was performed with multiple unpaired Student’s t-test, *** p < 0.001; (D) FLC tolerance observed under CR conditions (SM 0.05% glucose) (H99 CR: dark blue line, Δafr3 CR: dark red line) is independent of Afr3 presence, as shown by the susceptibility under normal conditions (SM 2% glucose) (H99: blue line, Δafr3: red line); (E) expression of AFR3 is not increased under CR conditions (checkered blue bar) when compared to normal glucose conditions (blue bar); (F) the Δafr3 young cells (Δafr3 Y, blue bar) are more susceptible to FLC killing than H99 young cells (H99 Y, red bar). Furthermore, Δafr3 old cells (Δafr3 O, checkered blue bar) lose FLC killing tolerance when compared to H99 old cells (H99 O, checkered red bar). Statistical analysis was performed with multiple unpaired Student’s t-test, * p < 0.05, ** p < 0.01, ### p < 0.001, and $ p < 0.05; error bars represent the standard deviation between biological triplicates. Full article ">Figure 3
Afr3 Expression in Saccharomyces cerevisiae Increases Efflux and FLC Resistance. (A) Schematic diagram of Afr3 expression in S. cerevisiae ADΔ strain. The pYES2 plasmid contains a URA3 auxotrophic marker gene, a 2µ origin of replication, a GAL1 promoter, and a CYC1 terminator. Hind III was used as the cloning site between the GAL1 promoter and CYC1 terminator. AFR3 (CNAG_06909) cassette was inserted in this cloning site when transformed into S. cerevisiae ADΔ strain. The transformation was confirmed through plasmid PCR, qPCR for AFR3 expression, and sequencing of the AFR3 cassette. The figure was designed with BioRender. All subsequent experiments were performed at 30 °C; (B) ADΔ + Afr3 (orange line) shows increased efflux when compared to ADΔ (green line) when measured employing the Rhodamine 6G dye; (C) ADΔ + Afr3 (orange bar) has lower intracellular accumulation of Nile Red when compared to control ADΔ (green bar). A catalytically inactive NBD mutant of Afr3 (yellow bar) does not show a statistical difference in Nile Red accumulation from ADΔ; (D) a FLC E-Test strip assay shows that expression of Afr3 increases the strain resistance to FLC (MIC of 0.064 µg/mL vs. <0.016 µg/mL); (E) S. cerevisiae ADΔ cells expressing AFR3-GFP show protein expression by means of GFP fluorescence. Brightfield and epifluorescence images were obtained that were later superimposed; (F) AFR3 expression in ADΔ is 425-fold higher (orange bar) than the control (green bar) as measured by qPCR. Error bars represent the standard deviation between biological triplicates. Statistical analysis was performed with multiple unpaired Student’s t-test, * p < 0.05, ** p < 0.01, *** p < 0.001. Full article ">Figure 4
Afr3 Localizes in the Plasma Membrane. S. cerevisiae ADΔ cells expressing AFR3-GFP show fluorescence on the cell surface, suggesting localization at the level of the plasma membrane. White arrows point to localization within fungal cells. Images were obtained through the generation of ten Z stacks, six of which are represented in this image. Full article ">Figure 5
Afr3 Plays a Role in Virulence. (A) Phagocytosed Δafr3 (red bar) cells are better killed by J774A.1 murine macrophages than wild-type H99 cells (blue bar). Statistical analysis was performed with Student’s t-test, ** p < 0.01; (B) Galleria mellonella larvae survived longer when infected with mutant strain Δafr3 (red line), when compared to the survival of the larvae infected with wild-type H99 (blue line). Black line represents PBS uninfected controls. Statistical analysis was performed with log-rank (Mantel–Cox) test, **** p < 0.0001; (C) Δafr3 (red bar) has lower retention of C. neoformans cells in the larvae hemolymph than H99 (blue bar). Statistical analysis was performed with Student’s t-test, * p < 0.05; error bars signify standard deviations between the biological triplicate. Full article ">Figure 6
Afr3 Plays a Role in Aging. The C. neoformans Δafr3 mutant strain (red) has an expansion of the median lifespan compared to the H99 wild-type strain (blue), while Δafr1 (purple) and Δafr2 (brown) mutant strains do not show significant difference. Statistical analysis was performed with Student’s t-test, *** p < 0.001. Full article ">

15 pages, 2234 KiB

Open AccessArticle

Transcriptional and Translational Dynamics of Zika and Dengue Virus Infection

by Kamini Singh, Maria Guadalupe Martinez, Jianan Lin, James Gregory, Trang Uyen Nguyen, Rawan Abdelaal, Kristy Kang, Kristen Brennand, Arnold Grünweller, Zhengqing Ouyang, Hemali Phatnani, Margaret Kielian and Hans-Guido Wendel

Viruses 2022, 14(7), 1418; https://doi.org/10.3390/v14071418 - 28 Jun 2022

Cited by 7 | Viewed by 3735

Abstract

Zika virus (ZIKV) and dengue virus (DENV) are members of the Flaviviridae family of RNA viruses and cause severe disease in humans. ZIKV and DENV share over 90% of their genome sequences, however, the clinical features of Zika and dengue infections are very [...] Read more.

Zika virus (ZIKV) and dengue virus (DENV) are members of the Flaviviridae family of RNA viruses and cause severe disease in humans. ZIKV and DENV share over 90% of their genome sequences, however, the clinical features of Zika and dengue infections are very different reflecting tropism and cellular effects. Here, we used simultaneous RNA sequencing and ribosome footprinting to define the transcriptional and translational dynamics of ZIKV and DENV infection in human neuronal progenitor cells (hNPCs). The gene expression data showed induction of aminoacyl tRNA synthetases (ARS) and the translation activating PIM1 kinase, indicating an increase in RNA translation capacity. The data also reveal activation of different cell stress responses, with ZIKV triggering a BACH1/2 redox program, and DENV activating the ATF/CHOP endoplasmic reticulum (ER) stress program. The RNA translation data highlight activation of polyamine metabolism through changes in key enzymes and their regulators. This pathway is needed for eIF5A hypusination and has been implicated in viral translation and replication. Concerning the viral RNA genomes, ribosome occupancy readily identified highly translated open reading frames and a novel upstream ORF (uORF) in the DENV genome. Together, our data highlight both the cellular stress response and the activation of RNA translation and polyamine metabolism during DENV and ZIKV infection. Full article

(This article belongs to the Topic Infectious Diseases)

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ZIKV and DENV induced transcriptional changes in hNPCs. (A) Schematic of the RNA-seq and ribosome footprinting on hNPCs cells infected with ZIKV or DENV (72 h). Comparison of ribosome-protected sequences vs. total mRNA isolates the translational efficiency for each mRNA (TE). (B,C), RNA-Seq analysis identifies changes in transcription in hNPCs cells infected with ZIKV (B) and DENV (C) compared to uninfected samples. Using the statistical cut-off of 5% FDR (False Discovery Rate), we identify differential mRNAs with significantly decreased or increased (shown in red; q < 0.05) or unchanged transcription (background, shown in black); two biological replicates. (D,E), Venn diagram showing the number of shared or exclusive RNAs that are significantly downregulated (D) or upregulated (E) (q < 0.05) in ZIKV and DENV infected hNPCs (F,G), STRING: Functional Protein Association Networks (version 11.0) analysis of downregulated RNAs (n = 335; q < 0.05) in ZIKV-infected hNPCs shows (F) three enriched clusters I, II, and III related to histone genes (green), SLE, viral carcinogenesis, alcoholism (blue), and cell cycle (red), respectively. (G) Cluster III showed sub-clusters related to the cell cycle mitotic (green) and resolution of sister chromatid pathways (blue). (H), Gene Set Enrichment Analysis (GSEA) for chromosomal positional sets showed significant enrichment of genes clustered on chr6p22, chr1q21, and chr1p31 among the downregulated RNA (n = 335; q < 0.05) in ZIKV infected hNPCs. (I), GSEA for KEGG pathway enrichment in the subset of mRNA downregulated upon ZIKV infection. (J), GSEA of transcription factor motif enrichment in the subset of mRNAs downregulated in ZIKV infected samples. (K,L), GSEA for KEGG pathways show significant enrichment of mTOR (red) (K), histone (blue) genes (K), and MYC/E2F targets (L) in downregulated mRNA (n = 37; q < 0.05) in DENV infected hNPCs. Full article ">Figure 2
ZIKV and DENV infection-induced distinct transcription programs. (A,B), RNA-seq identified significantly up-regulated RNA at statistical cut off of q < 0.001 (red) and q < 0.05 (black) in ZIKV (A) and DENV (B) infected hNPCs. (C,D), GSEA for KEGG pathway enrichment in the subset of mRNA up-regulated upon ZIKV (C) and DENV (D) infection. Pathways enriched in both ZIKV and DENV infected hNPCs are indicated in bold. (E), RNA fold change of ZIKV and DENV induced aminoacyl tRNA synthetases (ARS) genes. (F), Gene expression analysis by qRT PCR for SHMT2, PIM1, and ATF3 in uninfected, ZIKV, and DENV infected hNPCs (biological replicates n = 3; experimental replicates n = 5–7; p < 0.05). Gene expression is normalized to beta-actin and fold change is plotted compared to uninfected samples. (G), ZIKV induced PIM1 expression that activates mTOR and mRNA translation. (H), ZIKV-induced transcription of genes involved in neurotrophin signaling, ZIKV targets are indicated in red. (I), DENV infection upregulates key enzymes involved in the one-carbon pool by the folate pathway, DENV targets are indicated in red. (J,K), GSEA transcription factor motif analysis identify common and distinct transcription factors involved in up-regulation of specific RNAs in ZIKV (n = 341; q < 0.05) (J) and DENV (n = 111; q < 0.05) (K) infected hNPCs. Full article ">Figure 3
Translational changes induced by ZIKV and DENV infection. (A,B), Ribosome footprinting identifies a specific subset of mRNAs that significantly affected translation efficiency (TE) in ZIKV (A) and DENV (B) infected hNPCs. Using the indicated statistical cut-offs we identify mRNAs with decreased (TE down, red), increased (TE up, blue), and unchanged translation (background, grey); three biological replicates; the most significantly affected genes (q < 0.05) are indicated on each side. (C), ZIKV and DENV regulated the translation of key enzymes OAZ2 and SMOX in the polyamine pathway. (D), DENV upregulated multiple ribosomal proteins, translation initiation, and elongation factors. (E,F), Unbiased search for significantly enriched sequences (TE up versus background) identifies four motifs enriched in upregulated mRNAs in ZIKV (E) and DENV (F) infected hNPCs. RNA binding proteins associated with each motif are indicated. Full article ">Figure 4
Analysis of translation efficiencies for the ZIKV and DENV viral genomes. (A,B), TE analysis revealed that ZIKV and DENV genomic RNAs (shown in red) are highly translated compared to host mRNAs. (C,D), RNA, and ribosome coverage on ZIKV (C) and DENV (D) showed a strong correlation except for the 5′ and 3′UTR regions of DENV (D). (E,F), RNA, and ribosome coverage across the ZIKV (E) and DENV (F) genome mapped to virus polyprotein. ZIKV and DENV showed relatively higher RNA reads at the 3′UTR and higher ribosomal coverage at 5′UTR suggesting differential RNA abundance and translation from UTR regions. Full article ">

13 pages, 4283 KiB

Open AccessArticle

Effective Infection with Dengue Virus in Experimental Neonate and Adult Mice through the Intranasal Route

by Minyue Qiu, Lixin Zhao, Junjie Zhang, Yalan Wang, Minchi Liu, Dong Hua, Xiaoyan Ding, Xiaoyang Zhou, Jie Zeng, Huacheng Yan and Jintao Li

Viruses 2022, 14(7), 1394; https://doi.org/10.3390/v14071394 - 26 Jun 2022

Cited by 1 | Viewed by 2030

Abstract

Dengue virus, the causative agent of dengue fever, life-threatening hemorrhagic fever, and shock syndrome, is mainly transmitted to humans through mosquito vectors. It can also be transmitted through atypical routes, including needle stick injury, vertical transmission, blood transfusion, and organ transplantation. In addition, [...] Read more.

Dengue virus, the causative agent of dengue fever, life-threatening hemorrhagic fever, and shock syndrome, is mainly transmitted to humans through mosquito vectors. It can also be transmitted through atypical routes, including needle stick injury, vertical transmission, blood transfusion, and organ transplantation. In addition, sporadic cases which have no clear infectious causes have raised the respiratory exposure concerns, and the risks remain unclear. Here, we analyze the respiratory infectivity of the dengue virus in BALB/c suckling and adult immunodeficient mice by the intranasal inoculation of dengue virus serotype 2. The infected mice presented with clinical symptoms, including excitement, emaciation, malaise, and death. Viremia was detected for 3 days post inoculation. Histopathological changes were observed in the brain, liver, and spleen. The virus showed evident brain tropism post inoculation and viral loads peaked at 7 days post inoculation. Furthermore, the virus was isolated from the infected mice; the sequence homology between the origin and isolates was 99.99%. Similar results were observed in adult IFN-α/β receptor-deficient mice. Overall, dengue virus can infect suckling mice and adult immune-deficient mice via the nasal route. This study broadens our perception of atypical dengue transmission routes and provides evidence of nasal transmission of dengue virus in the absence of mosquito vectors. Full article

(This article belongs to the Topic Infectious Diseases)

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DENV-2 infection via the intranasal route is lethal in BALB/c suckling mice. (A) Experimental scheme. Three days after birth, the newborn BALB/c suckling mice were challenged intracranially or intranasally with DENV-2. The body weight, clinical phenotypes, and mortality rates were evaluated. The organs (heart, liver, spleen, lung, kidney, and brain) and blood of the challenged suckling mice were harvested (black arrow). (B) Representative images of intracranially or intranasally challenged BALB/c suckling mice. (C) Survival probability of DENV-2 challenged suckling mice infected via intracranial or intranasal routes. Survival conditions were monitored daily after challenge (titer = 2.4 × 104 PFU; i.c., n = 21; i.n., n = 20; mock, n = 8). (D) Survival probability of intranasally infected suckling mice with different titers of DENV-2. Abbreviations: i.c., intracranial; i.n., intranasal; dpi, day post inoculation; PFU, plaque forming unit. Log rank test; ****, p < 0.0001; **, p < 0.01. Full article ">Figure 2
Infection status of DENV-2 challenged suckling mice. (A) Blood samples were harvested, and viremia was evaluated (each time point, n = 4 or n = 5). The dotted black line indicates the limits of detection. (B) Brain samples were harvested, and the virus titer was evaluated using RT-PCR (each time point, n = 4 or n = 5). (C) Immunostaining of the hippocampal CA1 and CA2 area from intracranially and intranasally challenged mice at the severe illness phase (5 and 9 dpi, respectively). Scale bar: 50 μm. (D) Representative transmission electron micrographs showing viral particles in DENV-2 challenged suckling mouse brains. Black arrows, viral particles. Abbreviations: i.c., intracranial; i.n., intranasal; dpi, day post inoculation. Full article ">Figure 3
DENV-2 infection results in pathological changes. (A) Selected organs were harvested from intracranially or intranasally challenged mice sacrificed in a late phase of illness (5 and 9 dpi, respectively) and stained with hematoxylin and eosin (H & E). Blue arrows, granulocytes; black arrows, multinucleated giant cells; yellow arrows, apoptotic bodies. (B) Brains were harvested from intracranially or intranasally challenged mice sacrificed in the late phases of illness (5 and 9 dpi, respectively) and stained with H & E. Blue arrows, gliocyte proliferation; black arrows, necrotic pyramidal cells; red arrows, necrotic neurons; yellow arrows, cytoplasmic vacuoles. Scale bar: 50 μm. Abbreviations: i.c., intracranial; i.n., intranasal. Full article ">Figure 4
Isolation of DENV-2 from Vero cells. (A) Experimental scheme. Three days old BALB/c suckling mice were intracranially or intranasally challenged with DENV-2. The brain tissues were harvested at 5 or 9 dpi. Isolates were passage cultured for three generations. (B) Plaque morphology of DENV-2 viral origin and isolates from intracranially or intranasally infected mouse. (C) DENV-2 was isolated from Vero cells and cultured for three passages; viral loads were evaluated by RT-qPCR. (D) The viral titer of each passage was evaluated in Vero cells. Abbreviations: i.c., intracranial; i.n., intranasal; PFU, plaque forming unit. Histograms: mean ± S.D. Two-way ANOVA test; ****, p < 0.0001; **, p < 0.01; *, p < 0.05; ns, not significant. Full article ">Figure 5
DENV-2 infection via the intranasal route is lethal in A6 mice. (A) Representative images of intranasally challenged A6 mice with neurological symptoms. (B) Survival probability of DENV-2 challenged A6 mice administered the virus via the intravenous or intranasal routes. Survival conditions were monitored daily after challenge (titer = 2.4 × 105 PFU; i.v., n = 4; i.n., n = 4; mock, n = 4). **, p < 0.01. (C) Viremia in A6 mice after DENV-2 inoculation. (i.v., n = 4; i.n., n = 4). Dotted lines indicate the limits of detection. (D) Internal organ samples were harvested, and the virus titer was evaluated (i.v., n = 4; i.n., n = 4). (E) Expression of pro-inflammatory factors in the brains and lungs of moribund A6 mice. Abbreviations: i.v., intravenous; i.n., intranasal; dpi, day post inoculation. Full article ">

9 pages, 608 KiB

Open AccessArticle

Implementation of Antibiotic Stewardship Improves the Quality of Blood Culture Diagnostics at an Intensive Care Unit of a University Hospital

by Sarah V. Walker, Benedict Steffens, David Sander and Wolfgang A. Wetsch

J. Clin. Med. 2022, 11(13), 3675; https://doi.org/10.3390/jcm11133675 - 25 Jun 2022

Cited by 2 | Viewed by 1649

Abstract

Background: Bloodstream infections increase morbidity and mortality in hospitalized patients and pose a significant burden for health care systems worldwide. Optimal blood culture diagnostics are essential for early detection and specific treatment. After assessing the quality parameters at a surgical intensive care [...] Read more.

Background: Bloodstream infections increase morbidity and mortality in hospitalized patients and pose a significant burden for health care systems worldwide. Optimal blood culture diagnostics are essential for early detection and specific treatment. After assessing the quality parameters at a surgical intensive care unit for six months, we implemented a diagnostic stewardship bundle (DSB) to optimize blood culture diagnostics and then reevaluated its effects after six months. Material and Methods: All patients ≥18 years old and on the ward were included: pre-DSB 137 and post-DSB 158. The standard quality parameters were defined as the number of blood culture sets per diagnostic episode (≥2), the rate of contamination (2–3%), the rate of positivity (5–15%), the collection site (≥1 venipuncture per episode) and the filling volume of the bottles (8–10 mL, only post-DSB). The DSB included an informational video, a standard operating procedure, and ready-to-use paper crates with three culture sets. Results: From pre- to post-interventional, the number of ≥2 culture sets per episode increased from 63.9% (257/402) to 81.3% (230/283), and venipunctures increased from 42.5% (171/402) to 77.4% (219/283). The positivity rate decreased from 15.1% (108/714) to 12.8% (83/650), as did the contamination rate (3.8% to 3.6%). The majority of the aerobic bottles were filled within the target range (255/471, 54.1%), but in 96.6%, the anaerobic bottles were overfilled (451/467). Conclusions: The implementation of DSB improved the quality parameters at the unit, thus optimizing the blood culture diagnostics. Further measures seem necessary to decrease the contamination rate and optimize bottle filling significantly. Full article

(This article belongs to the Topic Infectious Diseases)

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15 pages, 739 KiB

Open AccessArticle

Dynamics of HIV Reservoir and HIV-1 Viral Splicing in HCV-Exposed Individuals after Elimination with DAAs or Spontaneous Clearance

by Paula Martínez-Román, Celia Crespo-Bermejo, Daniel Valle-Millares, Violeta Lara-Aguilar, Sonia Arca-Lafuente, Luz Martín-Carbonero, Pablo Ryan, Ignacio de los Santos, María Rosa López-Huertas, Claudia Palladino, María Muñoz-Muñoz, Amanda Fernández-Rodríguez, Mayte Coiras, Verónica Briz and on behalf of the COVIHEP network

J. Clin. Med. 2022, 11(13), 3579; https://doi.org/10.3390/jcm11133579 - 21 Jun 2022

Cited by 2 | Viewed by 2218

Abstract

Background: Although human immunodeficiency virus type 1 (HIV-1) reservoir size is very stable under antiretroviral therapy (ART), individuals exposed to the Hepatitis C virus (HCV) (chronically coinfected and spontaneous clarifiers) show an increase in HIV reservoir size and in spliced viral RNA, which [...] Read more.

Background: Although human immunodeficiency virus type 1 (HIV-1) reservoir size is very stable under antiretroviral therapy (ART), individuals exposed to the Hepatitis C virus (HCV) (chronically coinfected and spontaneous clarifiers) show an increase in HIV reservoir size and in spliced viral RNA, which could indicate that the viral protein regulator Tat is being more actively synthesized and, thus, could lead to a higher yield of new HIV. However, it is still unknown whether the effect of HCV elimination with direct-acting antivirals (DAAs) could modify the HIV reservoir and splicing. Methods: This longitudinal study (48 weeks’ follow-up after sustained virological response) involves 22 HIV+-monoinfected individuals, 17 HIV+/HCV- spontaneous clarifiers, and 24 HIV+/HCV+ chronically infected subjects who eliminated HCV with DAAs (all of them aviremic, viral load < 50). Viral-spliced RNA transcripts and proviral DNA copies were quantified by qPCR. Paired samples were analyzed using a mixed generalized linear model. Results: A decrease in HIV proviral DNA was observed in HIV+/HCV- subjects, but no significant differences were found for the other study groups. An increased production of multiple spliced transcripts was found in HIV+ and HIV+/HCV+ individuals. Conclusions: We conclude that elimination of HCV by DAAs was unable to revert the consequences derived from chronic HCV infection for the reservoir size and viral splicing, which could indicate an increased risk of rapid HIV-reservoir reactivation. Moreover, spontaneous clarifiers showed a significant decrease in the HIV reservoir, likely due to an enhanced immune response in these individuals. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Evolution of HIV-reservoir size in (a) rCD4+ T cells and (b) rCD4 T- PBMCs. Footnote: The study groups were: (1) HIV+: PLWH; (2) HIV+/HCV-: PLWH and HCV, who spontaneously cleared HCV infection; and (3) HIV+/HCV+: PLWH and HCV, who were never treated for HCV at baseline but achieved a sustained viral response with direct-acting antivirals at endpoint. Symbols with connecting lines represent reservoir-size arithmetic mean and standard error of the mean. Differences between baseline and endpoint for the different study groups were calculated using a mixed-model Gamma-distributed GLM. Statistical significance was defined as p < 0.05 (2-tailed). HIV, human immunodeficiency virus; HCV, hepatitis C virus; rCD4+ T cells, resting CD4+ T cells; rCD4 T- PBMCs, resting CD4 T cells-depleted PBMCs; baseline, time of the study when HIV+/HCV+ individuals had never been treated for hepatitis; endpoint, time of the study when HIV+/HCV+ subjects had cleared HCV by treatment with direct-acting antivirals. HIV viral-splicing expression and dynamics. Full article ">Figure 2
Evolution of HIV viral splicing in (a) rCD4+ T cells and (b) rCD4 T- PBMCs. Footnote: The study groups were: (1) HIV+: PLWH; (2) HIV+/HCV-: PLWH and HCV, who spontaneously cleared HCV infection; and (3) HIV+/HCV+: PLWH and HCV, who were never treated for HCV at baseline but achieved a sustained viral response with direct-acting antivirals at endpoint. Symbols with connecting lines represent reservoir-size arithmetic mean and standard error of the mean. Differences between baseline and endpoint for the different study groups were calculated using a mixed-model Gamma-distributed GLM. Statistical significance was defined as p < 0.05 (2-tailed). HIV, human immunodeficiency virus; HCV, hepatitis C virus; rCD4+ T cells, resting CD4+ T cells; rCD4 T- PBMCs, resting CD4 T cells-depleted PBMCs; baseline, time of the study when HIV+/HCV+ individuals had never been treated for hepatitis; endpoint, time of the study when HIV+/HCV+ subjects had cleared HCV by treatment with direct-acting antivirals. Full article ">

11 pages, 554 KiB

Open AccessArticle

Effectiveness and Safety of High-Dose Dual Therapy: Results of the European Registry on the Management of Helicobacterpylori Infection (Hp-EuReg)

by Luis Fernández-Salazar, Ana Campillo, Luis Rodrigo, Ángeles Pérez-Aisa, Jesús M. González-Santiago, Xavier Segarra Ortega, Maja Denkovski, Natasa Brglez Jurecic, Luis Bujanda, Blas José Gómez Rodríguez, Juan Ortuño, Sotirios Georgopoulos, Laimas Jonaitis, Ignasi Puig, Olga P. Nyssen, Francis Megraud, Colm O’Morain and Javier P. Gisbert

J. Clin. Med. 2022, 11(12), 3544; https://doi.org/10.3390/jcm11123544 - 20 Jun 2022

Cited by 12 | Viewed by 2703

Abstract

Background: Randomized clinical trials and meta-analyses, primarily from Asian countries, have reported good effectiveness with high-dose dual therapy (HDDT) including a proton pump inhibitor (PPI) and amoxicillin when prescribed as H. pylori first-line or rescue treatment. However, combining amoxicillin with PPIs in the [...] Read more.

Background: Randomized clinical trials and meta-analyses, primarily from Asian countries, have reported good effectiveness with high-dose dual therapy (HDDT) including a proton pump inhibitor (PPI) and amoxicillin when prescribed as H. pylori first-line or rescue treatment. However, combining amoxicillin with PPIs in the 1990s in several European countries yielded suboptimal results. Methods: An international, multicenter, prospective non-interventional Registry (Hp-EuReg) aimed to evaluate the decisions and outcomes of H. pylori management by European gastroenterologists. All infected adult cases treated with HDDT were registered at e-CRF AEG-REDCap platform until June 2021. Sixty patients were prescribed with HDDT (98% compliance), 19 of them received a first-line therapy and 41 a rescue treatment (second- to sixth-line). Results: Overall HDDT effectiveness was 52% (per-protocol) and 51% (modified intention-to-treat). First-line and rescue treatment lines were equally effective, but the effectiveness was worse when patients had previously received metronidazole, tetracycline, or rifabutin. Adding bismuth to HDDT in rescue treatment did not yield better results. The incidence of adverse events was 30%, diarrhea being the most common (20% of patients); no serious adverse events were reported. Conclusion: Although HDDT is safe and has good compliance, it is not a good option in European first-line or rescue H. pylori treatment, even when adding bismuth. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 2004 KiB

Open AccessArticle

Comprehensive Clinical Characterisation of Brain Fog in Adults Reporting Long COVID Symptoms

by Glenn Jennings, Ann Monaghan, Feng Xue, Eoin Duggan and Román Romero-Ortuño

J. Clin. Med. 2022, 11(12), 3440; https://doi.org/10.3390/jcm11123440 - 15 Jun 2022

Cited by 39 | Viewed by 9218

Abstract

(1) Introduction: A subset of individuals experiencing long COVID symptoms are affected by ‘brain fog’, a lay term that often refers to general cognitive dysfunction but one that is still poorly characterised. In this study, a comprehensive clinical characterisation of self-reported brain fog [...] Read more.

(1) Introduction: A subset of individuals experiencing long COVID symptoms are affected by ‘brain fog’, a lay term that often refers to general cognitive dysfunction but one that is still poorly characterised. In this study, a comprehensive clinical characterisation of self-reported brain fog was conducted vis-à-vis other long COVID symptoms and parameters of mental, cognitive, and physical health. (2) Methodology: Adult participants reporting long COVID symptoms were recruited from hospital clinics and as self-referrals. Participants completed a battery of questionnaires and clinical assessments, including COVID-19 history, symptomatology, self-reported scales (Chalder Fatigue Scale [CFQ], Center for Epidemiological Studies Depression Scale, and Impact of Events Scale–Revised), computer-based cognitive assessments (simple response time and choice reaction time tasks), physical performance tests (gait velocity and muscle strength assessments), and an orthostatic active stand test. A systematic comparison between participants with and without self-reported brain fog was conducted, and a backwards binary logistic regression model was computed to identify the strongest independent associations with brain fog. This was complemented by an automatic cluster analysis to rank the importance of associations. Finally, a structural equation model was postulated with a causal model of key symptomatic indicators and functional consequences of brain fog as a latent variable. (3) Results: Of 108 participants assessed, brain fog was a self-reported symptom in 71 (65.7%) participants. Those with brain fog were at a longer point in time since COVID-19 onset and reported longer duration of low activity during the acute illness. When assessed, those with brain fog had higher frequencies of subjective memory impairment, word-finding difficulties, dizziness, myalgia, arthralgia, hyperhidrosis, cough, voice weakness, throat pain, visual and hearing problems, dysosmia, paraesthesia, chest pain, skin rashes, and hair loss; mean scores in fatigue, depression, and post-traumatic stress scales were higher; performance in both computer-based cognitive tasks was poorer; and measured gait speed and grip strength were lower. The logistic regression suggested that the best independent associations with brain fog were memory impairment, CFQ, and myalgia. The cluster analysis suggested that the most important associations with brain fog were CFQ, dizziness, myalgia, reduced gait speed, word-finding difficulties, reduced grip strength, and memory impairment. The SEM was consistent with key indicators of brain fog being CFQ, dizziness, myalgia, word-finding difficulties, and memory impairment; and reduced grip strength, gait speed, and cognitive response times its functional consequences. (4) Conclusions: The findings indicate that self-reported brain fog in long COVID is a recognisable symptom cluster primarily characterised by fatigue, dizziness, myalgia, word-finding difficulties, and memory impairment and has adverse psychological and psychomotor correlates. In long COVID, brain fog should be regarded as a wide-ranging symptom and addressed holistically with medical, psychological, and rehabilitative supports as guided by individual needs. Full article

(This article belongs to the Topic Infectious Diseases)

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26 pages, 1397 KiB

Open AccessArticle

C-Reactive Protein and Serum Albumin Ratio: A Feasible Prognostic Marker in Hospitalized Patients with COVID-19

by Vicente Giner-Galvañ, Francisco José Pomares-Gómez, José Antonio Quesada, Manuel Rubio-Rivas, Javier Tejada-Montes, Jesús Baltasar-Corral, María Luisa Taboada-Martínez, Blanca Sánchez-Mesa, Francisco Arnalich-Fernández, Esther Del Corral-Beamonte, Almudena López-Sampalo, Paula María Pesqueira-Fontán, Mar Fernández-Garcés, Ricardo Gómez-Huelgas, José Manuel Ramos-Rincón and on behalf of the SEMI-COVID-19 Network

Biomedicines 2022, 10(6), 1393; https://doi.org/10.3390/biomedicines10061393 - 13 Jun 2022

Cited by 5 | Viewed by 2371

Abstract

(1) Background: C-reactive protein (CRP) and albumin are inflammatory markers. We analyzed the prognostic capacity of serum albumin (SA) and CRP for an outcome comprising mortality, length of stay, ICU admission, and non-invasive mechanical ventilation in hospitalized COVID-19 patients. (2) Methods: We conducted [...] Read more.

(1) Background: C-reactive protein (CRP) and albumin are inflammatory markers. We analyzed the prognostic capacity of serum albumin (SA) and CRP for an outcome comprising mortality, length of stay, ICU admission, and non-invasive mechanical ventilation in hospitalized COVID-19 patients. (2) Methods: We conducted a retrospective cohort study based on the Spanish national SEMI-COVID-19 Registry. Two multivariate logistic models were adjusted for SA, CRP, and their combination. Training and testing samples were used to validate the models. (3) Results: The outcome was present in 41.1% of the 3471 participants, who had lower SA (mean [SD], 3.5 [0.6] g/dL vs. 3.8 [0.5] g/dL; p < 0.001) and higher CRP (108.9 [96.5] mg/L vs. 70.6 [70.3] mg/L; p < 0.001). In the adjusted multivariate model, both were associated with poorer evolution: SA, OR 0.674 (95% CI, 0.551–0.826; p < 0.001); CRP, OR 1.002 (95% CI, 1.001–1.004; p = 0.003). The CRP/SA model had a similar predictive capacity (honest AUC, 0.8135 [0.7865–0.8405]), with a continuously increasing risk and cutoff value of 25 showing the highest predictive capacity (OR, 1.470; 95% CI, 1.188–1.819; p < 0.001). (4) Conclusions: SA and CRP are good independent predictors of patients hospitalized with COVID-19. For the CRP/SA ratio value, 25 is the cutoff for poor clinical course. Full article

(This article belongs to the Topic Infectious Diseases)

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14 pages, 1649 KiB

Open AccessArticle

Development of a Singleplex Real-Time Reverse Transcriptase PCR Assay for Pan-Dengue Virus Detection and Quantification

by Adisak Songjaeng, Somchai Thiemmeca, Dumrong Mairiang, Nuntaya Punyadee, Kessiri Kongmanas, Prachya Hansuealueang, Nattaya Tangthawornchaikul, Thaneeya Duangchinda, Juthathip Mongkolsapaya, Kanokwan Sriruksa, Wannee Limpitikul, Prida Malasit and Panisadee Avirutnan

Viruses 2022, 14(6), 1271; https://doi.org/10.3390/v14061271 - 10 Jun 2022

Cited by 6 | Viewed by 3138

Abstract

Dengue virus (DENV) infection is a significant global health problem. There are no specific therapeutics or widely available vaccines. Early diagnosis is critical for patient management. Viral RNA detection by multiplex RT-PCR using multiple pairs of primers/probes allowing the simultaneous detection of all [...] Read more.

Dengue virus (DENV) infection is a significant global health problem. There are no specific therapeutics or widely available vaccines. Early diagnosis is critical for patient management. Viral RNA detection by multiplex RT-PCR using multiple pairs of primers/probes allowing the simultaneous detection of all four DENV serotypes is commonly used. However, increasing the number of primers in the RT-PCR reaction reduces the sensitivity of detection due to the increased possibility of primer dimer formation. Here, a one tube, singleplex real-time RT-PCR specific to DENV 3′-UTR was developed for the detection and quantification of pan-DENV with no cross reactivity to other flaviviruses. The sensitivity of DENV detection was as high as 96.9% in clinical specimens collected at the first day of hospitalization. Our assay provided equivalent PCR efficiency and RNA quantification among each DENV serotype. The assay’s performance was comparable with previously established real-time RT-PCR targeting coding sequences. Using both assays on the same specimens, our results indicate the presence of defective virus particles in the circulation of patients infected with all serotypes. Dual regions targeting RT-PCR enhanced the sensitivity of viral genome detection especially during the late acute phase when viremia rapidly decline and an incomplete viral genome was clinically evident. Full article

(This article belongs to the Topic Infectious Diseases)

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Performance of 3′-UTR primers/probes. Quantification cycle (Cq) of 3′-UTR region (a–e) was determined using serial 10-fold diluted (101 to 106 RNA copies) in vitro transcript DENV1-4RNA as template. Coefficient of determination (R2) and PCR amplification efficiency (E) for DENV1 (a), DENV2 (b), DENV3 (c), and DENV4 (d) were analyzed from 8 independent experiments. The variation of Cq values at each RNA concentration among serotypes was analyzed by Bonferroni’s Multiple Comparison Test (e). RNAs extracted from cultured supernatants of Japanese encephalitis virus (JEV, Nakayama strain), yellow fever virus (YFV, 17D strain), zika virus (ZIKV, ZV0127 strain), DENV1 Hawaii, DENV2 16681, DENV3 H87, and DENV4 H241 were used as RNA templates to verify the specificity of our 3′-UTR primers/probes (f). Primers specific to E gene of JEV, YFV, or ZIKV were used to confirm the existence of RNA templates of each virus type. The sizes of PCR products for DENV1, DENV2, DENV3, DENV4, JEV, YFV, and ZIKV were 185, 187, 184, 189, 333, 306, and 365 base pairs, respectively. No RNA template (Neg) was used as a negative control. The PCR product was run in 2% agarose gel electrophoresis and was stained with gel red before visualization under UV light (f). Full article ">Figure 2
Correlation of DENV genome levels quantified by RT-PCR specific to 3′-UTR and coding sequence. Quantification cycle (Cq) values or DENV genome levels (Log copies/mL) in various types of samples quantified by RT-PCR using the two types of probe/primer regions were compared and analyzed for correlation coefficient (R) and p values of linear regression. (a) A correlation plot showing Cq values from quantification of 144 samples of in vitro transcribed DENV1-4 RNA (ranging from 101–106 copies/mL) from 6 independent experiments. (b) A correlation plot showing DENV genome levels (Log copies/mL) in DENV1-4 infected cell cultured supernatants (2–200,000 ffu/mL) from 15 independent experiments. (c) A correlation plot showing DENV genome levels (Log copies/mL) measured in plasma of 161 DENV infected patients collected since the first day of hospitalization to the day to defervescence (499 samples in total). Full article ">Figure 3
Rate of DENV genome detection by real-time RT-PCR specific to only 3′-UTR or coding sequence. (a) Viral RNA levels in plasma of 161 DENV infected patients collected since the first day of hospitalization to the day to defervescence quantified by RT-PCR specific to 3′-UTR (gray circles) or coding sequence (white circles) were re-analyzed according to “Day to defervescence”. The number of samples are labeled on the top of each group. Detection rate of DENV detected by only 3′-UTR (gray bar) or only coding sequence (white bar) were analyzed according to “Day to defervescence” (b) or DENV serotypes (c). Full article ">Figure 4
Efficiency of DENV genome detection. Data from <a href="#viruses-14-01271-f002" class="html-fig">Figure 2</a>c were re-analyzed according to “Day to defervescence”. Detection rates of 3′-UTR assay (black bar) or coding sequence assay (white bar) or detected by either assay (gray bar) were analyzed according to “Day to defervescence”. Proportions of DENV detection rates among groups were analyzed by McNemar’s test. Asterisks (** and ***) represent McNemar’s p values < 0.01 and <0.001, respectively. Full article ">

16 pages, 611 KiB

Open AccessReview

Mechanism of Viral Suppression among HIV Elite Controllers and Long-Term Nonprogressors in Nigeria and South Africa

by Rahaman Ademolu Ahmed, Khalid Olajide Adekoya, Chika Kingsley Onwuamah, Bolanle Olufunmilayo Oboh, Smita Swaminathan Iyer, Ayomide Samuel Oluwatosin, Rosemary Ajuma Audu and Oliver Chukwujekwu Ezechi

Viruses 2022, 14(6), 1270; https://doi.org/10.3390/v14061270 - 10 Jun 2022

Cited by 2 | Viewed by 2894

Abstract

A subgroup among people living with HIV (PLHIV) experience viral suppression, sometimes to an undetectable level in the blood and/or are able to maintain a healthy CD4+ T-cell count without the influence of antiretroviral (ARV) therapy. One out of three hundred PLHIV fall [...] Read more.

A subgroup among people living with HIV (PLHIV) experience viral suppression, sometimes to an undetectable level in the blood and/or are able to maintain a healthy CD4+ T-cell count without the influence of antiretroviral (ARV) therapy. One out of three hundred PLHIV fall into this category, and a large sample of this group can be found in areas with a high prevalence of HIV infection such as Nigeria and South Africa. Understanding the mechanism underpinning the nonprogressive phenotype in this subgroup may provide insights into the control of the global HIV epidemic. This work provides mechanisms of the elite control and nonprogressive phenotype among PLHIV in Nigeria and South Africa and identifies research gaps that will contribute to a better understanding on HIV controllers among PLHIV. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 524 KiB

Open AccessArticle

Antibody Response Induced by BNT162b2 and mRNA-1273 Vaccines against the SARS-CoV-2 in a Cohort of Healthcare Workers

by Juan F. Delgado, Antoni Berenguer-Llergo, Germà Julià, Gema Navarro, Mateu Espasa, Sara Rodríguez, Noemí Sánchez, Eva Van Den Eynde, Marta Navarro, Joan Calvet, Jordi Gratacós, Rosa M. Serrano, Pilar Peña and María J. Amengual

Viruses 2022, 14(6), 1235; https://doi.org/10.3390/v14061235 - 7 Jun 2022

Cited by 5 | Viewed by 2650

Abstract

The aim of this study was to characterize the antibody response induced by SARS-CoV-2 mRNA vaccines in a cohort of healthcare workers. A total of 2247 serum samples were analyzed using the Elecsys^® Anti-SARS-CoV-2 S-test (Roche Diagnostics International Ltd., Rotkreuz, Switzerland). Sex, [...] Read more.

The aim of this study was to characterize the antibody response induced by SARS-CoV-2 mRNA vaccines in a cohort of healthcare workers. A total of 2247 serum samples were analyzed using the Elecsys^® Anti-SARS-CoV-2 S-test (Roche Diagnostics International Ltd., Rotkreuz, Switzerland). Sex, age, body mass index (BMI), arterial hypertension, smoking and time between infection and/or vaccination and serology were considered the confounding factors. Regarding the medians, subjects previously infected with SARS-CoV-2 who preserved their response to the nucleocapsid (N) protein showed higher humoral immunogenicity (BNT162b2: 6456.0 U/mL median; mRNA-1273: 2505.0 U/mL) compared with non-infected (BNT162b2: 867.0 U/mL; mRNA-1273: 2300.5 U/mL) and infected subjects with a lost response to N protein (BNT162b2: 2992.0 U/mL). After controlling for the confounders, a higher response was still observed for mRNA-1273 compared with BNT162b2 in uninfected individuals (FC = 2.35, p < 0.0001) but not in previously infected subjects (1.11 FC, p = 0.1862). The lowest levels of antibodies were detected in previously infected non-vaccinated individuals (39.4 U/mL). Clinical variables previously linked to poor prognoses regarding SARS-CoV-2 infection, such as age, BMI and arterial hypertension, were positively associated with increasing levels of anti-S protein antibody exclusively in infected subjects. The mRNA-1273 vaccine generated a higher antibody response to the S protein than BNT162b2 in non-infected subjects only. Full article

(This article belongs to the Topic Infectious Diseases)

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7 pages, 1378 KiB

Open AccessCommunication

Genomic Diversity of SARS-CoV-2 Omicron Variant in South American Countries

by Nicolas Luna, Marina Muñoz, Angie L. Ramírez, Luz H. Patiño, Sergio Andres Castañeda, Nathalia Ballesteros and Juan David Ramírez

Viruses 2022, 14(6), 1234; https://doi.org/10.3390/v14061234 - 7 Jun 2022

Cited by 6 | Viewed by 1976

Abstract

Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage’s genomic and epidemiological characteristics. However, in South America, this variant’s [...] Read more.

Genomic surveillance of SARS-CoV-2 is one of the tools that provide genomic information on circulating variants. Given the recent emergence of the Omicron (B.1.1.529) variant, this tool has provided data about this lineage’s genomic and epidemiological characteristics. However, in South America, this variant’s arrival and genomic diversity are scarcely known. Therefore, this study determined the genomic diversity and phylogenetic relationships of 21,615 Omicron genomes available in public databases. We found that in South America, BA.1 (n = 15,449, 71%) and BA.1.1 (n = 6257, 29%) are the dominant sublineages, with several mutations that favor transmission and antibody evasion. In addition, these lineages showed cryptic transmission arriving on the continent in late September 2021. This event may have contributed to the dispersal of Omicron sublineages and the acquisition of new mutations. Considering the genomic and epidemiological characteristics of these lineages, especially those with a high number of mutations in their genome, it is important to conduct studies and surveillance on the dynamics of these lineages to identify the mechanisms of mutation acquisition and their impact on public health. Full article

(This article belongs to the Topic Infectious Diseases)

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17 pages, 1868 KiB

Open AccessReview

Colistin Monotherapy versus Colistin plus Meropenem Combination Therapy for the Treatment of Multidrug-Resistant Acinetobacter baumannii Infection: A Meta-Analysis

by Chienhsiu Huang, Ihung Chen and Tiju Tang

J. Clin. Med. 2022, 11(11), 3239; https://doi.org/10.3390/jcm11113239 - 6 Jun 2022

Cited by 11 | Viewed by 4869

Abstract

(1) Introduction: Colistin combination therapy with other antibiotics is a way to enhance colistin activity. The purpose of this meta-analysis was to compare the efficacy and safety of treatment with colistin monotherapy versus colistin plus meropenem combination therapy in patients with drug-resistant Acinetobacter [...] Read more.

(1) Introduction: Colistin combination therapy with other antibiotics is a way to enhance colistin activity. The purpose of this meta-analysis was to compare the efficacy and safety of treatment with colistin monotherapy versus colistin plus meropenem combination therapy in patients with drug-resistant Acinetobacter baumannii infection. (2) Methods: All studies were included if they reported one or more of the following outcomes: clinical improvement, complete microbiological response, 14-day mortality, hospital mortality, or nephrotoxicity. (3) Results: Three randomized controlled trials and seven retrospective studies were included in the meta-analysis. Colistin monotherapy has similar rates of clinical improvement, 14-day mortality, hospital mortality, and nephrotoxicity as colistin plus meropenem combination therapy. Regarding complete microbiological response, the colistin plus meropenem combination was better than colistin monotherapy. (4) Discussion: Previous meta-analyses demonstrated heterogeneity in study quality and a lack of evidence supporting the use of colistin-based combination therapy. Our meta-analysis clearly showed that colistin combined with meropenem was not superior to colistin monotherapy for the treatment of Acinetobacter baumannii infection. (5) Conclusions: The efficacy and safety of treatment with colistin monotherapy and that of colistin plus meropenem combination therapy in patients with drug-resistant Acinetobacter baumannii infection were comparable. The majority of the evidence was obtained from nonrandomized studies, and high-quality randomized controlled trials are needed to confirm the role of colistin plus meropenem combination therapy in the treatment of multidrug-resistant Acinetobacter baumannii infection. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 3231 KiB

Open AccessArticle

Deletion of Toxoplasma Rhoptry Protein 38 (PruΔrop38) as a Vaccine Candidate for Toxoplasmosis in a Murine Model

by Yayun Wu, Zihui Zhou, Zhu Ying, Ying Xu, Jing Liu and Qun Liu

Biomedicines 2022, 10(6), 1336; https://doi.org/10.3390/biomedicines10061336 - 6 Jun 2022

Cited by 3 | Viewed by 1798

Abstract

Toxoplasmosis is a serious zoonotic disease that threatens human and animal health. Here, we evaluated the vaccine potential of the deletion of Toxoplasma rhoptry protein 38 (PruΔrop38) through its pathogenicity and immunoprotective efficacy in mice. Mice inoculated intraperitoneally with 1 × [...] Read more.

Toxoplasmosis is a serious zoonotic disease that threatens human and animal health. Here, we evaluated the vaccine potential of the deletion of Toxoplasma rhoptry protein 38 (PruΔrop38) through its pathogenicity and immunoprotective efficacy in mice. Mice inoculated intraperitoneally with 1 × 10³, 2 × 10³, or 4 × 10³ PruΔrop38 showed no visible signs, whereas mice inoculated with 1 × 10³ parental Pru strain showed obvious wasting and bow-back, suggesting a significantly lower pathogenicity of PruΔrop38 in mice. Vaccination with 1 × 10² PruΔrop38 triggered a mixed Th1/Th2 response (Th1 response predominant), with higher IgG, IgG2a, and IgG1 levels in serum from week 3 to week 12, and a significant increase in IFN-γ, IL-12, and IL-10 in suspensions of splenocytes at 30 or 60 days post-immunization. All vaccinated mice survived when infected intraperitoneally with tachyzoites (RH, Pru, VEG, or TgcatBJ1) or when infected orally with cysts (Pru or ME49). The brain parasite burden during Pru tachyzoite, Pru cyst and ME49 cyst challenges were significantly reduced in vaccinated mice. The duration of immunization showed that vaccination with PruΔrop38 could protect mice from challenge with different varied genotypes of Toxoplasma strains against different routes of infection. Collectively, these findings indicate that PruΔrop38 is an attenuated strain that provides long-term protective efficacy against acute or chronic toxoplasmosis in mice. Full article

(This article belongs to the Topic Infectious Diseases)

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Pathogenicity of PruΔrop38 in mice. (A) Survival rate and (B) body weight gain of CD-1 mice infected with the parental Pru strain or the PruΔrop38 strain. Pru (1 × 103 and 2 × 103) or PruΔrop38 (1 × 103, 2 × 103, 4 × 103, and 8 × 103) tachyzoites were injected intraperitoneally (i.p.) into mice (n = 5), and daily monitoring of mice for 30 days (presented as the mean of body weight ± SD; * p < 0.05; one-way ANOVA with Tukey). Full article ">Figure 2
Dynamic distribution and effect on brain parasite burden of PruΔrop38 in mice. Amplification results of T. gondii-specific genes from organs and tissues in mice. Injections of (A) 1 × 102, (B) 5 × 102, and (C) 1 × 103 PruΔrop38 tachyzoites, respectively. (D) Cyst counts were performed on brain homogenates by DBA-FITC staining, brain cyst from mice injected with PruΔrop38 and Pru were observed using a fluorescence microscope. (E) Immunofluorescence assays determined the number of brain cysts of Pru and PruΔrop38. Pru (1 × 103) or PruΔrop38 (1 × 102, 5 × 102, and 1 × 103) tachyzoites were injected intraperitoneally (i.p.) into mice (n = 5) for 30 days. (Cyst walls of T. gondii were labeled with DBA-FITC (green), Scale bar = 50 µm). (F) The number of parasites and DNA concentration in each brain tissue were detected by calculating the 529 gene of Toxoplasma and the 28S rRNA gene of the brain with quantitative real-time PCR, the load of parasites = number of parasites/DNA concentration of brain tissue (presented as the mean ± SD; *** p < 0.001; one-way ANOVA with Tukey). Full article ">Figure 3
Humoral and cellular immune responses induced by PruΔrop38. Levels of IgG and its subtype (IgG2a and IgG1) antibodies in the serum obtained from vaccinated and control mice. (A) IgG, (B) IgG2a, and (C) IgG1, respectively (n = 3; weekly serum collection after immunization). The levels of cytokines in the suspension of splenocyte in vaccinated and control mice. Splenocytes were collected at 30 or 60 days post-vaccination and co-incubated with TSA (50 μg/mL), and the levels of (D) IFN-γ, (E) IL-12, and (F) IL-10 were analyzed by ELISA (n = 3; presented as the mean ± SD; *** p < 0.001; Student’s t-test). Full article ">Figure 4
Protective efficacy against varied genotypes of tachyzoite challenge. Survival rate and body weight gain of vaccinated and control mice re-challenged with (A,B) RH (1 × 102) and VEG (1 × 105) tachyzoites, (C,D) Pru (1 × 103 and 5 × 103) tachyzoites, and (E,F) TgCatBj1 (1 × 103 and 5 × 103) tachyzoites, respectively. (n = 5; mice were injected intraperitoneally (i.p.); daily monitoring of mice for 30 days; presented as the mean of body weight ± SD; * p < 0.05; one-way ANOVA with Tukey). Full article ">Figure 5
Protective efficacy against varied genotypes of cyst challenge. Survival rate and body weight gain of vaccinated and control mice re-challenged with (A,B) Pru (20 and 10) cysts and (C,D) ME49 (20 and 5) cysts (n = 5; mice were injected orally; daily monitoring of mice for 30 days; presented as the mean of body weight ± SD; * p < 0.05; one-way ANOVA with Tukey). Full article ">Figure 6
Effect on brain parasite burden when challenged with T. gondii type II strains. The brain from vaccinated and control mice were harvested after challenge with 30 days, and cysts were observed by IFA and then the number of cysts were determined by DBA-FITC staining. (A) Pru cyst challenge (20 and 10), (B) ME49 cyst challenge (20 and 5), and (C) Pru tachyzoite (5 × 103 and 1 × 103) challenge, respectively. (n = 5; presented as the mean of cyst number ± SD; *** p < 0.001; one-way ANOVA with Tukey). Full article ">Figure 7
The duration of immunity with PruΔrop38. Survival rate of vaccinated and control mice re-challenged with (A) RH (1 × 102) and VEG (1 × 105) tachyzoites, (B) Pru (1 × 103 and 5 × 103) tachyzoites, and (C) TgCatBj1 (1 × 103 and 5 × 103) tachyzoites, (D) Pru (20 and 10) cysts, and (E) ME49 (20 and 5) cysts, respectively (n = 5; mice were injected with tachyzoites intraperitoneally (i.p.) or with cysts orally; daily monitoring of mice for 30 days). Full article ">

18 pages, 1666 KiB

Open AccessReview

Pediatric Infective Endocarditis: A Literature Review

by Lourdes Vicent, Raquel Luna and Manuel Martínez-Sellés

J. Clin. Med. 2022, 11(11), 3217; https://doi.org/10.3390/jcm11113217 - 5 Jun 2022

Cited by 25 | Viewed by 5944

Abstract

Infective endocarditis in children is a rare entity that poses multiple challenges. A history of congenital heart disease is the most common risk factor, although in recent years, other emerging predisposing conditions have gained relevance, such as central venous catheters carriers or children [...] Read more.

Infective endocarditis in children is a rare entity that poses multiple challenges. A history of congenital heart disease is the most common risk factor, although in recent years, other emerging predisposing conditions have gained relevance, such as central venous catheters carriers or children with chronic debilitating conditions; cases in previously healthy children with no medical history are also seen. Diagnosis is complex, although it has improved with the use of multimodal imaging techniques. Antibiotic treatment should be started early, according to causative microorganism and risk factors. Complications are frequent and continue to cause significant morbidity. Most studies have been conducted in adults and have been generalized to the pediatric population, with subsequent limitations. Our manuscript presents a comprehensive review of pediatric infective endocarditis, including recent advances in diagnosis and management. Full article

(This article belongs to the Topic Infectious Diseases)

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13 pages, 2894 KiB

Open AccessArticle

Identification of a Novel HBV Encoded miRNA Using Next Generation Sequencing

by Vladimir Loukachov, Karel A. van Dort, Louis Jansen, Henk W. Reesink and Neeltje A. Kootstra

Viruses 2022, 14(6), 1223; https://doi.org/10.3390/v14061223 - 5 Jun 2022

Cited by 8 | Viewed by 2242

Abstract

Hepatitis B Virus (HBV) encoded miRNAs were previously described and suggested to play a role in HBV replication and pathogenesis. In this study we aim to identify novel HBV encoded miRNAs in plasma and liver tissue samples from chronic hepatitis B (CHB) patients [...] Read more.

Hepatitis B Virus (HBV) encoded miRNAs were previously described and suggested to play a role in HBV replication and pathogenesis. In this study we aim to identify novel HBV encoded miRNAs in plasma and liver tissue samples from chronic hepatitis B (CHB) patients and determine their role in CHB pathogenesis and HBV replication. RNA next generation sequencing was performed on plasma and liver tissue samples from ten CHB patients and uninfected controls. The interaction of the potential miRNA-like structures with the RNA-induced silencing complex (RISC) was determined using RNA immunoprecipitation. Expression levels of the HBV encoded miRNAs were measured in liver tissue samples derived from a conformation cohort. The effect of HBV encoded miRNAs overexpression on HBV replication, expression of predicted target genes, and induction of interferon stimulated genes in cell lines were assessed. Three potential miRNA-like structures transcribed by HBV were identified in liver tissue, of which one miRNA, HBV-miR-6, was recognized using RISC. HBV-miR-6 expression was demonstrated in liver tissue samples from 52 of the 87 CHB patients. HBV-miR-6 levels correlated with hepatic HBV-DNA and plasma HBsAg levels. Overexpression of HBV-miR-6 in vitro did not affect HBV replication, and predicted both target genes expression and interferon stimulated genes expression after stimulation. A potential novel HBV encoded miRNA was identified and validated in liver tissue from CHB patients. It is suggested that HBV-miR-6 may play a role in the process of viral excretion or particle formation in vivo. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Secondary structure prediction of potential HBV encoded miRNAs. Small NGS of liver tissue from CHB patients revealed three pre-miRNA-like hairpin structures encoded by the HBV genome. The RNA secondary structures of the small RNAs named HBV-miR-6 (A), HBV-miR-7 (B), and HBV-miR-8 (C) were assessed using the mfold web server online tool. A: adenine; C: cytosine; G; guanine; U: uracil. Optimal base pairs are represented by red line between the two nucleotides. The intensity of the blue color represents the level of promiscuity in the association of any given nucleotide or helix with alternative complementary pairs (dark blue been lower and white higher). The numbers indicate the corresponding nucleotide position in the total sequence. Full article ">Figure 2
HBV-miR-6 interacts with RICS. RNA immunoprecipitation using either an AGO2, NRNP70 (positive control), or IgG control antibodies was performed in HepG2.2.15 cells (black bars) and HepG2 cells (grey bars). The binding of HBV-miR-6 (A), HBV-miR-7 (B), and HBV-miR-8 (C) to AGO2, and U1 snRNA to SNRNP70, were measured using RT-qPCR. The graphs represent averages of results from two independent experiments. Full article ">Figure 3
Hepatic HBV-miR-6 expression levels in CHB patients. HBV-miR-6 expression levels were measured in liver tissue derived from 87 CHB patients and 13 HBV negative controls using qPCR. Relative expression levels of HBV-miR-6 were normalized to GAPDH expression using the 2^−ΔCt method; the data are presented as a boxplot and whiskers. Full article ">Figure 4
Effect of HBV-miR-6 on the expression of predicted host targets and HBV replication. (A) HepG2 cells were transduced with a lentiviral vector expressing HBV-miR-6 or GFP. The expression levels of potential HBV-miR-6 target genes were measured using qPCR at day 6 after transduction. HepG2.2.15 cells were transduced using a lentiviral expressing HBV-miR-6 or GFP. HBV replication was determined at day 6 after transduction using qPCR detecting intracellular pgRNA (B) and encapsidated HBV-DNA (C) in culture supernatant. Relative gene expression levels were normalized to GFP control using the 2^−ΔΔCt method. Relative expression levels of pgRNA and HBV-DNA were normalized to GAPDH expression using the 2^−ΔCt method and groups were compared using a Mann–Whitney U test. Data are presented as a boxplot and whiskers; graphs represent averages of results from three independent experiments. Full article ">Figure 5
Effect of HBV-miR-6 on innate signaling. HepG2 cells were transduced with a lentiviral vector expressing GFP (grey) or HBV-miR-6 (black). After 48 h, the cells were stimulated with either IFNa (A,B), R848 (C,D) or ODN2216 (E,F). The expression levels of IFNa, IFNb, and ISGs (RASD2, ISG15, IFI44L, IFI27) were measured using qPCR at 6 h (A,C,E) or 16 h (B,D,F) after stimulation. Relative expression levels of mRNA were normalized to B-actin expression using the 2^−ΔCt method and groups were compared using a Mann–Whitney U test. Data are presented as a boxplot and whiskers; graphs represent averages of results from three independent experiments. Full article ">

10 pages, 2610 KiB

Open AccessArticle

Age-Specific Characteristics of Adult and Pediatric Respiratory Viral Infections: A Retrospective Single-Center Study

by Jae Kyoon Hwang, Jae Yoon Na, Jihye Kim, Jae-Won Oh, Yong Joo Kim and Young-Jin Choi

J. Clin. Med. 2022, 11(11), 3197; https://doi.org/10.3390/jcm11113197 - 3 Jun 2022

Cited by 4 | Viewed by 1694

Abstract

This study aimed to identify age-specific characteristics of respiratory viral infections. Hospitalized patients with confirmed viral respiratory infections were included in the sample. The patients were divided into the pediatric group (<19 years old) and the adult group (≥19 years old). The groups [...] Read more.

This study aimed to identify age-specific characteristics of respiratory viral infections. Hospitalized patients with confirmed viral respiratory infections were included in the sample. The patients were divided into the pediatric group (<19 years old) and the adult group (≥19 years old). The groups were then subdivided based on age: 0–6, 7–12, 13–18, 19–49, 50–64, and ≥65 years old. These groups were compared to evaluate the differences in the pattern of respiratory viral infections. Among a total of 4058 pediatric patients (mean age 3.0 ± 2.9 years, n = 1793 females), 2829 (48.9%) had mono-infections, while 1229 (51.1%) had co-infections. Co-infections were the most common in the 0–6-year-old group (31.6%). Among 1550 adult patients (mean age 70.2 ± 15.3 years, n = 710 females), 1307 (85.6%) had mono-infections and 243 (14.4%) had co-infections. Co-infections were most common in the ≥65-year-old group (16.8%). Viral infection and co-infection rates decreased with age in pediatric patients but increased with increasing age in adults. In pediatric patients, the rates of viral infections and co-infections were high; the rate of co-infections was higher in younger patients. In adult patients, the rates of viral infections and co-infections were lower than those in pediatric patients; the rate of co-infections was higher in older patients. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 1690 KiB

Open AccessArticle

Agrobacterium tumefaciens-Mediated Transformation of Candida glabrata

by Samantha D’Spain, Pilar I. Andrade, Nohelli E. Brockman, Jianmin Fu and Brian L. Wickes

J. Fungi 2022, 8(6), 596; https://doi.org/10.3390/jof8060596 - 2 Jun 2022

Cited by 3 | Viewed by 2059

Abstract

The use of broad-spectrum antimycotic therapy, immunosuppressive therapy, and indwelling medical devices has contributed to the increased frequency of mucosal and systemic infections caused by Candida glabrata. A major concern for C. glabrata and other Candida spp. infections is the increase in [...] Read more.

The use of broad-spectrum antimycotic therapy, immunosuppressive therapy, and indwelling medical devices has contributed to the increased frequency of mucosal and systemic infections caused by Candida glabrata. A major concern for C. glabrata and other Candida spp. infections is the increase in drug resistance. To address these issues, additional molecular tools for the study of C. glabrata are needed. In this investigation, we developed an Agrobacterium tumefaciens transformation system for C. glabrata. A number of parameters were investigated to determine their effect on transformation frequency, and then an optimized protocol was developed. The optimal conditions for the transformation of C. glabrata were found to be an infection incubation temperature of 26 °C, 0.2 mM acetosyringone in both induction media and co-culture media, 0.7% agar concentration, and a multiplicity of infection of 50:1 A. tumefaciens to C. glabrata. Importantly, the frequency of multiple integrations was low (5%), demonstrating that A. tumefaciens generally integrates at single sites in C. glabrata, which is consistent with other fungal A. tumefaciens transformation systems. The development of this system in C. glabrata adds another tool for the molecular manipulation of this increasingly important fungal pathogen. Full article

(This article belongs to the Topic Infectious Diseases)

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Flowchart of the ATMT protocol. Full article ">Figure 2
Wild-type C. glabrata was co-cultivated with A. tumefaciens containing plasmid p624 for 72 h at a variety of temperatures to determine the optimal temperature for transformant yield. Brackets with * above bars indicate groups with statistically significant differences. No significant difference indicated with ns. ns = p > 0.05, * = p ≤ 0.05. Full article ">Figure 3
The influence of acetosyringone concentration on transformation frequency. (A). Agrobacterium tumefaciens strain with plasmid p624 was cultured in induction media with various concentrations of acetosyringone and shaken for 6 h at 28 °C at 250 RPM and then mixed with wild-type C. glabrata, which were then placed onto nitrocellulose membranes and plated onto co-culture medium with an acetosyringone concentration of 1 × AS for 72 h at 26 °C. Brackets with **** above bars indicate groups with statistically significant differences. No significant difference indicated with ns. **** = p ≤ 0.0001, ns = p > 0.05. (B). Wild-type C. glabrata and A. tumefaciens were incubated on co-culture medium with various concentrations of acetosyringone for 72 h at 26 °C (the acetosyringone concentration in induction media was 1 × AS). Brackets with **** above bars indicate groups with statistically significant differences. **** = p ≤ 0.0001 (C) Combined acetosyringone conditions from (A,B). Brackets with **** above bars indicate groups with statistically significant differences. **** = p ≤ 0.0001. Full article ">Figure 4
The effect of agar concentration in co-culture media on transformation efficiency. Wild-type C. glabrata and A. tumefaciens were mixed onto nitrocellulose membranes and plated onto co-culture media with different percentages of agar. Brackets with **** or *** above bars indicate groups with statistically significant differences. *** = p ≤ 0.001, **** = p ≤ 0.0001. Full article ">Figure 5
The influence of the ratio of A. tumefaciens cells to C. glabrata cells. One hundred microliters of wild-type C. glabrata were placed on nitrocellulose membranes with various amounts of A. tumefaciens to determine the best ratio of cells to achieve the highest transformant yield. The membranes with C. glabrata and A. tumefaciens were then placed on to co-culture media and incubated for 72 h at 26 °C. Brackets with **** above bars indicate groups with statistically significant differences. **** = p ≤ 0.0001. Full article ">Figure 6
Identification of insertion site of 50:1 ratio of A. tumefaciens to C. glabrata transformants using vectorette PCR. (A). To confirm that increasing the ratio of A. tumefaciens to C. glabrata did not cause double insertions vectorette PCR was used to identify the insertion sites. One out of twenty samples showed a double insertion (Lane 5), meaning multiple insertions occurred at a 5% rate. The samples were flanked on each side with a 1.0 Kb Plus ladder size standard (L) (New England Biolabs, Ipswich, MA, USA). Full article ">Figure 7
Comparison of optimized conditions to standard baseline conditions. Using the data above, optimal conditions were chosen and compared to the standard protocol. Transformation frequency improved roughly 4-fold. Brackets with **** above bars indicate groups with statistically significant differences. **** = p ≤ 0.0001. Full article ">

9 pages, 266 KiB

Open AccessArticle

Risk Factors Leading to Enucleation or Evisceration in Infectious Endophthalmitis

by Ambar N. Lugo Merly, Lorena A. Montalvo Toledo, Guillermo A. Requejo, Alexander Meléndez, Samuel Álvarez, Andrés López, Radames Ríos, Victor M. Villegas and Armando L. Oliver

J. Clin. Med. 2022, 11(11), 3145; https://doi.org/10.3390/jcm11113145 - 1 Jun 2022

Viewed by 1937

Abstract

Endophthalmitis treatment consists of intravitreal antibiotics injections and, in selected circumstances, pars plana vitrectomy. However, severe or refractory cases may require an enucleation or evisceration (ENEV). Our study seeks to identify risk factors leading to enucleation or evisceration in patients with infectious endophthalmitis. [...] Read more.

Endophthalmitis treatment consists of intravitreal antibiotics injections and, in selected circumstances, pars plana vitrectomy. However, severe or refractory cases may require an enucleation or evisceration (ENEV). Our study seeks to identify risk factors leading to enucleation or evisceration in patients with infectious endophthalmitis. A retrospective chart review of subjects with a clinical diagnosis of infectious endophthalmitis was undertaken. The affected eyes were stratified into groups: those that underwent ENEV and those in which the eyeball was preserved (EP). The groups were compared using statistical analyses. In total, 69 eyes diagnosed with infectious endophthalmitis were included in the study. There was a higher frequency of exogenous infectious endophthalmitis in the ENEV group versus the EP group. Postsurgical infectious endophthalmitis was lower in the ENEV than in the EP group. A visual acuity of no light perception was more common in the ENEV compared to the EP group. Panophthalmitis was more frequent in the ENEV versus the EP group. Our findings suggest that eyes with endophthalmitis presenting with a visual acuity of no light perception, panophthalmitis, or exogenous etiology have a higher risk of requiring ENEV. In addition, eyes with a postsurgical etiology may be at a lower risk of requiring ENEV. Full article

(This article belongs to the Topic Infectious Diseases)

10 pages, 516 KiB

Open AccessArticle

Clinical Characteristics, Outcomes, and Risk Factors for Mortality in Patients with Stenotrophomonas maltophilia Bacteremia

by Siripen Kanchanasuwan, Jakkapan Rongmuang, Pisud Siripaitoon, Narongdet Kositpantawong, Boonsri Charoenmak, Thanaporn Hortiwakul, Ozioma Forstinus Nwabor and Sarunyou Chusri

J. Clin. Med. 2022, 11(11), 3085; https://doi.org/10.3390/jcm11113085 - 30 May 2022

Cited by 12 | Viewed by 2006

Abstract

This study aimed to establish the clinical features, outcomes, and factors associated with mortality in patients with Stenotrophomonas maltophilia (S. maltophilia) septicemia. The characteristics and outcome data used in this retrospective study were collected from medical records at Songklanagarind Hospital. [...] Read more.

This study aimed to establish the clinical features, outcomes, and factors associated with mortality in patients with Stenotrophomonas maltophilia (S. maltophilia) septicemia. The characteristics and outcome data used in this retrospective study were collected from medical records at Songklanagarind Hospital. Risk factors for survival were analyzed using χ²-tests, Kaplan–Meier curves, and Cox regression. A total of 117 patients with S. maltophilia bacteremia were analyzed. The patients’ median age was 45 years, 77 (70%) were male, 105 (90%) had comorbidities, 112 (96%) had previously undergone carbapenem therapy, and over half of the patients were on invasive medical devices. Trimethoprim-sulfamethoxazole (TMP-SMX) and fluoroquinolone showed high susceptibility rates to S. maltophilia, with 93% and 88% susceptibility, respectively. Patients who received appropriate empirical antibiotic treatment had significantly reduced 14-day, 30-day, and in-hospital mortality rates than those who did not (p < 0.001). The days of hospital stay and costs for those who received appropriate and inappropriate empirical antimicrobial treatment were 21 and 34 days (p < 0.001) and 142,463 and 185,663 baht, respectively (p < 0.002). Our results suggest that an appropriate empirical antibiotic(s) is significantly associated with lower 30-day mortality in hospitalized patients with S. maltophilia septicemia. Full article

(This article belongs to the Topic Infectious Diseases)

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13 pages, 1482 KiB

Open AccessArticle

Reinforcement of the Standard Therapy with Two Infusions of Convalescent Plasma for Patients with COVID-19: A Randomized Clinical Trial

by Joan Bargay-Lleonart, Fiorella Sarubbo, Maria Arrizabalaga, José Maria Guerra, Josep Borràs, Khaoulah El Haji, Magdalena Flexas, Jorge Perales, Victoria Fernández-Baca, Carmen Gallegos, Manuel Raya Cruz, Sonia Velasco, Víctor López, Ana Cruz, Antonia Bautista-Gili, Teresa Jimenez-Marco, Enric Girona-Llobera, Laia Vilaplana, Laura Calonge, Juan Tena, Maria Pilar Galán and Antoni Payeras Show full author list Hide full author list

J. Clin. Med. 2022, 11(11), 3039; https://doi.org/10.3390/jcm11113039 - 27 May 2022

Cited by 4 | Viewed by 2718

Abstract

Background: The aim was to evaluate the reinforcement of the standard therapy with hyperimmune plasma (HP) in Coronavirus-19 disease (COVID-19) patients. Methods: Open-label, multicenter, randomized clinical trial performed in three hospitals in the Balearic Islands. Non-severe COVID-19 hospitalized patients with clinical time evolution [...] Read more.

Background: The aim was to evaluate the reinforcement of the standard therapy with hyperimmune plasma (HP) in Coronavirus-19 disease (COVID-19) patients. Methods: Open-label, multicenter, randomized clinical trial performed in three hospitals in the Balearic Islands. Non-severe COVID-19 hospitalized patients with clinical time evolution equal to/less than 7 days were included, and randomized in: plasma group (PG) (n = 37), receiving 600 mL divided into two doses from convalescent plasma donor, administered on days 1 and 2 after the enrollment; and control group (CG) (n = 17). Primary outcome was the time for clinical improvement within 21 days, defined as patient achievement of categories 8, 7, and 6 in the Adaptive COVID-19 Treatment Trial scale (ACTT). The trial was terminated early due to the impossibility of recruitment due to the pandemic. Results: PG presented better scores on the ACTT scale at 7 days after HP infusion, whereas CG was needed 14 days to achieve similar results. The plasma infusion was safe. Conclusions: Despite the tendency observed in the plasma group to achieve slightly earlier better physical condition compared with the standard treatment alone. The administration of HP has been shown to be a safe therapy. No robust evidence was found to affirm a therapeutic effect of the early administration of two infusions of HP for non-severe COVID-19 infected patients. The interpretation is limited by the early termination of the trial, which resulted in a small sample size. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Patient Screening, Enrollment, Randomization, Follow-up, and Analysis Population. Full article ">Figure 2
Distribution of the Adaptive COVID-19 Treatment Trial scale (ACTT) score results in: (A) control group (CG) n = 17 and (B) plasma group (PG) n = 37, over the follow-up period (1, 3, 7, 14, and 21 days after the first infusion). Bars represent the percentage of patients with respect to the total in each group that present each score (from 8 to 1) in the time-point mentioned. The meaning of each score is explained in the ACTT Scale legend. *** p < 0.001, when using the χ2 test to compare the scores at 7, 14, and 21 days with respect to day 1 in each group; ††† p < 0.001, when using the χ2 test to compare the scores at 7 and 14 days in the PG with respect to the scores at 7 and 14 days in the CG. Scores considered as a clinical improvement are marked in bold. Full article ">Figure 3
Changes in immunity parameters at baseline, 1, 3, 7, 14, and 21 days after the first plasma infusion comparing the control group (CG) with the plasma group (PG). (A) Evolution of anti-SARS-CoV-2 S IgG serum titer (AU/mL) in CG and PG patients, expressed as mean ± SEM at each time point. *** p < 0.001, ** p < 0.01, when compared by two-way ANOVA repeat measures followed by the post hoc Tukey test, the levels of anti-SARS-CoV-2 S IgG serum titer at 21 days with respect to the baseline in each group. (B) Comparison of the anti-SARS-CoV-2 IgG serum titer (AU/mL) at 21 days respect the baseline, expressed as mean ± SEM, in CG and PG. *** p < 0.001, ** p < 0.01, when compared by one-way ANOVA followed by the post hoc Tukey test, the levels of anti-SARS-CoV-2 S IgG serum titer at 21 days with respect to the baseline in each group. (C) Correlation between the levels of anti-SARS-CoV-2 S IgG titers in PG serum vs. donor plasma bag received at 24 h after the last infusion; the correlation was performed using the Pearson test r2 = 0.5, p < 0.05. (D) Distribution of the levels of anti-SARS-CoV-2 S IgG titers (AU/mL) in each group 24 h after the last plasma infusion. The horizontal bars indicate medians and the dotted line interquartile ranges. Each circle represents one patient. Full article ">Figure 4
Evolution of the vital signs in control group (CG) and plasma group (PG), from baseline and at 1, 3, 7, 14, and 21 days after the enrollment, including: (A) diastolic blood pressure (mmHg), (B) systolic blood pressure (mmHg), (C) temperature (°C), (D) cardiac frequency (beat/min), (E) respiratory frequency (breath/min), and (F) oxygen saturation (%). Each variable is expressed as the mean ± SEM obtained in each group. There were no statistical differences by one-way ANOVA followed by the Tukey post hoc test. Full article ">

7 pages, 2312 KiB

Open AccessCase Report

Isavuconazole Treatment of Spinal Cord Invasive Aspergillosis Guided by Cerebrospinal Fluid (1,3)-β-d-Glucan Levels in a Patient with Low Interferon-Gamma and Ulcerative Colitis

by Siobhan O’Regan, Brendan O’Kelly, Paul Reidy, Aoibhlinn O’Toole, John Caird, Cora McNally, Samuel McConkey and Eoghan De Barra

J. Fungi 2022, 8(6), 557; https://doi.org/10.3390/jof8060557 - 25 May 2022

Viewed by 2188

Abstract

This case highlights the use of (1,3)-beta-d glucan to direct treatment of a cervical spinal cord Aspergillus fumigatus infection in a 22-year-old woman immunocompromised due to steroid and anti-TNF therapy in the context of ulcerative colitis and interferon gamma deficiency. A 4-year treatment [...] Read more.

This case highlights the use of (1,3)-beta-d glucan to direct treatment of a cervical spinal cord Aspergillus fumigatus infection in a 22-year-old woman immunocompromised due to steroid and anti-TNF therapy in the context of ulcerative colitis and interferon gamma deficiency. A 4-year treatment course requiring neurosurgical intervention on four occasions and prolonged antifungal therapy, including isavuconazole, resulted in clinical cure with a corresponding decrease in CSF beta-d-glucan to <30 pg/mL. Serum and CSF galactomannan levels were not elevated at any point during the clinical course. Full article

(This article belongs to the Topic Infectious Diseases)

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15 pages, 3042 KiB

Open AccessArticle

Mongolia Gerbils Are Broadly Susceptible to Hepatitis E Virus

by Wenjing Zhang, Yasushi Ami, Yuriko Suzaki, Yen Hai Doan, Masamichi Muramatsu and Tian-Cheng Li

Viruses 2022, 14(6), 1125; https://doi.org/10.3390/v14061125 - 24 May 2022

Cited by 13 | Viewed by 1952

Abstract

Although cell culture systems for hepatitis E virus (HEV) have been established by using cell lines such as PLC/PRF/5 and A549, small-animal models for this virus are limited. Since Mongolia gerbils are susceptible to genotype 1, 3 and 4 HEV (HEV-1, HEV-3 and [...] Read more.

Although cell culture systems for hepatitis E virus (HEV) have been established by using cell lines such as PLC/PRF/5 and A549, small-animal models for this virus are limited. Since Mongolia gerbils are susceptible to genotype 1, 3 and 4 HEV (HEV-1, HEV-3 and HEV4), we intraperitoneally inoculated Mongolia gerbils with HEV-5, HEV-7, HEV-8, rabbit HEV or rat HEV in addition to the above three genotypes to investigate the infectivity and to assess whether Mongolia gerbil is an appropriate animal model for HEV infection. The results indicated that (i) HEV-5 and rat HEV were effectively replicated in the Mongolia gerbils in the same manner as HEV-4: large amounts of the viral RNA were detected in the feces and livers, and high titers of the serum anti-HEV IgG antibodies were induced in all animals. The feces were shown to contain HEV that is infectious to naïve gerbils. Furthermore, HEV-4, HEV-5 and rat HEV were successfully transmitted to the gerbils by oral inoculation. (ii) Although the viral RNA and serum anti-HEV IgG antibodies were detected in all animals inoculated with HEV-1 and HEV-8, both titers were low. The viral RNA was detected in the feces collected from two of three HEV-3-inoculated, and one of three HEV-7-inoculated gerbils, but the titers were low. The serum antibody titers were also low. The viruses excreted into the feces of HEV-1-, HEV-3-, HEV-7- and HEV-8-inoculated gerbils failed to infect naïve Mongolia gerbils. (iii) No infection sign was observed in the rabbit HEV-inoculated gerbils. These results demonstrated that Mongolia gerbils are broadly susceptible to HEV, and their degree of sensitivity was dependent on the genotype. Mongolia gerbils were observed to be susceptible to not only HEVs belonging to HEV-A but also to rat HEV belonging to HEV-C1, and thus Mongolia gerbil could be useful as a small-animal model for cross-protection experiments between HEV-A and HEV-C1. Mongolia gerbils may also be useful for the evaluation of the efficacy of vaccines against HEV. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
HEV replication in Mongolia gerbils. Twenty-seven Mongolia gerbils were randomly separated into nine groups (n = 3 per group). Individual gerbils are indicated by ○, △ and ☐ (a,b) or white, gray and black bars (c). Each group received HEV-1, HEV-3, HEV-4, HEV-5, HEV-7, HEV-8, rabbit HEV, rat HEV or phosphate-buffered saline (PBS) via intraperitoneal injection. The kinetics of the viral RNA in the fecal specimens were measured by RT-qPCR (a). The serum and tissue samples were collected at the end of the experiment (day 28 p.i.), and the anti-HEV-IgG antibody titers were determined using an ELISA with the VLPs of HEV-1 (to detect HEV-1, HEV-3, HEV-4, HEV-5, HEV-7, HEV-8 or rabbit HEV) or those of rat HEV (to detect rat HEV) as the antigens (b). Dotted lines: the cut-off values. The minimum endpoints of the antibody titers are blackened (●, ▲, ■) (b). The viral RNA titers in the liver, spleen and serum samples (c). Full article ">Figure 1 Cont.
HEV replication in Mongolia gerbils. Twenty-seven Mongolia gerbils were randomly separated into nine groups (n = 3 per group). Individual gerbils are indicated by ○, △ and ☐ (a,b) or white, gray and black bars (c). Each group received HEV-1, HEV-3, HEV-4, HEV-5, HEV-7, HEV-8, rabbit HEV, rat HEV or phosphate-buffered saline (PBS) via intraperitoneal injection. The kinetics of the viral RNA in the fecal specimens were measured by RT-qPCR (a). The serum and tissue samples were collected at the end of the experiment (day 28 p.i.), and the anti-HEV-IgG antibody titers were determined using an ELISA with the VLPs of HEV-1 (to detect HEV-1, HEV-3, HEV-4, HEV-5, HEV-7, HEV-8 or rabbit HEV) or those of rat HEV (to detect rat HEV) as the antigens (b). Dotted lines: the cut-off values. The minimum endpoints of the antibody titers are blackened (●, ▲, ■) (b). The viral RNA titers in the liver, spleen and serum samples (c). Full article ">Figure 2
Infectivity of HEV discharged into the feces. Three groups of Mongolia gerbils (n = 3 per group) were inoculated with the 10% stool suspension prepared from the HEV-4-inoculated, HEV-5-inoculated or rat HEV-inoculated gerbils. Individual gerbils are indicated by ○, △ and ☐ (a,b,d,e,g,h) or white, gray and black bars (c,f,i). The kinetics of the viral RNA in the fecal specimens were determined by RT-qPCR (a,d,g). The serum and tissue samples were collected at the end of the experiment (day 42 p.i.). The serum anti-HEV IgG antibodies were measured using an ELISA with either VLPs of HEV-1 (to detect HEV-4 and HEV-5) or those of rat HEV (to detect rat HEV) as the antigens. Dotted lines: the cut-off values and the minimum endpoints of the antibody titers are blackened (●, ▲, ■) (b,e,h). The viral RNA titers detected in the liver, spleen and serum (c,f,i). Full article ">Figure 3
Detection of the viral RNA in the tissues in the early stage of infection. Six Mongolia gerbils were randomly separated into two groups (n = 3 per group). Individual gerbils are indicated by white, gray and black bars. One group was inoculated with HEV-4 (a) and the other with rat HEV (b) via intraperitoneal injection. All gerbils were euthanized on day 14 p.i. The serum samples, intestinal contents, liver, spleen, heart, lung, kidney, pancreas, salivary gland, thymus, muscle and brain were collected, and the viral RNA was measured by RT-qPCR. Full article ">Figure 4
HEV-4, HEV-5 and rat HEV orally transmitted to Mongolia gerbils. Nine Mongolia gerbils were randomly separated into three groups (n = 3 per group). Individual gerbils are indicated by ○, △ and ☐ (a,b,d,e,g,h) or white, gray and black bars (c,f,i). Each group was orally inoculated with HEV-4, HEV-5 or rat HEV. The kinetics of the viral RNA in the fecal specimens were determined by RT-qPCR (a,d,g). The liver, spleen, bile and serum samples were collected at the end of the experiment (day 26 p.i.). The serum anti-HEV IgG antibodies were detected by using an ELISA with either the VLPs of HEV-1 (to detect HEV-4 and HEV-5) or those of rat HEV (to detect rat HEV) as the antigens. Dotted lines: the cut-off value and the minimum endpoints of the antibody titers were blackened (●, ▲, ■) (b,e,h). The viral RNA titers in the liver, spleen, bile and serum (c,f,i). Full article ">

13 pages, 764 KiB

Open AccessArticle

Association between Following the ESCMID Guidelines for the Management of Candidemia and Mortality: A Retrospective Cohort Study

by Charles Maurille, Julie Bonhomme, Anaïs R. Briant, Jean-Jacques Parienti, Renaud Verdon and Anna Lucie Fournier

J. Fungi 2022, 8(5), 541; https://doi.org/10.3390/jof8050541 - 23 May 2022

Cited by 3 | Viewed by 2271

Abstract

Objectives: The objective of this study was to evaluate the association between ESCMID adherence and 30-day mortality in candidemia. Methods: We performed a retrospective cohort study in two French tertiary-care hospitals. All patients with at least one positive blood culture (BC) for Candida [...] Read more.

Objectives: The objective of this study was to evaluate the association between ESCMID adherence and 30-day mortality in candidemia. Methods: We performed a retrospective cohort study in two French tertiary-care hospitals. All patients with at least one positive blood culture (BC) for Candida spp. between January 2013 and December 2019 were included. An adherent case was defined as a candidemia case for which the treatment fulfilled a bundle of defined criteria based on the latest ESCMID recommendations. We explored factors associated with adherence to ESCMID recommendations in an unadjusted model, and we used a propensity score method to address potential channeling biases with regard to 30-day mortality. Results: During the study period, 165 cases of candidemia were included. Among the ESCMID criteria, funduscopic examination was not performed in 45% and neither was echocardiography in 31%, while the ESCMID criteria were fully implemented in 44 cases (27%). In the propensity score analysis, the all-cause 30-day mortality rate was significantly lower among adherent cases (3.4/36.6, 9%) than among nonadherent cases (42.4/119.5, 36%) (OR = 5.3 95% CI [1.6–17.1]). Conclusions: In our study, adherence to the bundle of criteria for candidemia management was associated with increased survival, supporting additional efforts to implement these recommendations. Full article

(This article belongs to the Topic Infectious Diseases)

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18 pages, 2124 KiB

Open AccessArticle

Elevated Ozone Concentration and Nitrogen Addition Increase Poplar Rust Severity by Shifting the Phyllosphere Microbial Community

by Siqi Tao, Yunxia Zhang, Chengming Tian, Sébastien Duplessis and Naili Zhang

J. Fungi 2022, 8(5), 523; https://doi.org/10.3390/jof8050523 - 18 May 2022

Cited by 8 | Viewed by 2540

Abstract

Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O₃ and the complementary effect of soil N addition on the physiological properties of trees. However, it has been [...] Read more.

Tropospheric ozone and nitrogen deposition are two major environmental pollutants. A great deal of research has focused on the negative impacts of elevated O₃ and the complementary effect of soil N addition on the physiological properties of trees. However, it has been overlooked how elevated O₃ and N addition affect tree immunity in face of pathogen infection, as well as of the important roles of phyllosphere microbiome community in host–pathogen–environment interplay. Here, we examined the effects of elevated O₃ and soil N addition on poplar leaf rust [Melampsora larici-populina] severity of two susceptible hybrid poplars [clone ‘107’: Populus euramericana cv. ‘74/76’; clone ‘546’: P. deltoides Í P. cathayana] in Free-Air-Controlled-Environment plots, in addition, the link between Mlp-susceptibility and changes in microbial community was determined using Miseq amplicon sequencing. Rust severity of clone ‘107’ significantly increased under elevated O₃ or N addition only; however, the negative impact of elevated O₃ could be significantly mitigated when accompanied by N addition, likewise, this trade-off was reflected in its phyllosphere microbial α-diversity responding to elevated O₃ and N addition. However, rust severity of clone ‘546’ did not differ significantly in the cases of elevated O₃ and N addition. Mlp infection altered microbial community composition and increased its sensitivity to elevated O₃, as determined by the markedly different abundance of taxa. Elevated O₃ and N addition reduced the complexity of microbial community, which may explain the increased severity of poplar rust. These findings suggest that poplars require a changing phyllosphere microbial associations to optimize plant immunity in response to environmental changes. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Rust severity of poplar foliar rust in four ambient ozone concentration FACE plots (A-O3) and four elevated ozone concentration FACE plots (E-O3) under two N treatments (N0 = no addition of nitrogen, N60 = addition of 60 kg/ha nitrogen every month). The significant differences between treatments at the 0.05 probability were indicated as the asterisk (*) according to the two-tailed Wilcoxon test; ns: not significant. Full article ">Figure 2
Taxonomic structures of phyllosphere bacterial microbiota at the class level (a) and fungal microbiota at the genus level (b). Only the 12 families with the largest mean relative abundance are shown. Full article ">Figure 3
Shannon indices of phyllosphere communities of non-infected leaves and Mlp-infected leaves of the clone ‘107’ (a,b) and the clone ‘546’ clone (c,d) from ambient ozone concentration plots (A-O3) and elevated ozone concentration plots (E-O3) with nitrogen addition (N60) and without nitrogen addition (N0). Box plots showed the range of estimated values between 25% and 75%, the median, the minimum, and the maximum observed values within each dataset. Full article ">Figure 4
PCoA of bacterial and fungal communities using the weighted_unifrac distance for bacteria (a) and unweighted unifrac distance for fungi (b). Samples are sorted for ozone concentration (A-O3 vs. E-O3) and nitrogen treatment (N0 vs. N60). Full article ">Figure 5
The Mental tests and Spearman’s correlation coefficients between α-diversity indices of Melampsora larici-populina-infected poplar phyllosphere fungal and bacterial communities with nitrogen addition, ozone concentration (Ozone), leaf dry weight (DW), leaf nitrogen and carbon content, and rust severity. Full article ">Figure 6
The co-occurrence networks (a) and trends of microbial network association indices (b) of phyllosphere microbiome for two hybrid poplars (‘107’ and ‘546’) in five conditions. No (a) biotic stresses (control), N addition (N), elevated O3 (O3), N addition with elevated O3 (N + O3), N addition, elevated O3 with Melampsora-larici populina infection (N + O3 + Mlp). Full article ">

21 pages, 2999 KiB

Open AccessArticle

Heme Oxygenase-1 (HMX1) Loss of Function Increases the In-Host Fitness of the Saccharomyces ‘boulardii’ Probiotic Yeast in a Mouse Fungemia Model

by Alexandra Imre, Renátó Kovács, Zoltán Tóth, László Majoros, Zsigmond Benkő, Walter P. Pfliegler and István Pócsi

J. Fungi 2022, 8(5), 522; https://doi.org/10.3390/jof8050522 - 18 May 2022

Viewed by 3253

Abstract

The use of yeast-containing probiotics is on the rise; however, these products occasionally cause fungal infections and possibly even fungemia among susceptible probiotic-treated patients. The incidence of such cases is probably underestimated, which is why it is important to delve deeper into the [...] Read more.

The use of yeast-containing probiotics is on the rise; however, these products occasionally cause fungal infections and possibly even fungemia among susceptible probiotic-treated patients. The incidence of such cases is probably underestimated, which is why it is important to delve deeper into the pathomechanism and the adaptive features of S. ‘boulardii’. Here in this study, the potential role of the gene heme oxygenase-1 (HMX1) in probiotic yeast bloodstream-derived infections was studied by generating marker-free HMX1 deletion mutants with CRISPR/Cas9 technology from both commercial and clinical S. ‘boulardii’ isolates. The six commercial and clinical yeasts used here represented closely related but different genetic backgrounds as revealed by comparative genomic analysis. We compared the wild-type isolates against deletion mutants for their tolerance of iron starvation, hemolytic activity, as well as kidney burden in immunosuppressed BALB/c mice after lateral tail vein injection. Our results reveal that the lack of HMX1 in S. ‘boulardii’ significantly (p < 0.0001) increases the kidney burden of the mice in most genetic backgrounds, while at the same time causes decreased growth in iron-deprived media in vitro. These findings indicate that even a single-gene loss-of-function mutation can, surprisingly, cause elevated fitness in the host during an opportunistic systemic infection. Our findings indicate that the safety assessment of S. ‘boulardii’ strains should not only take strain-to-strain variation into account, but also avoid extrapolating in vitro results to in vivo virulence factor determination. Full article

(This article belongs to the Topic Infectious Diseases)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Schematic depiction of free heme and hemoglobin-heme acquisition and utilization in C. albicans and S. cerevisiae: (a) C. albicans have heme-binding, GPI anchored CFEM cell surface proteins, with which uptake of external heme is possible through endocytosis. CaHmx1 is able to break down heme; however, several steps of heme-iron utilization have not yet been fully understood (indicated by question marks); (b) S. cerevisiae does not have heme-binding cell surface molecules, and thus it is unable to utilize external free heme or hemoglobin-heme. In this yeast, Hmx1 is an ER-bound enzyme that utilizes intracellular heme as an iron source. Full article ">Figure 2
Genomic comparison of the yeast isolates used for the deletion of HMX1. (a) Heterozygous variant density (per 10 kb) across chromosomes for the isolate PY0001 (top) and changes in allele ratios, i.e., gains and losses of heterozygous regions in the other five isolates (bottom). (b) Gene copy number variations in the six sequenced isolates. (c) The distribution of protein-coding genes affected by high- and medium-effect mutations. The total number of affected genes for combinations of isolates are shown at the bottom, each genome is represented by a circle colored according to isolate type (commercial, non-mycosis, mycosis). Full article ">Figure 3
Relative yeast growth under iron starvation: (a) bars show the mean results for the wild type S. ‘boulardii’ isolate triplicates (full grey bars) and for the ΔΔHMX1 mutant strain triplicates (striped bars) (for the second spot with 5000 plated cells). Individual data points are shown in blue (40 µM BPS), orange (80 µM BPS), and red (120 µM BPS), and whiskers show the standard deviation of the data. Comparisons with significant differences are marked (*: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001). (b) Photos of iron deprivation spot plate assay. Columns represent the wild type isolate vs. ΔΔHMX1 mutant strain pairs by BPS concentration. Raw photographs, including control plates without BPS, are uploaded to FigShare. Full article ">Figure 4
Comparison of growth curves of the isolates and HMX1 deletion strains in medium of 50% RPMI-1640 and 50% human serum. Individual data points for wild-type strains are indicated with black, while data for the knockout mutants are indicated with red. Data points of each replicate are connected by a line. Comparisons with significant differences are marked (*: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001). Full article ">Figure 5
Hemolytic index. Bars show the mean results for the wild type S. ‘boulardii’ isolates (full grey) and for the ΔΔHMX1 mutant strains (striped). Individual data points are shown in green (α-hemolysis) and black (β-hemolysis), and whiskers show the standard deviation of the data. Comparisons with significant differences are marked (*: p < 0.05; **: p < 0.01). Full article ">Figure 6
Kidney burden of mice injected with yeast probiotic isolates and HMX1 deletion mutant strains. Individual data points represent the colony forming units per kidney weight (g) for every mouse. Data from mice that died during or were killed at the end of the experiment are both plotted. Horizontal black lines show the median of the datapoints within a dataset. Comparisons with significant differences are marked (*: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001). Full article ">

18 pages, 1703 KiB

Open AccessArticle

Hepatitis B Virus Infection among Japanese Immigrants and Descendants: The Need to Strengthen Preventive and Control Measures

by Luiz Henrique Ferraz Demarchi, Larissa Melo Bandeira, Deborah Ledesma Taira, Marina Castilhos Souza Umaki Zardin, Mary Luizia Ibanhes, Ana Olivia Pascoto Esposito, Larissa Domingues Castilho De Arruda, Crhistinne Cavalheiro Maymone Gonçalves, Sabrina Moreira dos Santos Weis-Torres, Gabriela Alves Cesar, Rivaldo Venâncio Da Cunha, Tayana Serpa Ortiz Tanaka, Marco Antonio Moreira Puga, Grazielli Rocha De Rezende, Roberta Barbosa Lopes, Silvia Naomi de Oliveira Uehara, João Renato Rebello Pinho, Flair Jose Carrilho, Michele Soares Gomes-Gouvêa and Ana Rita Coimbra Motta-Castro

Viruses 2022, 14(5), 1085; https://doi.org/10.3390/v14051085 - 18 May 2022

Cited by 1 | Viewed by 2541

Abstract

This cross-sectional study aimed to investigate the prevalence and risk factors of Hepatitis B virus infection among Japanese immigrants and their descendants from São Paulo (SP), and to verify the occurrence of occult hepatitis B and coinfection with HCV, Delta, and HTLV. All [...] Read more.

This cross-sectional study aimed to investigate the prevalence and risk factors of Hepatitis B virus infection among Japanese immigrants and their descendants from São Paulo (SP), and to verify the occurrence of occult hepatitis B and coinfection with HCV, Delta, and HTLV. All samples (n = 2.127) were tested for HBV serological markers by electrochemiluminescence. HBsAg and/or total anti-HBc positive samples were tested for HBV DNA by real-time PCR, and genotyped by sequencing using the Sanger methodology. The prevalence rate of HBV exposure was 13.4% (CI 95%: 11.9–14.9%), and 22 (1.1%) were HBsAg positive. A high rate of susceptibility to HBV infection was found (67.4%; CI 95%: 65.4–69.4%). In contrast, only 19.2% (CI 95%: 17.6–20.9%) presented a serological profile analogous to that elicited by Hepatitis B vaccination. HBV isolates (n = 8) were classified as genotypes HBV/B1 (62.5%), HBV/C2 (12.5%), HBV/F1b (12.5%), and HBV/A1 (12.5%). Hepatitis B vaccination strategies and educational measures to control this infection should be considered. Full article

(This article belongs to the Topic Infectious Diseases)

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HBV serological profile among Japanese immigrants and their descendants according to age (years), Brazil (n = 2.127). Full article ">Figure 2
The maximum clade credibility (MCC) tree estimated by Bayesian analysis of S/POL sequences with 1270 bp of HBV strains characterized from Japanese immigrants and descendants living in São Paulo, Brazil. For better visualization, only clades of HBV/B1 and C2 are shown in this figure. Sequences characterized in this study are in red; sequences obtained from GenBank (n = 306) are indicated by their corresponding accession number, genotype, and geographic origin. The values of posterior probability are shown for key nodes. Full article ">Figure 3
Pedigree of 12 families of index cases (HBsAg-positive) under study, São Paulo—SP. Full article ">Figure 4
The maximum clade credibility (MCC) tree estimated by Bayesian analysis of S/POL sequences with 1270 bp of HBV strains characterized from Japanese immigrants and descendants living in São Paulo, Brazil. For better visualization, only clades of HBV/A1 and F1b are shown in this figure. Sequences characterized in this study are in red; sequences obtained from GenBank (n = 306) are indicated by their corresponding accession number, genotype, and geographic origin. The values of posterior probability are shown for key nodes. Full article ">

12 pages, 280 KiB

Open AccessArticle

Predictors of Poor Outcome among Critically Ill COVID-19 Patients: A Nationally Representative Sample of the Saudi Arabian Population

by Masaad Saeed Almutairi, Ahmed M. Assiri and Omar A. Almohammed

J. Clin. Med. 2022, 11(10), 2818; https://doi.org/10.3390/jcm11102818 - 17 May 2022

Cited by 1 | Viewed by 1751

Abstract

The outbreak and continuing impact of COVID-19 have significantly increased the rates of hospitalization and admissions to intensive care units (ICU). This study evaluates clinical outcomes in critically ill patients and investigates variables tied to poor prognosis. A secondary database analysis was conducted [...] Read more.

The outbreak and continuing impact of COVID-19 have significantly increased the rates of hospitalization and admissions to intensive care units (ICU). This study evaluates clinical outcomes in critically ill patients and investigates variables tied to poor prognosis. A secondary database analysis was conducted to investigate the predictors of poor outcome among critically ill COVID-19 patients in Saudi Arabia. Multivariable logistic regression analysis was used to assess the association between various demographic characteristics, comorbidities, and COVID-19 symptoms and patients’ poor prognosis, as a composite outcome. A total of 2257 critically ill patients were identified (male (71.8%), and elderly (37.3%)). The mortality rate was 50.0%, and the composite poor outcome was 68.4%. The predictors of poor outcome were being elderly (OR = 4.79, 95%CI 3.19–7.18), obesity (OR = 1.43, 95%CI 1.1–1.87), having a severe or critical case at admission (OR = 6.46, 95%CI 2.34–17.8; OR = 22.3, 95%CI 11.0–45, respectively), and some signs and symptoms of COVID-19 such as shortness of breath, feeling fatigued or headache, respiratory rate ≥ 30/min, PaO₂/FiO₂ ratio < 300, and altered consciousness. In conclusion, identifying high-risk populations that are expected to have a poor prognosis based on their criteria upon admission helps policymakers and practitioners better triage patients when faced with limited healthcare resources. Full article

(This article belongs to the Topic Infectious Diseases)

12 pages, 1589 KiB

Open AccessArticle

Epidemiology and Molecular Analyses of Influenza B Viruses in Senegal from 2010 to 2019

by Cheikh Talibouya Touré, Amary Fall, Soa Fy Andriamandimby, Mamadou Malado Jallow, Deborah Goudiaby, Davy Kiori, Sara Sy, Yague Diaw, Koba Ndiende Ndiaye, Fatimata Mbaye, Mbayang Ndiaye Niang, Jean Michel Heraud and Ndongo Dia

Viruses 2022, 14(5), 1063; https://doi.org/10.3390/v14051063 - 16 May 2022

Cited by 4 | Viewed by 2653

Abstract

Influenza virus types A and B are responsible for acute viral infections that affect annually 1 billion people, with 290,000 to 650,000 deaths worldwide. In this study, we investigated the circulation of influenza B viruses over a 10-year period (2010–2019). Specimens from patients [...] Read more.

Influenza virus types A and B are responsible for acute viral infections that affect annually 1 billion people, with 290,000 to 650,000 deaths worldwide. In this study, we investigated the circulation of influenza B viruses over a 10-year period (2010–2019). Specimens from patients suspected of influenza infection were collected. Influenza detection was performed following RNA extraction and real-time RT-PCR. Genes coding for hemagglutinin (HA) and neuraminidase (NA) of influenza B viruses were partially sequenced, and phylogenetic analyses were carried out subsequently. During the study period, we received and tested a total of 15,156 specimens. Influenza B virus was detected in 1322 (8.7%) specimens. The mean age of influenza B positive patients was 10.9 years. When compared to reference viruses, HA genes from Senegalese circulating viruses showed deletions in the HA1 region. Phylogenetic analysis highlighted the co-circulation of B/Victoria and B/Yamagata lineage viruses with reassortant viruses. We also noted a clear seasonal pattern of circulation of influenza B viruses in Senegal. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 4819 KiB

Open AccessArticle

In Vivo Efficacy of Amphotericin B against Four Candida auris Clades

by Lajos Forgács, Andrew M. Borman, Renátó Kovács, Dávid Balázsi, Zoltán Tóth, Bence Balázs, Chiu Chun-Ju, Gábor Kardos, Ilona Kovacs and László Majoros

J. Fungi 2022, 8(5), 499; https://doi.org/10.3390/jof8050499 - 11 May 2022

Cited by 2 | Viewed by 2756

Abstract

Candida auris is a multidrug-resistant fungus against which in some clinical situations amphotericin B (AMB) remains the alternative or first line drug. We compared daily 1 mg/kg of AMB efficacy in a neutropenic murine bloodstream infection model against 10 isolates representing four C. [...] Read more.

Candida auris is a multidrug-resistant fungus against which in some clinical situations amphotericin B (AMB) remains the alternative or first line drug. We compared daily 1 mg/kg of AMB efficacy in a neutropenic murine bloodstream infection model against 10 isolates representing four C. auris clades (South Asian n = 2; East Asian n = 2; South African n = 2; South American n = 4; two of which were of environmental origin). Five days of AMB treatment significantly increased the survival rates in mice infected with isolates of the East Asian clade, and 1 isolate each from the South African and South American clades (originated from bloodstream), but not in mice infected with the South Asian and 2 environmental isolates from the South American clades. AMB treatment decreased the fungal burden in mice infected with the 2 isolates each from East Asian and South African, and 1 out of 2 bloodstream isolates from South American clades in the hearts (p < 0.01), kidneys (p < 0.01) and brain (p < 0.05). AMB treatment, regardless of clades, significantly decreased colony forming units in the urine at day 3. However, histopathological examination in AMB-treated mice revealed large aggregates of yeast cells in the kidneys and hearts, and focal lesions in the cerebra and cerebelli, regardless of precise C. auris clade. Our clade-specific data confirm that the efficacy of AMB against C. auris is weak, explaining the therapeutic failures in clinical situations. Our results draw attention to the necessity to maximize the killing at the start of treatment to avoid later complications in the heart and central nervous system. Full article

(This article belongs to the Topic Infectious Diseases)

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9 pages, 4619 KiB

Open AccessCommunication

Evaluation of a Novel Chromogenic Medium for the Detection of Pseudomonas aeruginosa in Respiratory Samples from Patients with Cystic Fibrosis

by Thang V. Truong, Alexander Twist, Andrey Zaytsev, Emma C. L. Marrs, Audrey Perry, Graeme Turnbull, Sylvain Orenga, Stephen P. Stanforth and John D. Perry

Microorganisms 2022, 10(5), 1004; https://doi.org/10.3390/microorganisms10051004 - 10 May 2022

Cited by 2 | Viewed by 5647

Abstract

Pseudomonas aeruginosa is a dominant cause of respiratory infection in individuals with cystic fibrosis (CF), leading to significant morbidity and mortality. Detection of P. aeruginosa is conducted by culture of respiratory samples but this process may occasionally be compromised due to overgrowth by [...] Read more.

Pseudomonas aeruginosa is a dominant cause of respiratory infection in individuals with cystic fibrosis (CF), leading to significant morbidity and mortality. Detection of P. aeruginosa is conducted by culture of respiratory samples but this process may occasionally be compromised due to overgrowth by other bacteria and fungi. We aimed to evaluate a novel chromogenic medium, Pseudomonas aeruginosa chromogenic agar (PACA), for culture of P. aeruginosa from respiratory samples, from patients with CF. A total of 198 respiratory samples were cultured onto PACA and three other media: CHROMID^®P. aeruginosa, CHROMagar™ Pseudomonas and MacConkey agar. P. aeruginosa was recovered from 66 samples (33%), using a combination of all media. After 72 h incubation, the sensitivity of the four chromogenic media was as follows: 91% for PACA and CHROMagar™ Pseudomonas, 85% for CHROMID^®P. aeruginosa and 83% for MacConkey agar. For the three chromogenic media, the positive predictive value after 72 h was as follows: 95% for PACA, 56% for CHROMagar™ Pseudomonas and 86% for CHROMID^®P. aeruginosa. PACA proved to be a highly effective culture medium for the isolation and specific detection of P. aeruginosa from respiratory samples. Full article

(This article belongs to the Topic Infectious Diseases)

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14 pages, 485 KiB

Open AccessArticle

Differences in Expression of Selected Interleukins in HIV-Infected Subjects Undergoing Antiretroviral Therapy

by Beata Szymańska, Karolina Jurkowska, Brygida Knysz and Agnieszka Piwowar

Viruses 2022, 14(5), 997; https://doi.org/10.3390/v14050997 - 7 May 2022

Cited by 3 | Viewed by 1899

Abstract

The use of combined antiretroviral therapy (cART) inhibits the replication of the Human Immunodeficiency Virus (HIV) and thus may affect the functioning of the immune system, e.g., induce changes in the expression of certain cytokines. The aim was to examine the effect of [...] Read more.

The use of combined antiretroviral therapy (cART) inhibits the replication of the Human Immunodeficiency Virus (HIV) and thus may affect the functioning of the immune system, e.g., induce changes in the expression of certain cytokines. The aim was to examine the effect of cART on the expression of selected cytokines: interleukin -4, -7 and -15 in HIV-infected subjects. The test material was the plasma of HIV-infected men and healthy men (C, control group). The levels of interleukin were measured by immunoenzymatic method before cART and one year after treatment in relation to the C group. HIV-infected men were analyzed in subgroups depending on the HIV-RNA viral load, CD4⁺ and CD8⁺T-cell counts, and the type of therapeutic regimen. A significantly higher level of IL-4 was demonstrated in HIV-infected men before cART compared to those after treatment and in the control group. The use of cART resulted in a significant decrease in the level of IL-7 in HIV-infected men; however, high levels of IL-7 were associated with a low number of CD4⁺ T cells and CD8⁺ T cells. An increase in the level of IL-15 in HIV-infected men was noted after the use of cART. There was no difference in the expression of interleukins depending on the treatment regimen used. The study showed the effect of cART on the expression of interleukins, especially IL-4 and IL-7. Further research in this direction seems promising, confirming the role of these interleukins in the course of the disease. Full article

(This article belongs to the Topic Infectious Diseases)

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15 pages, 3538 KiB

Open AccessArticle

A Unique Robust Dual-Promoter-Driven and Dual-Reporter-Expressing SARS-CoV-2 Replicon: Construction and Characterization

by Ying Liu, Lu Li, Khalid A. Timani and Johnny J. He

Viruses 2022, 14(5), 974; https://doi.org/10.3390/v14050974 - 5 May 2022

Cited by 1 | Viewed by 2368

Abstract

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2, SARS2) remains a great global health threat and demands identification of more effective and SARS2-targeted antiviral drugs, even with successful development of anti-SARS2 vaccines. Viral replicons have proven to be a rapid, safe, and readily scalable [...] Read more.

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2, SARS2) remains a great global health threat and demands identification of more effective and SARS2-targeted antiviral drugs, even with successful development of anti-SARS2 vaccines. Viral replicons have proven to be a rapid, safe, and readily scalable platform for high-throughput screening, identification, and evaluation of antiviral drugs against positive-stranded RNA viruses. In the study, we report a unique robust HIV long terminal repeat (LTR)/T7 dual-promoter-driven and dual-reporter firefly luciferase (fLuc) and green fluorescent protein (GFP)-expressing SARS2 replicon. The genomic organization of the replicon was designed with quite a few features that were to ensure the replication fidelity of the replicon, to maximize the expression of the full-length replicon, and to offer the monitoring flexibility of the replicon replication. We showed the success of the construction of the replicon and expression of reporter genes fLuc and GFP and SARS structural N from the replicon DNA or the RNA that was in vitro transcribed from the replicon DNA. We also showed detection of the negative-stranded genomic RNA (gRNA) and subgenomic RNA (sgRNA) intermediates, a hallmark of replication of positive-stranded RNA viruses from the replicon. Lastly, we showed that expression of the reporter genes, N gene, gRNA, and sgRNA from the replicon was sensitive to inhibition by Remdesivir. Taken together, our results support use of the replicon for identification of anti-SARS2 drugs and development of new anti-SARS strategies targeted at the step of virus replication. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Scheme of SARS2 genome and the SARS2 replicon DNA construct. (A). The full-length of SARS2 genome from the Wuhan-Hu-1 isolate (GenBank accession No. NC_045512.2) encodes 5′ untranslated region (UTR), nonstructural proteins NSP1-16, structural proteins S, E, M, and N, accessory proteins ORF3-10, and 3′UTR. (B). Several genetic elements were included in the recombinant replicon DNA construct for various purposes. These include HIV long terminal repeat (LTR) promoter, T7 promoter, hammerhead virus ribozyme (HHV Rz) at the 5′ end, porcine teschovirus-1 self-cleaving peptide 2A (P2A) between NSP1 aa1-183 and firefly luciferase, encephalomyocarditis virus internal ribosome entry site (IRES) before NSP2-16, green fluorescence protein-blasticidine (GFP::Bsr) in place of S/E/M, and hepatitis delta virus ribozyme (HDV Rz) and bovine growth hormone polyadenylation signal (BGH pA) at the 3′ end. Full article ">Figure 2
Construction of the SARS2 replicon DNA. (A) The full-length of the recombinant SARS2 replicon DNA (27,952 bp) was divided into and synthesized in 5 fragments (F1/F6 and F2-F5) in the backbone of pMX backbone vector (for F2-5) or pMK backbone vector (for F1/6) with approximate nucleotide sequences for BsaI or SalI restriction sites at both 5′ and 3′ end. (B) Fragments F2-5 in pMX were ligated to create pMX.F2-5 construct using a Golden Gate Assembly kit. (C) pMXF2-5 and pMKF1/6 were digested with SalI and ligated to create the full-length recombinant non-infectious SARS2 replicon DNA construct using a homology recombination-based Gibson Assembly kit. Full article ">Figure 3
Recombinant SARS2 replicon DNA and its transcribed replicon RNA. (A). The intermediate product pMXF2-5 DNA from the Golden Gate Assembly and pMK.F1/6 DNA were confirmed using 0.5% agarose gel electrophoresis. (B). The SARS replicon DNA was obtained from pMX.F2-5 and pMK.F1/6 using a Golden Gate Assembly kit and confirmed using 0.5% agarose gel electrophoresis, marked by an arrow. (C). The full-length recombinant SARS2 replicon DNA was confirmed by PCR using primer pairs spanning specific junctions between two adjacent DNA fragments. (D). SARS2 DNA replicon was used to synthesize SARS2 RNA replicon using an in vitro T7 transcription kit, and the RNA replicon was confirmed using denatured agarose electrophoresis (0.7%), marked by an arrow. Stand’s: DNA size markers. Full article ">Figure 4
Luciferase reporter gene expression from recombinant SARS2 replicon DNA in response to HIV Tat expression (A,B). The 293T were plated at a density of 1.5 × 105 cells/well in a 24-well plate, transfected with 0.4 μg SARS2 replicon DNA and an increasing amount of pc3.Tat, cultured for 24 h, and harvested for the luciferase activity assay (A), or transfected with 0.4 μg SARS2 replicon DNA and 0.12 μg pc3.Tat, cultured for different lengths of time, and harvested for the luciferase activity assay (B,C). Vero E6 were transfected with 0.4 μg SARS2 replicon DNA and 0.12 μg pc3.Tat, cultured for different lengths of time, and harvested for the luciferase activity assay. pcDNA3 was used to equalize the total amount of DNA among all transfections. The data were Mean ± SEM and representative of at least three independent experiments. All differences were highly significant compared to Tat (0 μg) (A), and compared to Time (0 h), except Time (6 h) and between Replicon DNA and Replicon DNA + Tat (B,C). Full article ">Figure 5
Luciferase reporter gene expression from SARS2 replicon RNA in response to HIV Tat expression. The 293T (A) or Vero E6 (B) were plated at a density of 1.5 × 105 cells/well for 293T and 1.5 × 105 cells/well for Vero E6 in a 24-well plate, transfected with 0.3 μg SARS2 replicon RNA and 0.1 μg pc3.Tat, cultured for different lengths of time, and harvested for the luciferase activity assay. pcDNA3 was used to equalize the total amount of DNA among all transfections. The data were Mean ± SEM and representative of at least three independent experiments. All differences were highly significant compared to Time (0 h) and insignificant between Replicon RNA and Replicon RNA + Tat. Full article ">Figure 6
Expression of the GFP reporter gene and SARS2 N (A,B). The 293T were plated at a density of 4 × 106 cells/plate in a 10 cm plate, transfected with 10 μg SARS2 replicon DNA and 3.3 μg pc3.Tat, cultured for different lengths of time, and harvested for Western blotting and direct imaging of the GFP signal on the blots at 488 nM (A), or for Western blotting against an anti-SARS2 N antibody (B). Untx: 293T were only transfected with pcDNA3. (C). The 293T were at a density of 4 × 106 cells/plate in a 10 cm plate, transfected with 7.5 μg SARS2 replicon RNA, cultured for different lengths of time, and harvested for Western blotting against an anti-SARS2 N antibody. Western blotting against an anti-β-actin antibody was included as the equal loading control. The data were representative of at least three independent experiments. Full article ">Figure 7
Expression of positive/negative-stranded genomic RNA (gRNA) and N subgenomic RNA (sgRNA) from the SARS2 replicon and its response to Remdesivir. (A) Different RT primers (N3′ and LRS-L) in combination with different PCR primers (N5′/N3′ and TSR-L/N3′) were designed to distinguish positive-stranded from negative-stranded gRNA and N sgRNA. RT with N3′, followed by PCR with N5′/N3′ and TSR-L/N3′ represented positive-stranded gRNA and N sgRNA, respectively. RT with TSR-L, followed by PCR with N5′/N3′ and TSR-L/N3′, represented negative-stranded gRNA and N sgRNA, respectively. (B) The 293T were plated at a density of 6.5 × 105 cells/well in a 6-well plate, treated with 0, 5, or 10 μM Remdesivir for 1 h, transfected with 1.5 μg SARS2 replicon DNA and 0.5 μg pcDNA3, 1.5 μg SARS2 DNA and 0.5 μg pc3.Tat, or 1.2 μg SARS2 replicon RNA, cultured in the presence of Remdesivir for 24 h, and harvested for RNA isolation. RT was performed using N3′ or TRS-L5′ as the primer and 0.5 μg RNA in a 25 μL reaction. An aliquot RT reaction (2 μL from N3′ RT reaction; 2 μL from TSR-L5′ RT reaction) was used as the template for PCR, with indicated primer pairs. The PCR products were analyzed on 1% agarose gel electrophoresis. RT was performed using 0.1 μg RNA. RT with oligo d(T)23 as the RT primer and PCR with β-actin-specific primers were performed and included as the equal loading control. Stand’s: DNA size markers. Ctrl: untransfected cells. The data were representative of at least three independent experiments. Full article ">Figure 8
Effects of Remdesivir on gene expression from the SARS2 replicon DNA and RNA (A,B). The 293T were at a density of 4 × 106 cells/plate in a 10 cm plate, treated with Remdesivir for 1 h, transfected with 10 μg SARS2 replicon DNA, cultured in the presence of Remdesivir for 24 h, and harvested for the luciferase activity assay (A), or for Western blotting against an anti-SARS2 N antibody or anti-β-actin antibody, or by direct imaging of the GFP signal at 488 nm (B). (C). The 293T were at a density of 1.5 × 105 cells/well in a 24-well plate, treated with 10 μM Remdesivir for 1 h, transfected with 0.4 μg SARS2 replicon DNA and 0.12 μg pcDNA3, 0.4 μg SARS2 DNA and 0.12 μg pc3.Tat, or 0.3 μg SARS2 replicon RNA and 0.1 μg yeast tRNA, cultured in the presence of Remdesivir for 24 h, and harvested for the luciferase activity assay. The controls for Remdesivir treatment were DMSO, the solvent for Remdesivir. The data were Mean ± SEM and representative of at least three independent experiments (A,C) and representative of at least three independent experiments (B). All differences were highly significant compared to Remdesivir (0 μM) (A) and between ± Remdesivir (C). Full article ">

11 pages, 1740 KiB

Open AccessArticle

Pathogen- and Type-Specific Changes in Invasive Bacterial Disease Epidemiology during the First Year of the COVID-19 Pandemic in The Netherlands

by Anneke Steens, Mirjam J. Knol, Wieke Freudenburg-de Graaf, Hester E. de Melker, Arie van der Ende and Nina M. van Sorge

Microorganisms 2022, 10(5), 972; https://doi.org/10.3390/microorganisms10050972 - 5 May 2022

Cited by 18 | Viewed by 2369

Abstract

COVID-19 control measures have resulted in a decline in invasive bacterial disease caused by Neisseria meningitidis (IMD), Streptococcus pneumoniae (IPD), and Haemophilus influenzae (Hi-D). These species comprise different serogroups and serotypes that impact transmissibility and virulence. We evaluated type- and pathogen-specific changes in [...] Read more.

COVID-19 control measures have resulted in a decline in invasive bacterial disease caused by Neisseria meningitidis (IMD), Streptococcus pneumoniae (IPD), and Haemophilus influenzae (Hi-D). These species comprise different serogroups and serotypes that impact transmissibility and virulence. We evaluated type- and pathogen-specific changes in invasive bacterial disease epidemiology in the Netherlands during the first year of the SARS-CoV-2 pandemic. Cases were based on nationwide surveillance for five bacterial species with either respiratory (IMD, IPD, Hi-D) or non-respiratory (controls) transmission routes and were compared from the pre-COVID period (April 2015–March 2020) to the first COVID-19 year (April 2020–March 2021). IMD, IPD, and Hi-D cases decreased by 78%, 67%, and 35%, respectively, in the first COVID-19 year compared to the pre-COVID period, although effects differed per age group. Serogroup B-IMD declined by 61%, while serogroup W and Y-IMD decreased >90%. IPD caused by serotypes 7F, 15A, 12F, 33F, and 8 showed the most pronounced decline (≥76%). In contrast to an overall decrease in Hi-D cases, vaccine-preventable serotype b (Hib) increased by 51%. COVID-19 control measures had pathogen- and type-specific effects related to invasive infections. Continued surveillance is critical to monitor potential rebound effects once restriction measures are lifted and transmission is resumed. Full article

(This article belongs to the Topic Infectious Diseases)

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Number of invasive disease cases by month in the first COVID-19 year (2020–2021; bars) based on bacteriological surveillance, the 5-year moving average in pre-COVID years (solid line) and its standard deviation for the pre-COVID period (dashed line) for (A): N. meningitidis (IMD); (B): S. pneumoniae (IPD); (C): H. influenzae (Hi-D); (D): E. coli; (E): S. agalactiae. Note that the y-axis differs between pathogens. Full article ">Figure 2
Cumulative number of cases of invasive meningococcal disease caused by (A): serogroup B; (B): serogroup W; and (C): serogroup Y in the first COVID-19 year (2020–2021; black) compared to the previous five pre-COVID-19 years (blue). Full article ">Figure 3
Percentage of IPD cases caused by vaccine serotypes during the years 2015–2021, in all age groups except those aged 73–79 years old. Full article ">Figure 4
Cumulative number of cases (left) and monthly number of cases (right) for the first COVID-19 year (bars) compared to the 5-year moving average in pre-COVID-19 years (solid line) and the moving average plus/minus its standard deviation for the pre-COVID-19 period (dashed line) for (A): Haemophilus influenzae serotype b (Hib); and (B): non-typeable H. influenzae (NTHi). Full article ">

7 pages, 238 KiB

Open AccessArticle

Sartans and ACE Inhibitors: Mortality in Patients Hospitalized with COVID-19. Retrospective Study in Patients on Long-Term Treatment Who Died in the Italian Hospitals of Area Vasta n.5—Marche Region

by Tony Mazzoni, Zaira Maraia, Benedetta Ruggeri, Carlo Polidori, Maria Vittoria Micioni Di Bonaventura, Laura Armillei, Irene Pomilio and Isidoro Mazzoni

J. Clin. Med. 2022, 11(9), 2580; https://doi.org/10.3390/jcm11092580 - 5 May 2022

Cited by 2 | Viewed by 2191

Abstract

Introduction: During the 2019 Coronavirus pandemic (COVID-19), a concern emerged regarding a possible correlation between the severe form of SARS-CoV-2 infection and administration of ACE-Inhibitors (ACE-I) and Sartans (ARB), since long-term use of these drugs may potentially result in an adaptive response with [...] Read more.

Introduction: During the 2019 Coronavirus pandemic (COVID-19), a concern emerged regarding a possible correlation between the severe form of SARS-CoV-2 infection and administration of ACE-Inhibitors (ACE-I) and Sartans (ARB), since long-term use of these drugs may potentially result in an adaptive response with up-regulation of the ACE 2 receptor. Given the crucial role of ACE2, being the main target for virus entry into the cell, the potential consequences of ACE2 up-regulation have been a source of debate. The aim of this retrospective cohort study on COVID-19-positive patients who died is to investigate whether previous long-term exposure to ACE-I and/or ARB was associated with higher mortality due to COVID-19 infection, compared to all other types of drug treatment. Methods: We analysed the clinical and demographic data of 615 patients hospitalized for COVID-19 at the two hospitals of the Vasta Area n.5, between March 2020 and April 2021. Among them, 86 patients, treated with ACE-Is and/0 ARBs for about 12 months, died during hospitalization following a diagnosis of acute respiratory failure. Several quantitative and qualitative variables were recorded for all patients by reading their medical records. Results: The logistic model showed that the variables that increase mortality are age and comorbid diseases. There were no demonstrable mortality effects with ACE-I and ARB intake. Conclusions: The apparent increase in morbidity in patients with COVID-19 who received long-term treatment with ACE-I or ARB is not due to the drugs themselves, but to the conditions associated with their use. Full article

(This article belongs to the Topic Infectious Diseases)

17 pages, 3934 KiB

Open AccessArticle

The Velvet Protein UvVEA Regulates Conidiation and Chlamydospore Formation in Ustilaginoidea virens

by Mina Yu, Junjie Yu, Huijuan Cao, Xiayan Pan, Tianqiao Song, Zhongqiang Qi, Yan Du, Shiwen Huang and Yongfeng Liu

J. Fungi 2022, 8(5), 479; https://doi.org/10.3390/jof8050479 - 4 May 2022

Cited by 7 | Viewed by 1804

Abstract

Rice false smut, caused by Ustilaginoidea virens, is a serious disease of rice worldwide, severely reducing the quantity and quality of rice production. The conserved fungal velvet proteins are global regulators of diverse cellular processes. We identified and functionally characterized two velvet [...] Read more.

Rice false smut, caused by Ustilaginoidea virens, is a serious disease of rice worldwide, severely reducing the quantity and quality of rice production. The conserved fungal velvet proteins are global regulators of diverse cellular processes. We identified and functionally characterized two velvet genes, UvVEA and UvVELB, in U. virens. The deletion of these genes affected the conidiation of U. virens but had no effect on the virulence of this pathogen. Interestingly, the ΔUvVEA mutants appeared in the form of smaller false smut balls with a reduced number of chlamydospores compared with the wide-type strains. In addition, the deletion of UvVEA affected the expression of some transmembrane transport genes during chlamydospore formation and rice false smut balls development. Furthermore, the ΔUvVEA mutants were shown to be defective in the utilization of glucose. These findings proved the regulatory mechanism underlying the formation of rice false smut balls and chlamydospores and provided a basis for the further exploration of the mechanism of these processes. Full article

(This article belongs to the Topic Infectious Diseases)

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21 pages, 1384 KiB

Open AccessArticle

Seroprevalence of SARS-CoV-2 IgG Antibodies and Factors Associated with SARS-CoV-2 IgG Neutralizing Activity among Primary Health Care Workers 6 Months after Vaccination Rollout in France

by Dorine Decarreaux, Marie Pouquet, Cecile Souty, Ana-Maria Vilcu, Pol Prévot-Monsacre, Toscane Fourié, Paola Mariela Saba Villarroel, Stephane Priet, Hélène Blanché, Jean-Marc Sebaoun, Jean-François Deleuze, Clément Turbelin, Andréas Werner, Fabienne Kochert, Brigitte Grosgogeat, Pascaline Rabiega, Julien Laupie, Nathalie Abraham, Caroline Guerrisi, Harold Noël, Sylvie Van der Werf, Fabrice Carrat, Thomas Hanslik, Remi Charrel, Xavier De Lamballerie, Thierry Blanchon and Alessandra Falchi Show full author list Hide full author list

Viruses 2022, 14(5), 957; https://doi.org/10.3390/v14050957 - 3 May 2022

Cited by 5 | Viewed by 3050

Abstract

We aimed to investigate the immunoglobulin G response and neutralizing activity against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) among primary health care workers (PHCW) in France and assess the association between the neutralizing activity and several factors, including the coronavirus disease 2019 (COVID-19) [...] Read more.

We aimed to investigate the immunoglobulin G response and neutralizing activity against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) among primary health care workers (PHCW) in France and assess the association between the neutralizing activity and several factors, including the coronavirus disease 2019 (COVID-19) vaccination scheme. A cross-sectional survey was conducted between 10 May 2021 and 31 August 2021. Participants underwent capillary blood sampling and completed a questionnaire. Sera were tested for the presence of antibodies against the nucleocapsid (N) protein and the S-1 portion of the spike (S) protein and neutralizing antibodies. In total, 1612 PHCW were included. The overall seroprevalences were: 23.6% (95% confidence interval (CI) 21.6–25.7%) for antibodies against the N protein, 94.7% (93.6–95.7%) for antibodies against the S protein, and 81.3% (79.4–83.2%) for neutralizing antibodies. Multivariate regression analyses showed that detection of neutralizing antibodies was significantly more likely in PHCW with previous SARS-CoV-2 infection than in those with no such history among the unvaccinated (odds ratio (OR) 16.57, 95% CI 5.96–59.36) and those vaccinated with one vaccine dose (OR 41.66, 95% CI 16.05–120.78). Among PHCW vaccinated with two vaccine doses, the detection of neutralizing antibodies was not significantly associated with previous SARS-CoV-2 infection (OR 1.31, 95% CI 0.86–2.07), but was more likely in those that received their second vaccine dose within the three months before study entry than in those vaccinated more than three months earlier (OR 5.28, 95% CI 3.51–8.23). This study highlights that previous SARS-CoV-2 infection and the time since vaccination should be considered when planning booster doses and the design of COVID-19 vaccine strategies. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Flow chart of the primary healthcare worker (PHCW) participants enrolled from May to August 2021 (COVID-SéroPRIM study, France, 2021). Full article ">Figure 2
Antibody levels (BAU/mL) for IgG antibodies against the S protein according to (a) the number of COVID-19 vaccine doses received along with the presence or absence of self-reported SARS-CoV-2 infection among the PHCWs; (b) time since the last vaccination among vaccinees; (c) age (years) of the PHCWs, May 2021 to August 2021 (n = 1602; COVID-SéroPRIM study, France, 2021). Full article ">Figure 2 Cont.
Antibody levels (BAU/mL) for IgG antibodies against the S protein according to (a) the number of COVID-19 vaccine doses received along with the presence or absence of self-reported SARS-CoV-2 infection among the PHCWs; (b) time since the last vaccination among vaccinees; (c) age (years) of the PHCWs, May 2021 to August 2021 (n = 1602; COVID-SéroPRIM study, France, 2021). Full article ">Figure 3
Distribution of seroneutralization titers among the PHCWs, May 2021 to August 2021 (N = 1602; COVID-SéroPRIM study, France, 2021). Full article ">Figure 4
Boxplot of the quantitative ELISA-S results according to neutralizing antibody titers among the PHCWs (N = 1602; COVID-SéroPRIM study, France, 2021). Full article ">

21 pages, 953 KiB

Open AccessReview

Role of Microbiota in Viral Infections and Pathological Progression

by Taketoshi Mizutani, Aya Ishizaka, Michiko Koga, Takeya Tsutsumi and Hiroshi Yotsuyanagi

Viruses 2022, 14(5), 950; https://doi.org/10.3390/v14050950 - 1 May 2022

Cited by 22 | Viewed by 4502

Abstract

Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or [...] Read more.

Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or promote viral infection, while others are involved in pathogenicity. It is also becoming evident that the profile of the commensal microbiota under normal conditions influences the progression of viral diseases. Thus, to understand the pathogenesis underlying viral infections, it is important to elucidate the interactions among viruses, target tissues, and the surrounding environment, including the commensal microbiota, which should have different relationships with each virus. In this review, we outline the role of microorganisms in viral infections. Particularly, we focus on gaining an in-depth understanding of the correlations among viral infections, target tissues, and the surrounding environment, including the commensal microbiota and the gut virome, and discussing the impact of changes in the microbiota (dysbiosis) on the pathological progression of viral infections. Full article

(This article belongs to the Topic Infectious Diseases)

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17 pages, 17278 KiB

Open AccessArticle

A Denture Use Model Associated with Candida spp. in Immunocompetent Male and Female Rats

by Vinicius Tatsuyuji Sakima, Yuliana Vega-Chacón, Paulo Sergio Cerri, Bhumika Shokeen, Renate Lux and Ewerton Garcia de Oliveira Mima

J. Fungi 2022, 8(5), 466; https://doi.org/10.3390/jof8050466 - 30 Apr 2022

Cited by 1 | Viewed by 1932

Abstract

Denture stomatitis (DS) is a common infection in denture wearers, especially women. This study evaluated the induction of DS using acrylic devices attached to the palate of rats combined with inoculation of Candida spp. Immunocompetent male and female rats received a carbohydrate-rich diet. [...] Read more.

Denture stomatitis (DS) is a common infection in denture wearers, especially women. This study evaluated the induction of DS using acrylic devices attached to the palate of rats combined with inoculation of Candida spp. Immunocompetent male and female rats received a carbohydrate-rich diet. Impressions were taken from the rats’ palate to individually fabricate acrylic devices. Mono- and multispecies biofilms of C. albicans, C. glabrata, and C. tropicalis were grown on the devices, which were then cemented on posterior teeth and kept in the rats’ palate for four weeks. Microbial samples from the palate and the device were quantified. Oral microbiome of rats inoculated with C. albicans was analyzed by 16S rRNA gene sequencing. Log₁₀(CFU/mL) were analyzed by mixed or two-way MANOVA (α = 0.05). Candida spp. and acrylic device did not induce palatal inflammation macroscopically nor microscopically. Although there was an increase (p < 0.001) of the total microbiota and female rats demonstrated higher (p = 0.007) recovery of Candida spp. from the palate, the gender differences were not biologically relevant. The microbiome results indicate an increase in inflammatory microbiota and reduction in health-associated micro-organisms. Although Candida spp. and acrylic device did not induce DS in immunocompetent rats, the shift in microbiota may precede manifestation of inflammation. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 531 KiB

Open AccessArticle

Surgical Procedure Time and Mortality in Patients with Infective Endocarditis Caused by Staphylococcus aureus or Streptococcus Species

by Gregor Paul, Laurin Ochs, Christopher Hohmann, Stephan Baldus, Guido Michels, Charlotte Meyer-Schwickerath, Gerd Fätkenheuer, Navid Mader, Thorsten Wahlers, Carolyn Weber and Norma Jung

J. Clin. Med. 2022, 11(9), 2538; https://doi.org/10.3390/jcm11092538 - 30 Apr 2022

Cited by 5 | Viewed by 1930

Abstract

Staphylococcus aureus (SA) and Streptococcus species (SS) show different clinical manifestations in infective endocarditis (IE), but the impact on the complexity of surgical treatment remains unclear. All patients with surgically treated IE due to SA or SS between July 2013 and December 2016 [...] Read more.

Staphylococcus aureus (SA) and Streptococcus species (SS) show different clinical manifestations in infective endocarditis (IE), but the impact on the complexity of surgical treatment remains unclear. All patients with surgically treated IE due to SA or SS between July 2013 and December 2016 were extracted from a prospectively collected, single-center registry. Data on patient characteristics, surgical procedures, and postprocedural outcomes were collected. SA-IE was more common with prosthetic valves (26.3% vs. 7.3%, p = 0.04), cardiac devices (14.3% vs. 0%, p = 0.03), previous cardiac surgery (28.6% vs. 9.8%, p = 0.03), intravenous drug abuse (14.3% vs. 0%, p = 0.03), and embolic events (57.1% vs. 26.8%, p = 0.007). Preoperative CRP was significantly higher in SA-IE (median 96.1 mg/L vs. 42.4 mg/L, p = 0.002). Otherwise, SS-IE affected more cusps/leaflets (mean 2.4 vs. 1.8, p = 0.03) and led to more valve dysfunction (83.8% vs. 54.3%, p = 0.007). Surgery times did not differ between the groups, though patients with SA spent more time in the intensive care unit (median 7 vs. 4.5 days, p = 0.04). Hospital mortality did not differ, but patients with SA-IE had unfavorable long-term survival (p = 0.001). Future studies need to be larger and focus on the mechanism behind the reduced long-term survival to mitigate the deleterious effect of SA in surgically treated patients with IE. Full article

(This article belongs to the Topic Infectious Diseases)

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9 pages, 244 KiB

Open AccessArticle

Prostatic Abscess Caused by Klebsiella pneumoniae: A 6-Year Single-Center Study

by Joo-Hee Hwang, Jeong-Hwan Hwang, Seung Yeob Lee and Jaehyeon Lee

J. Clin. Med. 2022, 11(9), 2521; https://doi.org/10.3390/jcm11092521 - 29 Apr 2022

Cited by 4 | Viewed by 1922

Abstract

Hypervirulent Klebsiella pneumoniae (hvKp) is an important strain that can cause multiple organ infections. Although hvKp infection cases are increasing, there is limited information on the prostatic abscesses caused by K. pneumoniae. Furthermore, the clinical significance of hvKp associated with K1 or [...] Read more.

Hypervirulent Klebsiella pneumoniae (hvKp) is an important strain that can cause multiple organ infections. Although hvKp infection cases are increasing, there is limited information on the prostatic abscesses caused by K. pneumoniae. Furthermore, the clinical significance of hvKp associated with K1 or K2 capsular types or virulence genes in prostatic abscesses remains unclear. Therefore, we aimed to elucidate the clinical and microbiological characteristics of prostatic abscesses caused by K. pneumoniae in relation to various virulence genes. A retrospective study was performed at a 1200-bed tertiary hospital between January 2014 and December 2019. Patients diagnosed with prostatic abscesses with K. pneumoniae isolated from blood, urine, pus, or tissue cultures were enrolled in this study. Our results demonstrate that 30.3% (10/33) of the prostatic abscesses were caused by K. pneumoniae. All strains isolated from patients with prostatic abscesses due to K. pneumoniae were the K1 capsular type, and eight patients (80.0%) carried rmpA and iutA genes that identified hvKp. These findings suggest that hvKp is an important pathogen in prostatic abscesses. Therefore, when treating patients with K. pneumoniae prostatic abscesses, attention should be paid to the characteristics of hvKp, such as bacteremia, multiorgan abscess formation, and metastatic spread. Full article

(This article belongs to the Topic Infectious Diseases)

20 pages, 1456 KiB

Open AccessReview

Do Triclosan Sutures Modify the Microbial Diversity of Surgical Site Infections? A Systematic Review and Meta-Analysis

by Frederic C. Daoud, Maïder Coppry, Nicholas Moore and Anne-Marie Rogues

Microorganisms 2022, 10(5), 927; https://doi.org/10.3390/microorganisms10050927 - 28 Apr 2022

Cited by 5 | Viewed by 2077

Abstract

Randomised controlled clinical trials (RCTs) report a lower incidence rate of surgical site infections (SSIs) with triclosan sutures (TSs) compared with non-triclosan sutures (NTSs). Do triclosan sutures modify the microbial diversity of culture-confirmed SSIs (ccSSIs)? If so, this would support the association between [...] Read more.

Randomised controlled clinical trials (RCTs) report a lower incidence rate of surgical site infections (SSIs) with triclosan sutures (TSs) compared with non-triclosan sutures (NTSs). Do triclosan sutures modify the microbial diversity of culture-confirmed SSIs (ccSSIs)? If so, this would support the association between TS antimicrobial activity and the SSI incidence rate. This prospective systematic literature review (PROSPERO CRD42019125099) was conducted according to PRISMA. RCTs that compared the incidence of SSIs with TSs and NTSs and reported microbial counts from SSI cultures per suture group were eligible. The microbial species were grouped by genus, and the association between genera and sutures was tested. The pooled relative risk (RR) of ccSSIs was also calculated. Twelve RCTs were eligible. No publication bias was identified. The microorganism count was 180 in 124 SSIs with TSs versus 246 in 199 SSIs with NTSs. No significant difference in microbial diversity was found, but statistical power was low for test results to support or challenge the association between the antimicrobial activity of TSs and the reduced rate of SSIs. The RR of the ccSSIs was significant and consistent with comprehensive meta-analyses. The certainty of the pooled RR was moderate. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 1390 KiB

Open AccessArticle

Longitudinal Randomized Cohort Study of SARS-CoV-2 Antibody Seroprevalence in the St. Petersburg Population

by Vyacheslav S. Smirnov, Liudmila V. Lyalina, Anzhelika M. Milichkina, Irina V. Khamitova, Elena V. Zueva, Valery A. Ivanov, Vitaly S. Zaguzov and Areg A. Totolian

Viruses 2022, 14(5), 913; https://doi.org/10.3390/v14050913 - 27 Apr 2022

Cited by 7 | Viewed by 2223

Abstract

Introduction. Since the detection of the first COVID-19 patient, 2 years have passed, during which more than 287,862,000 people have fallen ill globally, of which about 1.9% died. The implementation of SARS-CoV-2 control programs required efforts from almost all countries. An important direction [...] Read more.

Introduction. Since the detection of the first COVID-19 patient, 2 years have passed, during which more than 287,862,000 people have fallen ill globally, of which about 1.9% died. The implementation of SARS-CoV-2 control programs required efforts from almost all countries. An important direction in the fight against COVID-19 has been the formation of herd immunity, the main tool for managing the pandemic. Study goal. The aim of the study was to assess the seroprevalence of antibodies (Abs) to SARS-CoV-2 nucleocapsid (Nc) and receptor binding domain (RBD) in the St. Petersburg population during the COVID-19 pandemic. Materials and methods. A longitudinal cohort randomized monitoring study of Ab seroprevalence (SARS-CoV-2 Nc, RBD) was organized and conducted according to a unified methodology developed by Rospotrebnadzor with the participation of the St. Petersburg Pasteur Institute. For this purpose, a cohort was formed of 1000 volunteers who participated in all five stages of seromonitoring. The cohort was divided into seven age groups: 1–17; 18–29; 30–39; 40–49; 50–59; 60–69; 70; and older (70+) years. Seropositivity levels (Nc, RBD) were assessed by quantitative and qualitative enzyme immunoassays. During the second year of monitoring, some volunteers were vaccinated with the GamCOVIDVac (84%) or EpiVacCorona (11.6%) vaccines approved in Russia. Statistical processing was carried out using Excel 2010. Confidence intervals for shares and percentages (95% CI) were calculated using the method of A. Wald and J. Wolfowitz with adjustment (A. Agresti, B.A. Coull). The statistical significance of differences was calculated by z-test, using the appropriate online calculator (p < 0.05) unless indicated. Results. There was a trend toward an increase in Nc seropositivity in stages 1–3 of seromonitoring, with a decrease in stages 4–5 among children and adults. The share of RBD seropositive steadily increased during all five stages of seromonitoring. The most frequent finding was low anti-RBD Abs levels (22.6–220 BAU/mL). High Ab levels were recorded statistically significantly less frequently. Asymptomatic forms were observed in 84–88% of SARS-CoV-2 seropositive volunteers. By the fifth stage of monitoring, this indicator significantly decreased to 69.8% (95% CI: 66.1–73.4). The monitoring revealed a statistically significant increase in anti-RBD Abs alongside a statistically significant decrease in the proportion of Nc seropositives. This dynamic was especially characteristic of persons vaccinated with GamCOVIDVac. Conclusion. Prior to the use of specific vaccines, a seroprevalence of anti-Nc Abs was noted. After the introduction of the GamCOVIDVac vaccine in adults, a decrease in the level of anti-Nc Abs was noted due to an increase in the proportion of RBD seropositive persons. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Dynamics of SARS-CoV-2 infection and vaccination of the St. Petersburg population in 2021. The blue dotted line is the infection trend; the regression equation and the coefficient of determination are highlighted in blue and placed at the top center. The brown dotted line is the vaccination trend; the regression equation and the coefficient of determination are highlighted in brown and placed at the top center. The main vaccine used in the Russian Federation was GamCOVIDVac (Sputnik V). Full article ">Figure 2
Distribution of seropositivity to N and RBD antigens (ag) in children and adults, by seromonitoring stage. Colored curves are trend lines for the percent seropositive among 1—children (N ag); 2—children (RBD ag); 3—adults (N ag); and 4—adults (RBD ag). Regression equations and coefficients of determination, in their corresponding colors, are shown in the upper left (y2, y4) and lower right (y1, y3) corners. Black vertical bars are the 95% confidence intervals. The summarized data are given in <a href="#app1-viruses-14-00913" class="html-app">Table S1</a>. Full article ">Figure 3
Distribution of anti-Nc antibody levels among children and adults, by seromonitoring stage. Colored lines—dynamics of Ab distribution in children and adults in the dynamics of monitoring; colored dotted lines—trends in Ab levels in children; solid color lines are trends in Ab levels in adults. The equations for the trend curves in their respective colors are shown to the right of the curves and correspond to the sequences in which the end points of the trend lines are located. See additional <a href="#app1-viruses-14-00913" class="html-app">Table S2</a>. Full article ">Figure 4
Distribution dynamics of anti-RBD antibody levels among children and adults, by seromonitoring stage. Colored lines are Ab distribution trends in children (dashed) and adults (solid). Trend equations and determination coefficients, in their corresponding colors, are shown on the right side of the graph next to their curves. Black vertical lines are 95% confidence intervals. Antibody values are given in BAU/ml (<a href="#app1-viruses-14-00913" class="html-app">Table S3</a>). Full article ">Figure 5
Share of asymptomatic forms among Nc–seropositive volunteers. The solid curve is the median share of seropositive volunteers with asymptomatic infection. Key: black vertical lines— [IQR]; colored dots—averaged values in each age group. Age groups of seropositive, asymptomatic volunteers are in years. See <a href="#app1-viruses-14-00913" class="html-app">Table S4</a>. Full article ">Figure 6
Seroprevalence of anti-Nc and anti-RBD IgG in volunteer plasma, by seromonitoring stage. Key: RBD + Nc double-positive volunteers with both Abs; RBD Abs—volunteers with only RBD Abs; Nc Abs—volunteers with only Nc Abs; Total Abs—total number of seropositive volunteers (RBD + Nc Abs, RBD Abs, Nc Abs) relative to all examined; vertical black lines—95% CI. Full article ">

39 pages, 2617 KiB

Open AccessSystematic Review

Molecular Epidemiology and Evolutionary Dynamics of Human Influenza Type-A Viruses in Africa: A Systematic Review

by Grace Nabakooza, Ronald Galiwango, Simon D. W. Frost, David P. Kateete and John M. Kitayimbwa

Microorganisms 2022, 10(5), 900; https://doi.org/10.3390/microorganisms10050900 - 25 Apr 2022

Cited by 2 | Viewed by 4583

Abstract

Genomic characterization of circulating influenza type-A viruses (IAVs) directs the selection of appropriate vaccine formulations and early detection of potentially pandemic virus strains. However, longitudinal data on the genomic evolution and transmission of IAVs in Africa are scarce, limiting Africa’s benefits from potential [...] Read more.

Genomic characterization of circulating influenza type-A viruses (IAVs) directs the selection of appropriate vaccine formulations and early detection of potentially pandemic virus strains. However, longitudinal data on the genomic evolution and transmission of IAVs in Africa are scarce, limiting Africa’s benefits from potential influenza control strategies. We searched seven databases: African Journals Online, Embase, Global Health, Google Scholar, PubMed, Scopus, and Web of Science according to the PRISMA guidelines for studies that sequenced and/or genomically characterized Africa IAVs. Our review highlights the emergence and diversification of IAVs in Africa since 1993. Circulating strains continuously acquired new amino acid substitutions at the major antigenic and potential N-linked glycosylation sites in their hemagglutinin proteins, which dramatically affected vaccine protectiveness. Africa IAVs phylogenetically mixed with global strains forming strong temporal and geographical evolution structures. Phylogeographic analyses confirmed that viral migration into Africa from abroad, especially South Asia, Europe, and North America, and extensive local viral mixing sustained the genomic diversity, antigenic drift, and persistence of IAVs in Africa. However, the role of reassortment and zoonosis remains unknown. Interestingly, we observed substitutions and clades and persistent viral lineages unique to Africa. Therefore, Africa’s contribution to the global influenza ecology may be understated. Our results were geographically biased, with data from 63% (34/54) of African countries. Thus, there is a need to expand influenza surveillance across Africa and prioritize routine whole-genome sequencing and genomic analysis to detect new strains early for effective viral control. Full article

(This article belongs to the Topic Infectious Diseases)

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Flowchart showing the exclusion and inclusion criteria of studies analyzed. Full article ">Figure 2
The geographical distribution of studies that did genomic characterization of influenza type-A viruses (H1N1, H1N1pdm09, and H3N2) sampled in Africa. Each country is highlighted based on the absolute number of studies that analyzed sequences of influenza viruses collected from that country. For each country, the study count also includes any study that included at least one sequence from that country in their virus clade classification using the European Center for Disease Control (ECDC) guidelines [<a href="#B27-microorganisms-10-00900" class="html-bibr">27</a>]. Abbreviations: CAR = Central African Republic. Countries not shown: Cape Verde (n = 1), Reunion (n = 3), Seychelles (n = 4), Mauritania (n = 1), Mauritius (n = 10), and Mayotte (n = 1). Full article ">Figure 3
Temporal and geographical distribution of genetic clades of seasonal H1N1 virus strains that circulated in Africa between 2001 and 2009. Details on the characteristic genomic markers (amino acid substitutions in the HA1 proteins) for each clade are described in <a href="#app1-microorganisms-10-00900" class="html-app">Table S8</a>. Full article ">Figure 4
Temporal and geographical distribution of genetic clades of pandemic H1N1pdm09 (2009–2010) and seasonal H1N1pdm09 (2011 onwards) virus strains that circulated in Africa between 2009 and 2018. Abbreviations: Burkina Faso (BurkF), Cameroon (Cam), Cape Verde (CapeV), Central African Republic (CAR), Ivory Coast (IvoryC), Madagascar (Madg), Mauritania (Mauritn), Mozambique (Mozab), South Africa (SA), Tanzania (Tanz), and A/Madrid/SO8171/2010(H1N1)-like clade (Madrid). Details on the characteristic genomic markers (amino acid substitutions in the HA1 proteins) for each clade are described in <a href="#app1-microorganisms-10-00900" class="html-app">Table S9</a>. Full article ">Figure 5
Temporal and geographical distribution of genetic clades of seasonal H3N2 virus strains that circulated in Africa between 2003 and 2018. Abbreviations: Burkina Faso (BurkF), Cameroon (Cam), Cape Verde (CapeV), Central African Republic (CAR), Ivory Coast (IvoryC), Madagascar (Madg), Mozambique (Mozab), South Africa (SA), Tanzania (Tanz). A/Brisbane/10/2007(H3N2)-like clade (Brisbane), A/Fujian/411/2002(H3N2)-like clade (Fujian), A/Perth/16/2009(H3N2)-like clade (Perth), A/Victoria/208/2009(H3N2-like clade (Victoria), and A/Wellington/1/2004(H3N2)-like clade (Wellington). Details on the characteristic genomic markers (amino acid substitutions in the HA1 proteins) for each clade are described in <a href="#app1-microorganisms-10-00900" class="html-app">Table S11</a>. Full article ">

9 pages, 239 KiB

Open AccessArticle

GenoType CM Direct^® and VisionArray Myco^® for the Rapid Identification of Mycobacteria from Clinical Specimens

by Hans-Ulrich Schildhaus, Mathis Steindor, Bernd Kölsch, Thomas Herold, Jan Buer and Jan Kehrmann

J. Clin. Med. 2022, 11(9), 2404; https://doi.org/10.3390/jcm11092404 - 25 Apr 2022

Cited by 3 | Viewed by 1735

Abstract

M. tuberculosis is the single infectious agent responsible for most deaths worldwide outside of pandemics. Diseases due to non-tuberculous mycobacteria (NTM) are increasing in many regions of the world. The two molecular assays GenoType CM direct^® (GTCMd) (Bruker, Billerica, MA, USA) and [...] Read more.

M. tuberculosis is the single infectious agent responsible for most deaths worldwide outside of pandemics. Diseases due to non-tuberculous mycobacteria (NTM) are increasing in many regions of the world. The two molecular assays GenoType CM direct^® (GTCMd) (Bruker, Billerica, MA, USA) and VisionArray Myco^® (VAM) (ZytoVision, Bremerhaven, Germany) are based on the DNA/DNA hybridization technique, and allow for the identification of tuberculous and the most clinically relevant non-tuberculous mycobacterial species from clinical specimens. We evaluated the performance of both assays for the identification of mycobacteria from 65 clinical specimens of 65 patients and compared it with the results of conventional culture. Based on conventional culture that recovered 37 mycobacterial isolates including 11 tuberculous and 26 NTM isolates, sensitivity, specificity, positive predictive value and negative predictive value were 89.2%, 81.5%, 86.8% and 84.6% for GTCMd and 73.0%, 96.3%, 96.4% and 72.2% for VAM. Additionally, GTCMd identified mycobacteria from five and VAM from one culture-negative sample. Both assays identified a mycobacterium in one sample overgrown by other microorganisms. Two M. abscessus subsp. abscessus isolates grown from culture were identified as M. chelonae by GTCMd assay. In conclusion, both assays improve the rapid identification of mycobacteria directly from clinical specimens. Full article

(This article belongs to the Topic Infectious Diseases)

17 pages, 3884 KiB

Open AccessArticle

Therapeutic Potential of Green Synthesized Gold Nanoparticles Using Extract of Leptadenia hastata against Invasive Pulmonary Aspergillosis

by Basem M. Abdallah and Enas M. Ali

J. Fungi 2022, 8(5), 442; https://doi.org/10.3390/jof8050442 - 24 Apr 2022

Cited by 7 | Viewed by 2771

Abstract

Gold nanoparticles are widely used in the biomedical field for the treatment of several diseases, including cancer, inflammatory diseases, and immune system disorders, due to their distinctive physicochemical characteristics. In this study, we investigated the therapeutic potential of green synthesized gold nanoparticles using [...] Read more.

Gold nanoparticles are widely used in the biomedical field for the treatment of several diseases, including cancer, inflammatory diseases, and immune system disorders, due to their distinctive physicochemical characteristics. In this study, we investigated the therapeutic potential of green synthesized gold nanoparticles using ethanolic leaf extract of Leptadenia hastata (LH-AuNPs) against invasive pulmonary aspergillosis (IPA) in mice. UV/visible spectroscopy, Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDX), and zeta potential were used to characterize the biofabricated LH-AuNPs. Antifungal activity of LH-AuNPs was determined by MTT assay, (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide), time-kill assay, and radial growth inhibition. TEM and SEM were used to examine the mode of the antifungal action of LH-AuNPs. The in vivo activity of LH-AuNPs against IPA was studied using a well-established IPA mouse model. LH-AuNPs excreted antifungal activity against Aspergillus fumigatus with MIC 64 µg/mL and inhibited the radial growth of A. fumigatus by 30% compared to the control. LH-AuNPs caused distortion and collapse of fungal hyphae and deterioration of cell walls. Interestingly, LH-AuNPs did not display any cytotoxicity on cultured primary bone marrow stem cells (BMSCs) or A549 human lung cell line in vitro at MIC concentration. IPA mice treated with LH-AuNPs displayed significant lung tissue repair without any in vivo cytotoxicity. LH-AuNPs administration showed significant suppression of fungal burden and gliotoxin production in the lung. In addition, LH-AuNPs inhibited IPA-induced pro-inflammatory cytokines production, including interleukin-1 (IL-1), interleukin-17 (IL-17), and tumor necrosis factor-alpha (TNF-α), and reduced oxidative stress in lung. In conclusion, our data provide LH-AuNPs as a novel nanoparticle therapy for IPA. Full article

(This article belongs to the Topic Infectious Diseases)

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Biosynthesis of LH-AuNPs using L. hastate leaf extract. (A) The biosynthesis of LH-AuNPs was performed by combining L. hastate leaves powder (10 g) with 50 mL of 95% ethanol for 24 h at 37 °C in a 200 mL Erlenmeyer flask; 5 mL of the plant extract was added to 1 mM aqueous HAuCl4 solution (45 mL). The solution changed color from pale yellow to vivid ruby-red, signifying the formation of AuNPs. (B) TEM image of LH-AuNPs showed spherical or hexagonal shapes with lattice fringes s with sizes ranging from 5 to 30 nm. Full article ">Figure 2
Confirmation of biosynthesized LH-AuNPs. (A) UV–Vis spectrum of LH-AuNPs. Different ratios give different absorption peaks, but the most extreme peak with maximum absorbance was recorded 1:2 on 544 nm. (B) XRD spectrum recorded for LH-AuNPs showed clear peaks of cubic phases at 38.2 (111), 44.3 (200), 64.9 (220), 77.5 (311), and 81.5 (222), which confirms the crystalline nature of AuNPs. (C) FTIR spectrum of LH-AuNPs exhibited two peaks related to OH/NH and C=O groups. The presence of OH group could be ascribed to peak at 3444.6 cm−1. The peak of 1732.0 corresponded to C=O group. (D) EDX spectrum of LH-AuNPs shows strong signals in the gold region and confirms the formation of gold nanoparticles. A strong peak was displayed around 2.40 keV, which is the characteristic of gold nanoparticles. Full article ">Figure 3
Antimicrobial potential of LH-AuNPs. (A) Inverted microscope images of A. fumigatus treated with DMSO, LH-AuNPs, and AMB at their MIC values. Visual alterations in mycelial growth are obvious at three different treatments. (B) Radial growth of A. fumigatus was inhibited, where LH-AuNPs reduced the relative radial growth of A. fumigatus by 30% compared to the control. (C) Pigment formation defects after LH-AuNPs treatment. The LH-AuNPs treated colonies lacked green pigmentation, signifying they formed few conidia. (D) Time–kill curves of A. fumigatus following exposure to LH-AuNPs and AMB. Values are mean ± SD of three independent experiments. Full article ">Figure 4
Electron microscopy photographs of A. fumigatus after treatment with LH-AuNPs. (A) SEM images of A. fumigatus treated with saline (a,b) and LH-AuNPs (c,d) (64 μg/mL). Black arrows specify pitting and tearing destruction to the cell wall. White arrows show penetration of cell wall into the cytoplasm. Bar = 5 μm. (B) TEM images of A. fumigatus treated with saline (a,b) showing normal growth of A. fumigatus hyphae and treated with LH-AuNPs (c,d) showing reticular accumulations on the cell wall on the outer fibrillar layer (arrows) (c) and the outer fibrillar layer has a lattice-like structure that is thready (thick arrows). The inner fibrillar layer is not consistently observable (thin arrow) (d). Full article ">Figure 5
LH-AuNPs repair lung tissue damage in IPA mice. (A) Cytotoxicity of LH-AuNPs on human lung cancer cell line, A549, and primary mBMSCs. The dose-dependent effect of LH-AuNPs on cell viability was measured by MTT assay after 48h of treatment. Values are mean ± SD of three independent experiments (** p < 0.005, compared to control non-treated cells). (B) Histological analysis of lung tissues (3 days post-LH-AuNPs treatment) from control, IPA-non-treated, and IPA-treated mice with LH-AuNPs. Sections stained with H & E (a) and periodic acid–Schiff (PAS) (b). Extensive fungal growth and tissue damage are evident in the non-treated IPA mice. Arrows indicate fungal balls with great density fungi and proliferating hyphae, while there is a lack of fungal balls and hyphae in the lungs of animals with LH-AuNPs treatment. Full article ">Figure 6
LH-AuNPs suppress fungal burden and gliotoxin production in lung of IPA mice. In vivo cytotoxicity of LH-AuNPs in IPA mice. (A) H & E histological sections of liver and kidney from control, IPA-non-treated, and IPA-treated mice with LH-AuNPs. (B) Serum biochemical markers of liver function (a) AST and ALT and (b) renal function, including urea and creatinine. Biochemical analysis was performed after 3 days of treatment with LH-AuNPs. (C) Effect of LH-AuNPs on fungal load in lung homogenate of IPA mice. (D) Measurements of lung gliotoxin concentration in IPA mice after 3 days of LH-AuNPs. Values are expressed as means ± SD (n = 10 mice/group) (** p < 0.005, compared to control non-treated mice). Full article ">Figure 7
Inhibitory effect of LH-AuNPs on pro-inflammatory cytokines production and oxidative stress in IPA mice. Measurements of inflammatory cytokines, (A) TNF-α, (B) IL-1, and (C) IL-17 after 3 days of LH-AuNPs treatment in IPA mice. Effect LH-AuNPs on the antioxidant enzymes production, including (D) CAT, (E) SOD, and (F) MDA in the lung of IPA mice after 3 days of LH-AuNPs treatment. Data are expressed as means ± SD (n = 10 mice/group). (* p < 0.05 and ** p < 0.005, compared to control non-treated mice). Full article ">

15 pages, 3228 KiB

Open AccessReview

Mechanisms of Inhibition of Quorum Sensing as an Alternative for the Control of E. coli and Salmonella

by Esmeralda Escobar-Muciño, Margarita M. P. Arenas-Hernández and M. Lorena Luna-Guevara

Microorganisms 2022, 10(5), 884; https://doi.org/10.3390/microorganisms10050884 - 23 Apr 2022

Cited by 25 | Viewed by 6756

Abstract

Quorum sensing (QS) is a process of cell–cell communication for bacteria such as E. coli and Salmonella that cause foodborne diseases, with the production, release, and detection of autoinducer (AI) molecules that participate in the regulation of virulence genes. All of these proteins [...] Read more.

Quorum sensing (QS) is a process of cell–cell communication for bacteria such as E. coli and Salmonella that cause foodborne diseases, with the production, release, and detection of autoinducer (AI) molecules that participate in the regulation of virulence genes. All of these proteins are useful in coordinating collective behavior, the expression of virulence factors, and the pathogenicity of Gram-negative bacteria. In this work, we review the natural or synthetic inhibitor molecules of QS that inactivate the autoinducer and block QS regulatory proteins in E. coli and Salmonella. Furthermore, we describe mechanisms of QS inhibitors (QSIs) that act as competitive inhibitors, being a useful tool for preventing virulence gene expression through the downregulation of AI-2 production pathways and the disruption of signal uptake. In addition, we showed that QSIs have negative regulatory activity of genes related to bacterial biofilm formation on clinical artifacts, which confirms the therapeutic potential of QSIs in the control of infectious pathogens. Finally, we discuss resistance to QSIs, the design of next-generation QSIs, and how these molecules can be leveraged to provide a new antivirulence therapy to combat diseases caused by E. coli or Salmonella. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 849 KiB

Open AccessArticle

Frequency and Duration of, and Risk Factors for, Diagnostic Delays Associated with Histoplasmosis

by Aaron C. Miller, Alan T. Arakkal, Scott H. Koeneman, Joseph E. Cavanaugh, George R. Thompson, John W. Baddley and Philip M. Polgreen

J. Fungi 2022, 8(5), 438; https://doi.org/10.3390/jof8050438 - 23 Apr 2022

Cited by 14 | Viewed by 3508

Abstract

Histoplasmosis is often confused with other diseases leading to diagnostic delays. We estimated the incidence, length of, and risk factors for, diagnostic delays associated with histoplasmosis. Using data from IBM Marketscan, 2001–2017, we found all patients with a histoplasmosis diagnosis. We calculated the [...] Read more.

Histoplasmosis is often confused with other diseases leading to diagnostic delays. We estimated the incidence, length of, and risk factors for, diagnostic delays associated with histoplasmosis. Using data from IBM Marketscan, 2001–2017, we found all patients with a histoplasmosis diagnosis. We calculated the number of visits that occurred prior to the histoplasmosis diagnosis and the number of visits with symptomatically similar diagnoses (SSDs). Next, we estimated the number of visits that represented a delay using a simulation-based approach. We also computed the number of potential opportunities for diagnosis that were missed for each patient and the length of time between the first opportunity and the diagnosis. Finally, we identified risk factors for diagnostic delays using a logistic regression model. The number of SSD-related visits increased significantly in the 97 days prior to the histoplasmosis diagnosis. During this period, 97.4% of patients had a visit, and 90.1% had at least one SSD visit. We estimate that 82.9% of patients with histoplasmosis experienced at least one missed diagnostic opportunity. The average delay was 39.5 days with an average of 4.0 missed opportunities. Risk factors for diagnostic delays included prior antibiotic use, history of other pulmonary diseases, and emergency department and outpatient visits, especially during weekends. New diagnostic approaches for histoplasmosis are needed. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 869 KiB

Open AccessArticle

Serum Cytokines Usefulness for Understanding the Pathology in Allergic Bronchopulmonary Aspergillosis and Chronic Pulmonary Aspergillosis

by Yuya Ito, Takahiro Takazono, Yasushi Obase, Susumu Fukahori, Nobuyuki Ashizawa, Tatsuro Hirayama, Masato Tashiro, Kazuko Yamamoto, Yoshifumi Imamura, Naoki Hosogaya, Chizu Fukushima, Yoshitomo Morinaga, Katsunori Yanagihara, Koichi Izumikawa and Hiroshi Mukae

J. Fungi 2022, 8(5), 436; https://doi.org/10.3390/jof8050436 - 23 Apr 2022

Cited by 8 | Viewed by 2399

Abstract

Allergic bronchopulmonary aspergillosis (ABPA) and chronic pulmonary aspergillosis (CPA) are important fungal infections caused by Aspergillus species. An overlap of ABPA and CPA has been reported; therefore, it is critical to determine whether the main pathology is ABPA or CPA and whether antifungals [...] Read more.

Allergic bronchopulmonary aspergillosis (ABPA) and chronic pulmonary aspergillosis (CPA) are important fungal infections caused by Aspergillus species. An overlap of ABPA and CPA has been reported; therefore, it is critical to determine whether the main pathology is ABPA or CPA and whether antifungals are required. In this study, we investigated whether the serum cytokine profile is useful for understanding the pathology and for differentiating between these diseases. We compared the various serum cytokine levels among healthy subjects and patients diagnosed with asthma, ABPA, or CPA at Nagasaki University Hospital between January 2003 and December 2018. In total, 14 healthy subjects, 19 patients with asthma, 11 with ABPA, and 10 with CPA were enrolled. Interleukin (IL) -5 levels were significantly higher in patients with ABPA than in those with CPA, and IL-33 and tumor necrosis factor (TNF) levels were significantly higher in patients with CPA than in those with asthma (p < 0.05, Dunn’s multiple comparison test). The sensitivity and specificity of the IL-10/IL-5 ratio (cutoff index 2.47) for diagnosing CPA were 70% and 100%, respectively. The serum cytokine profile is useful in understanding the pathology of ABPA and CPA, and the IL-10/IL-5 ratio may be a novel supplemental biomarker for indicating the pathology of CPA. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Chest computed tomography (CT) findings and serum cytokine. Interleukin (IL)-5 levels were high in subjects with mucoid impaction and significantly lower in those with fungus ball and cavitary lesions on chest CT. IL-10, IL-33, tumor necrosis factor (TNF), and soluble CD40 ligand (sCD40L) levels were low in subjects with mucoid impaction and high in those with cavitary lesions on chest CT. IL-33 level was significantly higher in subjects with fungus balls. Data are expressed as the mean ± standard deviation. Error bars indicate standard deviation. Statistical analyses were performed using the Mann–Whitney U test. Asterisks indicate statistically significant differences (* p < 0.05; ** p < 0.01). Full article ">Figure 2
Serum cytokine ratio and receiver operating characteristic (ROC) curves. (a) The Interleukin (IL)-33/IL-5 ratio was not significantly different between allergic bronchopulmonary aspergillosis (ABPA) and chronic pulmonary aspergillosis (CPA) subjects, but the soluble CD40 ligand (sCD40L)/IL-5, tumor necrosis factor (TNF)/IL-5, and IL-10/IL-5 ratios were significantly higher in subjects with CPA than in those with ABPA. Data are expressed as the mean ± standard deviation. Error bars indicate standard deviation. Statistical analyses were performed using the Kruskal–Wallis test with Dunn’s multiple comparison post-test. Asterisks indicate statistically significant differences (* p < 0.05; ** p < 0.01; *** p < 0.001; **** p < 0.0001). (b) ROC curve analyses were performed on the serum cytokine ratio, and areas under the curves, including 95% confidence intervals, were evaluated. Areas under the curves (95% confidence interval) for sCD40L/IL-5, TNF/IL-5, and IL-10/IL-5 ratios were 0.818 (0.627–1.0000), 0.864 (0.709–1.000), and 0.909 (0.786–1.000), respectively. (c) ROC curve analyses were performed on the galactomannan (GM) antigen, and areas under the curves, including 95% confidence intervals, were evaluated. The area under the curve (95% confidence interval) for the GM antigen was 0.891 (0.751–1.000). Full article ">

17 pages, 715 KiB

Open AccessReview

Epidemiology and Characteristics of Elizabethkingia spp. Infections in Southeast Asia

by Asdren Zajmi, Jeanette Teo and Chew Chieng Yeo

Microorganisms 2022, 10(5), 882; https://doi.org/10.3390/microorganisms10050882 - 22 Apr 2022

Cited by 23 | Viewed by 4381

Abstract

Elizabethkingia spp. is a ubiquitous pathogenic bacterium that has been identified as the causal agent for a variety of conditions such as meningitis, pneumonia, necrotizing fasciitis, endophthalmitis, and sepsis and is emerging as a global threat including in Southeast Asia. Elizabethkingia infections tend [...] Read more.

Elizabethkingia spp. is a ubiquitous pathogenic bacterium that has been identified as the causal agent for a variety of conditions such as meningitis, pneumonia, necrotizing fasciitis, endophthalmitis, and sepsis and is emerging as a global threat including in Southeast Asia. Elizabethkingia infections tend to be associated with high mortality rates (18.2–41%) and are mostly observed in neonates and immunocompromised patients. Difficulties in precisely identifying Elizabethkingia at the species level by traditional methods have hampered our understanding of this genus in human infections. In Southeast Asian countries, hospital outbreaks have usually been ascribed to E. meningoseptica, whereas in Singapore, E. anophelis was reported as the main Elizabethkingia spp. associated with hospital settings. Misidentification of Elizabethkingia spp. could, however, underestimate the number of cases attributed to the bacterium, as precise identification requires tools such as MALDI-TOF MS, and particularly whole-genome sequencing, which are not available in most hospital laboratories. Elizabethkingia spp. has an unusual antibiotic resistance pattern for a Gram-negative bacterium with a limited number of horizontal gene transfers, which suggests an intrinsic origin for its multidrug resistance. Efforts to prevent and further understand Elizabethkingia spp. infections and limit its spread must rise to this new challenge. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 4413 KiB

Open AccessCase Report

Placental Alterations in a Chikungunya-Virus-Infected Pregnant Woman: A Case Report

by Natália Salomão, Luciana Araújo, Kíssila Rabelo, Elyzabeth Avvad-Portari, Luiz de Souza, Regina Fernandes, Nathália Valle, Luiz Ferreira, Carlos Basílio-de-Oliveira, Rodrigo Basílio-de-Oliveira, Thiara de Souza, Priscila Nunes, Jorge Carvalho, Flavia dos Santos and Marciano Paes

Microorganisms 2022, 10(5), 872; https://doi.org/10.3390/microorganisms10050872 - 22 Apr 2022

Cited by 5 | Viewed by 2469

Abstract

Chikungunya virus (CHIKV) is an arthropod-borne virus first isolated in Tanzania, Africa. The virus has spread to Asia as well as South and Central America through infected Aedes mosquitoes. Vertical transmission may also occur, and was first documented during a chikungunya outbreak in [...] Read more.

Chikungunya virus (CHIKV) is an arthropod-borne virus first isolated in Tanzania, Africa. The virus has spread to Asia as well as South and Central America through infected Aedes mosquitoes. Vertical transmission may also occur, and was first documented during a chikungunya outbreak in La Réunion Island in 2005. Since then, some authors have been discussing the role of the placenta in maternal–fetal CHIKV transmission. CHIKV infection is characterized by fever, headache, rash, and arthralgia. However, atypical manifestations and clinical complications, including neurological, cardiac, renal, ocular, and dermal, may occur in some cases. In this report, we describe the case of a pregnant woman infected by CHIKV during the third trimester of gestation, who presented with severe dermatological manifestations during the epidemic in Rio de Janeiro, Brazil in 2019. CHIKV RNA and antigens were detected in the placental tissue, which presented with histopathological (deciduitis, fibrin deposition, edema, fetal vessel thickening, and chorioamnionitis) and ultrastructural alterations (cytotrophoblast with mitochondrial swelling and dilated cisterns in endoplasmic reticulum, vesicles in syncytiotrophoblasts, and thickening of the basement membrane of the endothelium). Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Histopathological changes in the placenta. (A–C) Control placenta (uninfected) with regular aspects: (A) decidua and chorionic villi, (B) chorionic villi, and (C) decidua. (D–K) CHIKV-infected placenta: (D–E) deciduitis (Dec); (F) fibrin deposition (Fi) and fibrosis (Fs); (G) edema (E) in intervillous space (Is), edema inside fetal capillaries (Fc), and fibrin deposition (Fi); (H) fetal vessel thickening (Vs); (I) edema (E) in chorionic villi, extramedullary hematopoiesis (H); (J,K) chorioamnionitis (C) in lower and higher magnification, respectively. Scale bar—(A,D,G,H,J): 100 µm; (B,I): 20 µm; (C,F,K): 50 µm. Full article ">Figure 2
CHIKV antigen detection in the placenta. (A–B) Negative CHIKV antigen detection in the control placenta; (C–F) infected placenta with CHIKV antigen detection in: (C) decidual cells (DC), (D) trophoblast cells (TC), (E) endothelial cells (EC) and cell inside fetal capillary (H), and (F) cell inside fetal capillary (H). Scale bar—(A,B): 50 µm; (C–F): 10 µm). Full article ">Figure 3
Tissue expression and quantification of CD163+ cells in the placenta. (A,C) Control tissue (uninfected placenta in lower and higher magnification, respectively; (B,D) CHIKV placenta in lower and higher magnification, respectively; (E) quantification of CD163+, showing increased expression in the CHIKV-infected placenta compared to the control. The square (control) and the circle (infected placenta) represent each acquired image, and the number of positive cells is represented in y axis. * indicates statistically significant differences between groups (* p < 0.05). Full article ">Figure 4
Ultrastructure of CHIKV-infected placenta. (A) Electron microscopy of ultrathin sections of non-CHIKV placenta with regular cytotrophoblast organelles (mitochondria and endoplasmic reticulum), (B) syncytiotrophoblasts, and (C) endothelial cells. (D) Mitochondrial swelling with the endoplasmic reticulum exhibiting dilated cisterns in cytotrophoblast, (E) vesicles in syncytiotrophoblasts, and (F) thickening of the basement membrane of the endothelium. CTB—Cytotrophoblast; STB—syncytiotrophoblasts; ER—endoplasmic reticulum; M—mitochondria; N—nucleus; Ve—vesicles; En—endothelium; BM—basement membrane. Full article ">

12 pages, 1248 KiB

Open AccessArticle

Non-Achievement of Alanine Aminotransferase Normalization Associated with the Risk of Hepatocellular Carcinoma during Nucleos(t)ide Analogue Therapies: A Multicenter Retrospective Study

by Jun Inoue, Tomoo Kobayashi, Takehiro Akahane, Osamu Kimura, Kosuke Sato, Masashi Ninomiya, Tomoaki Iwata, Satoshi Takai, Norihiro Kisara, Toshihiro Sato, Futoshi Nagasaki, Masahito Miura, Takuya Nakamura, Teruyuki Umetsu, Akitoshi Sano, Mio Tsuruoka, Masazumi Onuki, Hirofumi Niitsuma, Atsushi Masamune and THERME Study Group

J. Clin. Med. 2022, 11(9), 2354; https://doi.org/10.3390/jcm11092354 - 22 Apr 2022

Cited by 4 | Viewed by 1953

Abstract

Patients with a chronic hepatitis B virus (HBV) infection who are treated with nucleos(t)ide analogues (NAs) are still at risk for hepatocellular carcinoma (HCC), and it has been clinically questioned whether patients with a high risk of HCC can be identified efficiently. We [...] Read more.

Patients with a chronic hepatitis B virus (HBV) infection who are treated with nucleos(t)ide analogues (NAs) are still at risk for hepatocellular carcinoma (HCC), and it has been clinically questioned whether patients with a high risk of HCC can be identified efficiently. We aimed to clarify the risk factors associated with the development of HCC during NA therapies. A total of 611 chronically HBV-infected patients without a history of HCC, who were treated with NAs for more than 6 months (median 72 months), from 2000 to 2021, were included from 16 hospitals in the Tohoku district in Japan. Incidences of HCC occurrence were analyzed with clinical factors, including on-treatment responses. Alanine aminotransferase (ALT) normalization, based on the criteria of three guidelines, was analyzed with other parameters, including the age–male–ALBI–platelets (aMAP) risk score. During the observation period, 48 patients developed HCC, and the cumulative HCC incidence was 10.6% at 10 years. Non-achievement of ALT normalization at 1 year of therapy was mostly associated with HCC development when ALT ≤ 30 U/L was used as the cut-off (cumulative incidence, 19.9% vs. 5.3% at 10 years, p < 0.001). The effectiveness of the aMAP risk score at the start of treatment was validated in this cohort. A combination of an aMAP risk score ≥ 50 and non-achievement of ALT normalization could stratify the risk of HCC significantly, and notably, there was no HCC development in 103 patients without these 2 factors. In conclusion, non-achievement of ALT normalization (≤30 U/L) at 1 year might be useful in predicting HCC during NA therapies and, in combination with the aMAP risk score, could stratify the risk more precisely. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 875 KiB

Open AccessArticle

Glycated Albumin and Glycated Albumin/HbA1c Predict the Progression of Coronavirus Disease 2019 from Mild to Severe Disease in Korean Patients with Type 2 Diabetes

by Jeongseon Yoo, Youngah Choi, Shin Ae Park, Ji Yeon Seo, Chul Woo Ahn and Jaehyun Han

J. Clin. Med. 2022, 11(9), 2327; https://doi.org/10.3390/jcm11092327 - 21 Apr 2022

Cited by 3 | Viewed by 1944

Abstract

Hyperglycemia is among the main risk factors for severe COVID-19. We evaluated the association of glycated albumin (GA) and GA/HbA1c ratio with progression of COVID-19 from mild to severe disease in patients with type 2 diabetes mellitus (T2DM). Our retrospective study included 129 [...] Read more.

Hyperglycemia is among the main risk factors for severe COVID-19. We evaluated the association of glycated albumin (GA) and GA/HbA1c ratio with progression of COVID-19 from mild to severe disease in patients with type 2 diabetes mellitus (T2DM). Our retrospective study included 129 patients aged over 18 years with COVID-19 and T2DM who did not have any need of oxygen supplement. Of these, 59 patients whose COVID-19 was aggravated and required oxygen supplementation eventually were classified as having severe disease. Clinical and laboratory data were compared between mild and severe cases. The median of GA (18.4% vs. 20.95%, p = 0.0013) and GA/HbA1c (2.55 vs. 2.68, p = 0.0145) were higher in severe disease than in mild disease and positively correlated with C-reactive protein (Kendal Tau coefficient 0.200 and 0.126, respectively; all p < 0.05). Multiple logistic regression analysis showed that GA (odds ratio (OR), 1.151; 95% confidence interval (CI), 1.024–1.294) and GA/HbA1c (OR, 8.330; 95% CI, 1.786–38.842) increased the risk of severe disease. Patients with GA 20% or higher were 4.03 times more likely to progress from mild to severe disease. GA and GA/HbA1c ratio predicted progression of COVID-19 from mild to severe disease in patients with T2DM. Full article

(This article belongs to the Topic Infectious Diseases)

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13 pages, 293 KiB

Open AccessArticle

Multidrug-Resistant Acinetobacter baumannii in Jordan

by Mohammad Al-Tamimi, Hadeel Albalawi, Mohamd Alkhawaldeh, Abdullah Alazzam, Hassan Ramadan, Majd Altalalwah, Ahmad Alma’aitah, Dua’a Al Balawi, Sharif Shalabi, Jumana Abu-Raideh, Ashraf I. Khasawneh, Farah Alhaj and Kamal Hijawi

Microorganisms 2022, 10(5), 849; https://doi.org/10.3390/microorganisms10050849 - 20 Apr 2022

Cited by 14 | Viewed by 3921

Abstract

Background: Acinetobacter baumannii is a common cause of multi-drug (MDR)-resistant infections worldwide. The epidemiological and molecular characteristics of MDR-A. baumannii in Jordan is not known. Methods: A. baumannii isolates were collected from 2010 to 2020 from three tertiary hospitals in Jordan. Demographic [...] Read more.

Background: Acinetobacter baumannii is a common cause of multi-drug (MDR)-resistant infections worldwide. The epidemiological and molecular characteristics of MDR-A. baumannii in Jordan is not known. Methods: A. baumannii isolates were collected from 2010 to 2020 from three tertiary hospitals in Jordan. Demographic and clinical data, isolates information, antibiotic susceptibility patterns, phenotypic, and molecular characterization of carbapenem resistance genes were performed. Results: A total of 622 A. baumannii isolates were collected during the study period. Most isolates were from males, aged 18–60 years, Jordanian, from infected wounds, and were patients in surgery or critical care units. Among patients from whom A. baumannii was isolated, associated risk factors for MDR were adults over 60, males, critically ill patients and infected wounds (OR 4.14, 2.45, 10, 7, respectively, p < 0.0001). Incidence rates from 2010 to 2015 showed a slight increase in MDR (3.75/1000 to 4.46/1000). Resistance patterns indicated high resistance for most cephalosporins, carbapenems, and fluoroquinolones, moderate resistance for trimethoprim/sulfamethoxazole and ampicillin/sulbactam, low resistance for aminoglycosides and tetracyclines, while colistin and tigecycline, have the lowest resistance rates. 76.8% of A. baumannii isolates were MDR and 99.2% were carbapenem-resistant. All isolates were positive for the OXA-51 gene (100%), 98.5% were positive for the OXA-23 gene, 26.6% for the VIM gene, while KPC and IMP genes were almost not detected (0% and 0.8% respectively). Conclusions: This is the first large, multicentric, prolonged study that provides insights into A. baumannii infections in Jordan. Attention to patients at higher risk is important for early identification. Colistin and tigecycline were the most effective antimicrobials. Full article

(This article belongs to the Topic Infectious Diseases)

20 pages, 2200 KiB

Open AccessArticle

A New Topical Candidate in Acne Treatment: Characterization of the Meclozine Hydrochloride as an Anti-Inflammatory Compound from In Vitro to a Preliminary Clinical Study

by Philippe A. Grange, Guillaume Ollagnier, Laurianne Beauvais Remigereau, Carole Nicco, Constance Mayslich, Anne-Geneviève Marcelin, Vincent Calvez and Nicolas Dupin

Biomedicines 2022, 10(5), 931; https://doi.org/10.3390/biomedicines10050931 - 19 Apr 2022

Cited by 2 | Viewed by 3119

Abstract

Acne is a chronic inflammatory multifactorial disease involving the anaerobic bacterium Cutibacterium acnes (C. acnes). Current acne treatments are associated with adverse effects, limiting treatment compliance and use. We showed that meclozine, an anti-histaminic H1 compound, has anti-inflammatory properties. In Vitro, [...] Read more.

Acne is a chronic inflammatory multifactorial disease involving the anaerobic bacterium Cutibacterium acnes (C. acnes). Current acne treatments are associated with adverse effects, limiting treatment compliance and use. We showed that meclozine, an anti-histaminic H1 compound, has anti-inflammatory properties. In Vitro, meclozine reduced the production of CXCL8/IL-8 and IL-1β mRNA and protein by C. acnes-stimulated human keratinocytes and monocytes. No cell toxicity was observed at the IC50. Meclozine prevented the phosphorylation of ERK and JNK. In Vivo, 1% meclozine gel significantly decreased C. acnes-mouse ear induced inflammation by 26.7% (p = 0.021). Ex vivo experiments on human skin explants showed that meclozine decreased the production of GM-CSF, IL-1β and TNF-α at transcriptional and translational levels. In a randomized, double-blind, placebo-controlled proof-of-concept clinical trial on 60 volunteers, 2% meclozine pharmaceutical gel decreased by 20.1% (p < 0.001) the ASI score in the treated group after 12 weeks of treatment. No adverse event was reported. Together, these results indicate that meclozine is a potent topical anti-inflammatory compound of potential value for acne treatment. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Chemical structure of meclozine. Meclozine hydrochloride or 1-(p-chloro-alpha-phenylbenzyl)-4-(m-methyl-benzyl)—piperazine dihydrochloride monohydrate. Full article ">Figure 2
Meclozine inhibits the CXCL8/IL-8 and IL-1β productions at the translational and transcriptional levels. (A–C) HaCaT cell, (D,E) primary keratinocyte (NHEK), (F–H) ThP-1 cell were pre-treated for 24 h with meclozine at concentrations ranging from 0.39 to 50 µM and then stimulated with C. acnes 6919 (gray bar). Control experiments were conducted with untreated and unstimulated cells (black bar) and with cells stimulated with C. acnes 6919 only (horizontal line bar); n = 4. (C,H) Total RNA was extracted from HaCaT and ThP-1 cells pre-treated with 10 µM meclozine and mRNA levels of CXCL8/IL-8 and IL-1β were quantitated by real-time RT-PCR and compared with GAPDH mRNA level (used as control) and are expressed as fold-change; n = 3. (I,J) HaCaT cells were pre-treated with meclozine at concentrations ranging from 0.39 to 50 µM for 1 h (dark bar), 6 h (dark gray bar), 24 h (middle gray bar), and 48 h (light gray bar), and then stimulated by C. acnes 6919 for 18 h. Measurement of CXCL8/IL-8 and IL-1β productions were realized by ELISA and cytotoxicity was determined by the MTT assay, n = 3. Data are means ± S.D. of separate experiments. Statistical significance was indicated by * (p < 0.05), ** (p < 0.01), *** (p < 0.001), and **** (p < 0.0001), respectively. ns: non-significant. Full article ">Figure 3
Meclozine inhibits CXCL8 and IL-1β productions in PGN and LTA stimulated keratinocytes and monocytes. HaCaT cells (A,B) and ThP1 cells (C,D) were pre-treated for 24 h with meclozine at concentrations ranging from 0.39 to 25 µM and then stimulated with PGN and LTA at 5 (dark gray bar), 10 (middle gray bar), and 20 µg/mL (light gray bar). Control experiments were conducted with cells stimulated with PGN and LTA only. Measurement of CXCL8/IL-8 and IL-1β productions were realized by ELISA. Data are means ± SEM of three separate experiments. Statistical analysis was done by using PGN and LTA alone for each concentration used as a reference and are indicated by * (p < 0.05), ** (p < 0.01), and *** (p < 0.001) respectively. Full article ">Figure 4
Meclozine inhibits inflammatory signaling pathways. HaCaT keratinocytes were pre-treated for 24 h with 10 µM meclozine and then stimulated with C. acnes (MOI of 15) for 30, 60, 120 and 180 min. (A) CXCL-8/IL-8 production was measured by ELISA in culture supernatant. Data represent mean ± SEM, n = 4. Representative blot analysis of relative phosphorylation of proteins (B) after C. acnes stimulation and (C) after meclozine pre-treatment and C. acnes stimulation. (D–H) Quantitative analysis of immunoblotting with C. acnes stimulation alone (dark bar) and meclozine pre-treatment followed by C. acnes stimulation (gray bar). Statistical significance is indicated by * (p < 0.05), *** (p < 0.001), and **** (p < 0.0001), respectively. Full article ">Figure 5
In vivo meclozine activity in C. acnes-stimulated ear mouse model. (A,E) Experimental setup of the in vivo training model used. BALB/c mice ears were injected with PBS (negative control) or stimulated with C. acnes suspension (1.5×106 CFU/20 µL). Both ears were topically treated with 30 mg of vehicle (positive control) or with (A–D) 30 mg of in-house meclozine gel formulation at 0.1 to 4% meclozine; and (E–G) 30 mg of pharmaceutical gel formulation at 1% meclozine. (B,F) Inflammatory score, including ear thickness, redness and peeling, was measured for each ear. Each bar represents the mean ± SEM, n = 8 biologically independent mice. (C,G) Pictures of ears. (D) Histological analysis of ears. The Mann–Whitney test was used to detect significant differences between groups with ns: non-significant; * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001. Scale bar = 50 μm. Full article ">Figure 6
Ex vivo meclozine activity. Human skin explants were left untreated and unstimulated (explant alone), stimulated by C. acnes 6919 (O.D.600nm = 1.0) (explant + C. acnes), and pre-treated with 15 µM meclozine for 48 h and then stimulated by C. acnes for 24 h. (A,C,E) IL-1β, TNF-α and GM-CSF productions were measured by ELISA in culture supernatant, respectively. (B,D,F) Total RNA was extracted and IL-1β, TNF-α and GM-CSF mRNA levels were determined by real-time RT-PCR and compared with GAPDH mRNA level (used as control), and are expressed as fold-change, respectively. Data are means ± SEM, n = 3. Statistical significance is indicated by *** (p < 0.001), and **** (p < 0.0001), respectively. Full article ">Figure 7
Clinical evaluation of meclozine in acne lesions in human. Double-blind, randomized, placebo-controlled clinical evaluation of 2% meclozine gel was evaluated over 12 weeks in 60 volunteers as described in Materials and Methods. Acne severity index (ASI) was determined at baseline and after 12 weeks treatment in the intention to treat (ITT) and per-protocol (PP) approaches. (A,C) Treated group and (B,D) control group. The Wilcoxon signed-rank test was used to detect significant differences between groups with ns: non-significant; *** p ≤ 0.001. Full article ">

19 pages, 3921 KiB

Open AccessArticle

Environmentally Acquired Bacillus and Their Role in C. difficile Colonization Resistance

by William T. Ferreira, Huynh A. Hong, James R. G. Adams, Mateusz Hess, Natalia K. Kotowicz, Sisareuth Tan, Enrico Ferrari, Alain Brisson, Jurgen Zentek, Mikhail Soloviev and Simon M. Cutting

Biomedicines 2022, 10(5), 930; https://doi.org/10.3390/biomedicines10050930 - 19 Apr 2022

Cited by 2 | Viewed by 2783

Abstract

Clostridioides difficile is an environmentally acquired, anaerobic, spore-forming bacterium which ordinarily causes disease following antibiotic-mediated dysbiosis of the intestinal microbiota. Although much is understood regarding the life cycle of C. difficile, the fate of C. difficile spores upon ingestion remains unclear, and [...] Read more.

Clostridioides difficile is an environmentally acquired, anaerobic, spore-forming bacterium which ordinarily causes disease following antibiotic-mediated dysbiosis of the intestinal microbiota. Although much is understood regarding the life cycle of C. difficile, the fate of C. difficile spores upon ingestion remains unclear, and the underlying factors that predispose an individual to colonization and subsequent development of C. difficile infection (CDI) are not fully understood. Here, we show that Bacillus, a ubiquitous and environmentally acquired, spore-forming bacterium is associated with colonization resistance to C. difficile. Using animal models, we first provide evidence that animals housed under conditions that mimic reduced environmental exposure have an increased susceptibility to CDI, correlating with a loss in Bacillus. Lipopeptide micelles (~10 nm) produced by some Bacilli isolated from the gastro-intestinal (GI)-tract and shown to have potent inhibitory activity to C. difficile have recently been reported. We show here that these micelles, that we refer to as heterogenous lipopeptide lytic micelles (HELMs), act synergistically with components present in the small intestine to augment inhibitory activity against C. difficile. Finally, we show that provision of HELM-producing Bacillus to microbiota-depleted animals suppresses C. difficile colonization thereby demonstrating the significant role played by Bacillus in colonization resistance. In the wider context, our study further demonstrates the importance of environmental microbes on susceptibility to pathogen colonization. Full article

(This article belongs to the Topic Infectious Diseases)

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C. difficile colonization is inversely correlated with the acquisition of environmental Bacillus. (A) C. difficile colonization in piglets decreased following environmental exposure after birth. Fecal samples of neonatal piglets were collected during days 1–13 following birth. C. difficile (red circles) and Bacillus spores (black circles) were enumerated from the same fecal sample, from each individual piglet. A statistically significant negative correlation (Spearman’s rank-order) was observed between counts of C. difficile and Bacillus spores in pig fecal samples (rs = −0.5464, p = 0.0127). A significant correlation also existed between days passed for both Bacillus (rs = 0.9270, p = 0.0001), and C. difficile counts (rs = −0.5138, p = 0.0205). The average for each sample from two CFU measurements was used; (B) Mice habituating in ‘super clean’ conditions were more susceptible to clindamycin-induced C. difficile colonization than ‘conventionally caged’ mice. Mice (n = 5/gp) kept in ‘super clean’ (IVC; sterile food, water and bedding) or ‘conventional cages’ (CC; non-sterile food, water and bedding) for 1 year were challenged with CD630 after dosing with various concentrations of clindamycin. Colonized animals were confirmed by enumerating ethanol-resistant C. difficile in cecum 24 h post-challenge. Mice with counts >103 CFU/g were considered colonized. The IC50 of IVC (‘super clean’) and CC mice were 0.8 mg/kg and 2.0 mg/kg, respectively; (C) Bacillus spores were absent in fecal samples of ‘Super clean’ mice. Fecal samples were collected before the challenge study (panel B), heated at 65 °C for 45 min., dilutions plated on LB and enumerated after incubation for 2 days at 37 °C. Significance calculated using an unpaired t-test. ****, p < 0.0001. Full article ">Figure 2
Bacillus-produced heterogenous lipopeptide lytic micelles (HELM) particles kill C. difficile. (A–C), SEC fractions from strains of three ‘active’ strains of Bacillus: B. velezensis strain Bv297 (A); B. licheniformis strain Bl130 (B) and B. subtilis strain Bs140 (C), were examined by RP-HPLC (orange line). Loading was normalized according to volume of initial culture supernatant. All strains showed inhibitory activity to CD630. Bv297 (A) and Bs140 (C) were human-derived (<a href="#app1-biomedicines-10-00930" class="html-app">Supplementary Table S1</a>) while Bl130 (B) was obtained from mouse faeces. The RP-HPLC profile of iturins (I), fengycins (F) and surfactins (S) are indicated and the Bv277 profile (blue line) is shown for comparison. Bl130 showed detectable levels of fengycin and iturin using MALDI-TOF analysis (data not shown); (D) HELM particles were analyzed by DLS. Analysis of the Bv277 active SEC fraction revealed the presence of a monodisperse population of micelles with an average diameter of 6.8 ± 0.16 nm (PDI = 0.18). Data points are the average of three measurements with error bars representing the standard error; (E,F), HELM bacteriolytic activity against CD630. The inhibitory activity to CD630 was determined using measurement of OD600 (E) or viable CFU (F) before and after addition (arrow) of HELM+ (Bv277) culture supernatant ( <img alt="Biomedicines 10 00930 i001" src="/biomedicines/biomedicines-10-00930/article_deploy/html/images/biomedicines-10-00930-i001.png"/>), HELM− (srfAA-) culture supernatant ( <img alt="Biomedicines 10 00930 i002" src="/biomedicines/biomedicines-10-00930/article_deploy/html/images/biomedicines-10-00930-i002.png"/>), HELM+ (Bv277) SEC-fractionated ‘active’ fraction ( <img alt="Biomedicines 10 00930 i003" src="/biomedicines/biomedicines-10-00930/article_deploy/html/images/biomedicines-10-00930-i003.png"/>) and untreated (PBS) ( <img alt="Biomedicines 10 00930 i004" src="/biomedicines/biomedicines-10-00930/article_deploy/html/images/biomedicines-10-00930-i004.png"/>). Full article ">Figure 3
Detection of HELMs in the SI. Panel A, MALDI-TOF analysis of 30 collected individual fractions following RP-HPLC analysis of pooled SI contents from naive mice (n = 3) (<a href="#app1-biomedicines-10-00930" class="html-app">Supplementary Figure S5</a>). Lipopeptides were identified in four fractions and representative mass spectra (colored arrows) are shown (B,C); (B) Representative MALDI-TOF spectra of an individual fraction (green arrow in A) containing iturins (highlighted in green). Displayed is a zoomed in mass spectrum of the detected C16IturinA/C16Mycosubtilin/C15BacillomycinF; (C) Representative MALDI-TOF spectra of an individual fraction (red arrow in A) containing surfactins (red) and fengycins (black). Displayed is a zoomed in mass spectrum of the detected surfactins (C12 to C15). Light blue color shows unidentified masses. Full article ">Figure 4
HELMs in the SI can inhibit C. difficile. Ex vivo analysis revealed CD630 inhibitory activity in the SI-extract of naïve and HELM+ (Bv277)-dosed mice. CD630 inhibitory activity was determined using methanol extracts taken from the SI contents of mice (n = 3) with or without clindamycin treatment (Clin and Naive). The contents were taken from the SI of mice treated with clindamycin followed by oral dosing with spores (2 × 109 CFU) of HELM+ (Bv277) or HELM− (srfAA-). The experiment was performed twice independently. Error bars represent standard deviation. Full article ">Figure 5
HELMs synergize with secondary bile acids. (A) HELMs synergize with SI extracts taken from mice. A sterile, cell-free Bv277 supernatant was incubated (3 h, RT) 1:1 with: PBS (HELMs) or methanol extracts in saline (1/3, w/v) taken from a naïve mouse SI (HELMs + SI) or SI taken from a mouse treated 24 h previously with 30 mg/kg clindamycin (HELMs + SI-Clin). The mixtures were serially diluted and inhibitory activity to CD630 was measured using the microdilution assay. At the dilution factors used in this experiment no activity was observed with the SI or SI-Clin extract only. The experiment was performed twice independently. Error bars represent standard deviation; (B,C), HELMs synergize with deoxycholate. Various dilutions of a sterile, cell-free Bv277 supernatant (containing 1 to 4 μg/mL HELMs) were mixed with different concentrations (50–400 μM) of secondary bile acid deoxycholate (DOC) (B) or primary bile acid cholate (CA) (C) and added to mid-logarithmic cultures of CD630 and incubated for 5 h at 37 °C. OD readings (600 nm) were taken, and relative growth determined as the percentage increase in OD600 from the time of addition of samples to CD630 culture. The experiment was performed twice independently. Error bars represent standard deviation. Significance calculated using an unpaired t-test. *, p < 0.05, **, p < 0.01, ***, p < 0.001, ****, p < 0.0001. Full article ">Figure 6
Exclusion of C. difficile colonization by HELM-producing Bacillus. (A,B) Bv-HELM+ spores inhibit C. difficile colonization in a dose-dependent manner using a microbiota depletion model. Mice (n = 6/gp) were treated with an antibiotic cocktail for 7 days, followed by a ‘washout’ period of 2 days before being challenged with 103 CD630 spores. Mice were dosed three times daily with spores of either 107, 106, 105, 104 or 103 CFU/dose of HELM+ (Bv277), HELM− (srfAA-) or PBS (naïve) during the two washout days and on the day of challenge. At 24 h post-challenge, ceca were removed for analysis of levels of ethanol-resistant spore counts (A) and toxin A (<a href="#app1-biomedicines-10-00930" class="html-app">Supplementary Figure S7A</a>). The percentage of colonized animals was calculated as the proportion of mice within each group with C. difficile spores (>103 CFU/g) and toxin present within the ceca (B). Significance was calculated using an unpaired t-test. *, p < 0.05; (C) Bv-HELM+ spores inhibit C. difficile colonization in a hamster clindamycin model. Golden Syrian hamsters were administered clindamycin and 13 h later dosed 3-times/day (6 h intervals) orally (i.g.) with ~2 × 109 CFU/dose of HELM+ (Bv277), HELM− (Bv378) or the cell-free supernatant of HELM+ (2 mL/dose) until study end. At 72 h post-clindamycin treatment animals were challenged with 102 spores of CD630. Animal survival is shown and toxin and CFU analysis is shown in <a href="#app1-biomedicines-10-00930" class="html-app">Supplementary Figure S6A,B</a>. Significance was tested with the log-rank (Mantel–Cox) test. **, p < 0.01. Full article ">

11 pages, 507 KiB

Open AccessArticle

Increased Risk to Develop Hypertension and Carotid Plaques in Patients with Long-Lasting Helicobacter pylori Gastritis

by Maria Pina Dore, Pier Sergio Saba, Giulia Tomassini, Caterina Niolu, Marco Monaco and Giovanni Mario Pes

J. Clin. Med. 2022, 11(9), 2282; https://doi.org/10.3390/jcm11092282 - 19 Apr 2022

Cited by 6 | Viewed by 4032

Abstract

Helicobacter pylori infection has been reported to be positively associated with hypertension, although with conflicting results. In this study, the relationship between H. pylori infection and hypertension, as well as atherosclerotic carotid lesions, was analyzed. Methods. Clinical records of patients referred to undergo [...] Read more.

Helicobacter pylori infection has been reported to be positively associated with hypertension, although with conflicting results. In this study, the relationship between H. pylori infection and hypertension, as well as atherosclerotic carotid lesions, was analyzed. Methods. Clinical records of patients referred to undergo upper endoscopy and gastric biopsy were retrieved. Information regarding the presence of H. pylori infection with atrophy/metaplasia/dysplasia (interpreted as a long-lasting infection), and current or past H. pylori infection was collected, as well as demographic variables, smoking habits, body mass index (BMI), dyslipidemia, diabetes, hypertension, presence of carotid lesions, and current treatment, and analyzed by multivariable regression models. Results. A total of 7152 clinical records from patients older than 30 years (63.4% women) were available for the study. Hypertension was present in 2039 (28.5%) patients and the risk was significantly increased in those with long-lasting H. pylori infection after adjusting for age decades, sex, BMI, cigarette smoking, diabetes, and dyslipidemia (OR 1.17, 95% CI 1.02–1.35). In addition, the long-lasting H. pylori infection was an independent risk for carotid plaques (OR 2.15, 95% CI 1.14–4.09). Conclusions. Our retrospective study demonstrated that long-lasting H. pylori infection is an independent risk factor for hypertension and the presence of carotid lesions after adjusting for potential confounders, although further validation our findings is needed from prospective studies. Full article

(This article belongs to the Topic Infectious Diseases)

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9 pages, 596 KiB

Open AccessArticle

Comparison of Efficacy of 2% Chlorhexidine Gluconate–Alcohol and 10% Povidone-Iodine–Alcohol against Catheter-Related Bloodstream Infections and Bacterial Colonization at Central Venous Catheter Insertion Sites: A Prospective, Single-Center, Open-Label, Crossover Study

by Ming-Ru Lin, Po-Jui Chang, Ping-Chih Hsu, Chun-Sui Lin, Cheng-Hsun Chiu and Chih-Jung Chen

J. Clin. Med. 2022, 11(8), 2242; https://doi.org/10.3390/jcm11082242 - 17 Apr 2022

Cited by 3 | Viewed by 4455

Abstract

An effective antiseptic agent is an essential component of a central venous catheter (CVC) care bundle, to protect against catheter-related bloodstream infections (CRBSIs). We conducted a trial to compare the incidences of CRBSI and the growth of insertion site flora in patients with [...] Read more.

An effective antiseptic agent is an essential component of a central venous catheter (CVC) care bundle, to protect against catheter-related bloodstream infections (CRBSIs). We conducted a trial to compare the incidences of CRBSI and the growth of insertion site flora in patients with CVC using 2% chlorhexidine gluconate–alcohol (CHG) or 10% povidone-iodine–alcohol (PVI) in the CVC care bundle. Patients who were admitted to two medical intensive care units (ICUs) and had CVC placement for >48 h were enrolled. Using a two-way crossover design with two six-month interventions, the ICUs were assigned to use either CHG or PVI in their care bundles. A total of 446 catheters in 390 subjects were enrolled in the study. The detection rate of flora was greater in the PVI group on both day 7 (26.6% versus 6.3%, p < 0.001) and day 14 (43.2% versus 15.8%, p < 0.001). The incidence rate of CRBSI was higher in the PVI group compared to the CHG group (2.15 vs. 0 events per 1000-catheter-days, p = 0.001), although the significance was lost in the multivariate analysis. In conclusion, 2% CHG was superior to 10% PVI in the CVC care bundle in terms of the inhibition of skin flora growth at CVC insertion sites and was potentially associated with lower incidence rates of CRBSI. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 3249 KiB

Open AccessArticle

Molecular Epidemiology and Evolution of Coxsackievirus A9

by Hehe Zhao, Jianxing Wang, Jianhua Chen, Ruifang Huang, Yong Zhang, Jinbo Xiao, Yang Song, Tianjiao Ji, Qian Yang, Shuangli Zhu, Dongyan Wang, Huanhuan Lu, Zhenzhi Han, Guoyan Zhang, Jichen Li and Dongmei Yan

Viruses 2022, 14(4), 822; https://doi.org/10.3390/v14040822 - 15 Apr 2022

Cited by 6 | Viewed by 2370

Abstract

Nineteen CVA9 isolates were obtained between 2010 and 2019 from six provinces of mainland China, using the HFMD surveillance network established in China. Nucleotide sequencing revealed that the full-length VP1 of 19 CVA9 isolates was 906 bases encoding 302 amino acids. The combination [...] Read more.

Nineteen CVA9 isolates were obtained between 2010 and 2019 from six provinces of mainland China, using the HFMD surveillance network established in China. Nucleotide sequencing revealed that the full-length VP1 of 19 CVA9 isolates was 906 bases encoding 302 amino acids. The combination of the thresholds of the phylogenetic tree and nucleotide divergence of different genotypes within the same serotype led to a value of 15–25%, and enabled CVA9 worldwide to be categorized into ten genotypes: A–J. The phylogenetic tree showed that the prototype strain was included in genotype A, and that the B, C, D, E, H, and J genotypes disappeared during virus evolution, whereas the F, I, and G genotypes showed co-circulation. Lineage G was the dominant genotype of CVA9 and included most of the strains from nine countries in Asia, North America, Oceania, and Europe. Most Chinese strains belonged to the G genotype, suggesting that the molecular epidemiology of China is consistent with that observed worldwide. The 165 partial VP1 strains (723 nt) showed a mean substitution rate of 3.27 × 10⁻³ substitution/site/year (95% HPD range 2.93–3.6 × 10⁻³), dating the tMRCA of CVA9 back to approximately 1922 (1911–1932). The spatiotemporal dynamics of CVA9 showed the spread of CVA9 obviously increased in recent years. Most CVA9 isolates originated in USA, but the epidemic areas of CVA9 are now concentrated in the Asia–Pacific region, European countries, and North America. Recombination analysis within the enterovirus B specie (59 serotypes) revealed eight recombination patterns in China at present, CVB4, CVB5, E30, CVB2, E11, HEV106, HEV85, and HEV75. E14, and E6 may act as recombinant donors in multiple regions. Comparison of temperature sensitivity revealed that temperature-insensitive strains have more amino acid substitutions in the RGD motif of the VP1 region, and the sites T283S, V284M, and R288K in the VP1 region may be related to the temperature tolerance of CVA9. Full article

(This article belongs to the Topic Infectious Diseases)

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Phylogenetic tree based on complete VP1 nucleotide sequences of coxsackievirus A9 (CVA9) strains. ● indicates the strains in this study. Full article ">Figure 2
(a) Time-scaled phylogenetic tree generated using the MCMC method for 165 partial VP1 CVA9 sequences from the worldwide. Bars at notes indicate 95% HPDs of tMRCAs. The tree was node-labeled with inferred dates of linage splits. (b) Bayesian skyline plot of the CVA9 strains. Full article ">Figure 3
Spatial diffusion pathways of state transition for CVA9. Epidemiology unidirectional pathways from one location to another are indicated on the maps. Shown are only the state transitions with supported BF ≥ 3. Orange arrows, decisive rates with BF ≥ 1000; red arrows, very strongly supported rates with 100 ≤ BF < 1000; green arrows, strongly supported rates with 10 ≤ BF < 100; purple arrows, supported rates with 3 ≤ BF < 10. Full article ">Figure 4
Neighbor-joining phylogenetic trees based on VP1, P1, P2, and P3 regions of the prototype sequence of all EV-B in the GenBank database and sequences of CVA9 strains in China. Numbers on codes indicate the bootstrap support of the node (1000 bootstrap replicate percentage). Scale bars represent the replacement of each site per year. Coding sequences of (a) VP1, (b) P1, (c) P2, and (d) P3 are shown. ● indicates CVA9 prototype strain (Griggs); ▲ indicates the Chinese CVA9 strains. Full article ">Figure 5
The genomic map of CVA9 representative strains recombination events predicted by RDP4. The grey band represents the full-length genome of the CVA9 strains; the numbers above indicate beginning and ending breakpoint positions. The different-colored bands represent the genomic regions where recombination events may have occurred; the numbers below indicate major and minor parents of the predicated recombination event. Full article ">Figure 6
A titer timeline chart of four CVA9 temperature sensitivity experiments. The green and red lines represent line charts of the virus titer changing over time at 36 °C and 39.5 °C, respectively. Xinjiang strain EV-B106 (HTPS-ODH11F/XJ/CHN/2011) and Xinjiang strain EV-B85 (HTYT-ARL-AFP02F/XJ/CHN/2011) were used as temperature-sensitive and temperature-insensitive controls, respectively. (a) temperature sensitivity of control strains; (b) temperature sensitivity of representative strains in genotype G; (c) temperature sensitivity of representative strains in genotype I. Full article ">Figure 7
CVA9 RGD binding site analysis showing the fully conserved nature of the RGD motif in the four representative strains. VP1 position 290 in the protype strain Griggs is equivalent to position 11 in the alignment. Full article ">

8 pages, 270 KiB

Open AccessArticle

Relationship among Streptococcus gallolyticus Subsp. gallolyticus, Enterococcus faecalis and Colorectal Neoplasms in Recurrent Endocarditis: A Historical Case Series

by Eva Romay, Juan Manuel Pericàs, María José García-País, Marta Hernández-Meneses, Blanca Ayuso, Javier García-González, Rodrigo Vicente Garcés-Durán, Ramón Rabuñal, Pilar Alonso-García, Fernando García-Garrote, Andrés Perissinotti, Bàrbara Vidal, Carles Falces, Eduard Quintana, Leticia Moreira, Manel Almela, Josep Llach, Asunción Moreno, Juan Corredoira, Jose María Miró and on behalf of Lucus Augusti and Hospital Clinic Endocarditis Teams Show full author list Hide full author list

J. Clin. Med. 2022, 11(8), 2181; https://doi.org/10.3390/jcm11082181 - 13 Apr 2022

Cited by 6 | Viewed by 2103

Abstract

Objectives: The role of colorectal neoplasms (CRN) as a common potential source of recurrent Streptococcus gallolyticus subsp. gallolyticus (SGG) and Enterococcus faecalis (EF) endocarditis remains unstudied. We aimed to investigate what proportion of episodes of recurrent endocarditis are caused by a succession of [...] Read more.

Objectives: The role of colorectal neoplasms (CRN) as a common potential source of recurrent Streptococcus gallolyticus subsp. gallolyticus (SGG) and Enterococcus faecalis (EF) endocarditis remains unstudied. We aimed to investigate what proportion of episodes of recurrent endocarditis are caused by a succession of SGG and EF, or vice versa, and to assess the role of a colonic source in such recurrent episodes. Methods: we conducted a retrospective analysis of two prospective endocarditis cohorts (1979–2019) from two Spanish hospitals, providing descriptive analyses of the major features of the endocarditis episodes, colonoscopy findings, and histologic results. Results: among 1552 IE episodes, 204 (13.1%) were caused by EF and 197 (12.7%) by SGG, respectively. There were 155 episodes (10%) of recurrent IE, 20 of which (12.9%) were due to a succession of SGG/EF IE in 10 patients (the first episode caused by SGG in eight cases, and by EF in two cases). The median follow-up was 86 (interquartile range 34–156) months. In 8/10 initial episodes, the causative microorganism was SGG, and all patients were diagnosed with CRN either during the initial episode or during follow-up. During the second episode of IE or follow-up, colonoscopies revealed CRN in six patients. Conclusions: There seems to be an association between SGG and EF in recurrent endocarditis that warrants further investigation. Our findings reinforce the need for systematically performing colonoscopy in the event of endocarditis caused by both microorganisms. Full article

(This article belongs to the Topic Infectious Diseases)

14 pages, 6578 KiB

Open AccessArticle

A Kinesin Vdkin2 Required for Vacuole Formation, Mycelium Growth, and Penetration Structure Formation of Verticillium dahliae

by Xing Yang, Cuimei Guo, Chi Chen, Zhijuan Hu, Xinyao Zheng, Shan Xu, Xingyong Yang and Chengjian Xie

J. Fungi 2022, 8(4), 391; https://doi.org/10.3390/jof8040391 - 12 Apr 2022

Cited by 5 | Viewed by 2265 | Correction

Abstract

The soil-borne vascular fungus Verticillium dahliae infects hundreds of dicotyledonous plants, causing severe wilt diseases. During the initial colonization, V. dahliae develops a penetration peg to enable infection of cotton roots. In some phytopathogenic fungi, vacuoles play a critical role in normal formation [...] Read more.

The soil-borne vascular fungus Verticillium dahliae infects hundreds of dicotyledonous plants, causing severe wilt diseases. During the initial colonization, V. dahliae develops a penetration peg to enable infection of cotton roots. In some phytopathogenic fungi, vacuoles play a critical role in normal formation of the infection structure. Kinesin 2 protein is associated with vacuole formation in Ustilago maydis. To identify the function of vacuoles in the V. dahliae infection structure, we identified VdKin2, an ortholog of kinesin 2, in V. dahliae and investigated its function through gene knockout. VdKin2 mutants showed severe defects in virulence and were suppressed during initial infection and root colonization based on observation of green fluorescent protein-labeled V. dahliae. We also found that deletion of VdKin2 compromised penetration peg formation and the derived septin neck. Disruption strains were viable and showed normal microsclerotia formation, whereas mycelium growth and conidial production were reduced, with shorter and more branched hyphae. Furthermore, the VdKin2 mutant, unlike wild-type V. dahliae, lacked a large basal vacuole, accompanied by a failure to generate concentrated lipid droplets. Taken together, VdKin2 regulates vacuole formation by V. dahliae, which is required for conidiation, mycelium growth, and penetration structure formation during initial plant root infection. Full article

(This article belongs to the Topic Infectious Diseases)

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Sequence analysis of VdKin2. (A) Phylogenetic tree of VdKin1 and VdKin2 in Verticillium dahliae v991 and their homologs from the annotated NCBI protein database in other fungi. The phylogenetic tree was constructed with the maximum likelihood method with MEGA X software. The protein evolutionary model was analyzed using the “find best protein model”, resulting in LG + G + I, and bootstrap values were based on 1000 replicates. (B) Genomic and cDNA of VdKin2 were compared using MultAlin. Gray and white represent exons and introns, respectively. Protein domains of VdKin2 were predicted using the NCBI Conserved Domain Database, which contain a motor domain and Smc superfamily domain (chromosome segregation ATPase). Multiple sequence alignments of the motor domains of Botrytis cinerea, Neurospora crassa, Ustilago maydis, Magnaporthe oryzae, Aspergillus niger and V. dahliae are included. Full article ">Figure 2
ΔVdKin2 strains exhibit severe defects in pathogenicity. (A) Four-week-old cotton seedlings were inoculated with wild-type (WT), ΔVdKin2-19, ΔVdKin2-43, ΔVdKin2comp, or sterile water (mock) at 107 spores/mL and cultured in a greenhouse. Symptoms of Verticillium wilt were photographed at 20 days after inoculation. (B) Discoloration of the inoculation shoot longitudinal sections. (C) Fungal outgrowth after one week of plating stem sections. The experiments were repeated 3 times. Full article ">Figure 3
Root colonization and penetration analyses of Verticillium dahliae. (A) Roots of 2-week-old cotton were inoculated with wild-type (WT)/eGFP and ΔVdKin2/eGFP strains at 105 spores/mL for 48 h to observe invasion and colonization. (B) Cellophane membranes were plated onto minimal medium and inoculated with conidia of WT, ΔVdKin2, and ΔVdKin2comp strains at 25 °C for 3 days, the cellophane was removed, and culture was continued for 2 days. The top panels show colonies of the strain grown on the cellophane membranes. The bottom panels show colonies grown from hyphae penetrating the membrane after removing the cellophane membrane. Full article ">Figure 4
VdKin2 is indispensable for penetration peg and septin ring formation in Verticillium dahliae. (A) Penetration pegs formed on the cellophane membrane by wild type (WT), ΔVdKin2, or ΔVdKin2comp strains. White arrows indicate penetration pegs. The ΔVdKin2 strain failed to form penetration pegs (white star). (B) Cellular localization of VdSep5-GFP in WT and ΔVdKin2 during development of the penetration peg. The red arrow indicates the septin ring. Full article ">Figure 5
VdKin2 affects septa development and vacuole morphology in Verticillium dahliae. (A) Hyphae of wild type (WT), ΔVdKin2, or ΔVdKin2comp strains were stained with Calcofluor White and the septa distance was observed. Scale bar = 10 μm. Measurement of septa using ImageJ software. The error bars represent standard deviations. Asterisks (****) indicate significance at p < 0.001. The experiments were performed three times independently. (B) Vacuoles were dyed with FM4-64 and photographs were acquired by fluorescence microscopy with DIC and RFP filters. Scale bar = 5 μm. Full article ">Figure 6
VdKin2 is required for high-salt stress resistance of Verticillium dahliae. (A) Colony morphology of wild type (WT), ΔVdKin2, and ΔVdKin2comp strains after 10 days of growth on potato dextrose agar (PDA) medium containing 1 M sorbitol or 0.75 M KCl. (B) Relative inhibition rate of growth of V. dahliae cultivated in PDA medium plus 1 M sorbitol. The data are shown as the mean ± standard error of the mean. ns, not significant. Full article ">Figure 7
Deletion of VdKin2 impairs lipid droplet development. Lipid droplets were stained using Nile red. Conidia and hyphae from the wild type (WT), ΔVdKin2, and ΔVdKin2comp strains. Full article ">Figure 8
Gene Ontology (GO) annotation (A) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis (B) for differentially expressed genes. GO enrichment (p < 0.05) and KEGG pathway enrichment (p < 0.05). (C) Heat maps of genes involved in “carbohydrate metabolic process” and “metabolism”. Log2 (FPKM) values are shown relative to the mean expression across all samples. Full article ">

15 pages, 3148 KiB

Open AccessArticle

Characterization and Public Health Insights of the New Delhi Metallo-β-Lactamase-Producing Enterobacterales from Laying Hens in China

by Hongcheng Wei, Linghan Kong, Yulong Wang, Zheren Huang, Xue Yang, Changyu Zhou, Chao Li, Boheng Ma, Cui Li, Changwei Lei and Hongning Wang

Microorganisms 2022, 10(4), 800; https://doi.org/10.3390/microorganisms10040800 - 11 Apr 2022

Cited by 3 | Viewed by 2122

Abstract

The New Delhi metallo-β-lactamase (NDM) is a major element for the rapid expansion of the carbapenem-resistant Enterobacterales, which poses a great challenge to public health security. NDM-producing Enterobacterales strains (50 Escherichia coli, 40 Klebsiella pneumoniae, and 5 Enterobacter cloacae) [...] Read more.

The New Delhi metallo-β-lactamase (NDM) is a major element for the rapid expansion of the carbapenem-resistant Enterobacterales, which poses a great challenge to public health security. NDM-producing Enterobacterales strains (50 Escherichia coli, 40 Klebsiella pneumoniae, and 5 Enterobacter cloacae) were isolated from laying hens in China for the surveillance of antibiotic-resistant pathogens, and all were found to be multi-drug resistant bacteria. The genomic analysis of these NDM-positive bacteria revealed the ST167, ST617, and ST410 of the fifteen ST-type E. coli clones and ST37 of the four ST-type K. pneumoniae clones to be the same types as the human-derived strains. Among them, some new clone types were also found. Most of the bla_NDM genes (bla_NDM-1 or bla_NDM-5) were on the IncX3 plasmids (n = 80) and were distributed in E. coli, K. pneumoniae, and E. cloacae, while the remaining bla_NDM-5 genes were harbored in the E. coli ST167 with IncFII plasmids (n = 15). The typeⅠ1 of the eight IncX3 plasmid subtypes was consistent with the human-derived pNDM5_020001 plasmid (accession no. CP032424). In addition, these two plasmids did not affect the growth of the host bacteria and could be reproduced stably without antibiotics. Our study revealed the high genetic propensity of the NDM-positive Enterobacterales from the laying hens and human commensal Enterobacterales, suggesting the potentially enormous risk of its transmission to humans. Full article

(This article belongs to the Topic Infectious Diseases)

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Antibiotic resistance genes (ARGs) and multilocus sequence typing (MLST) clustering of NDM-producing Enterobacterales. The species, STs, and antibiotic resistance genes (ARGs) were indicated by different colors. Full article ">Figure 2
Core genome evolution relationship of the blaNDM gene carrying E. coli strains (50 strains from this study, 39 strains from the database). The genomic sequence of E. coli K-12 (accession number CP025268) was selected as a reference genome. The SNPs, STs, NDM, host, and country were indicated by different colors and shapes. Full article ">Figure 3
Core genome evolution relationship of the blaNDM gene carrying K. pneumoniae strains (40 strains from this study, 97 strains from the database). The genomic sequence of K. Pneumoniae KCTC2242 (accession number CP002910) was selected as a reference genome. The SNPs, STs, NDM, host, and country were indicated by different colors and shapes. Full article ">Figure 4
Schematic map of the IncX3 plasmid and genetic environment of blaNDM genes. Regions of ≥99.0% nucleotide sequence identity were shaded in gray. (A) Genetic environment of pNDM-IncX3I1. (B) Comparative genomics of pSDCRK-IncFNDM5 and pNDM5_020001. Full article ">Figure 5
Comparison of the genomic genetic environment of blaNDM genes in IncX3. The arrows marked the direction of gene transcription, and the gene categories were differentiated by colors. The homologous regions were marked by grey shading. Full article ">Figure 6
Schematic map of blaNDM-IncFII plasmid. Regions with ≥99.0% nucleotide sequence identity were shaded in gray. (A) Genetic environment of pSDCRK-IncFNDM5. (B) Comparative genomics of pSDCRK-IncFNDM5 and pEC1188-NDM16. Full article ">Figure 7
Adaptability and stability of blaNDM-positive plasmid. (A) Growth curve of 9 kinds of transconjugant. (B) Competitive growth results obtained for blaNDM-IncX3 transconjugants and recipient bacteria EC600. (C) Competitive growth results obtained for carrying blaNDM-5-IncFⅡ transconjugants and recipient bacteria EC600. (D) Results obtained for continuous passage of blaNDM-IncX3 and blaNDM-IncFⅡ-carrying plasmid transconjugants. Full article ">

10 pages, 521 KiB

Open AccessArticle

Identification of Filamentous Fungi by MALDI-TOF Mass Spectrometry: Evaluation of Three Different Sample Preparation Methods and Validation of an In-House Species Cutoff

by Claudia Honsig, Brigitte Selitsch, Marlene Hollenstein, Matthias G. Vossen, Kathrin Spettel and Birgit Willinger

J. Fungi 2022, 8(4), 383; https://doi.org/10.3390/jof8040383 - 10 Apr 2022

Cited by 8 | Viewed by 2942

Abstract

Invasive infections caused by filamentous fungi constitute a leading cause of morbidity and mortality in immunocompromised patients. Rapid and reliable identification of filamentous fungi is essential for the early initiation of appropriate treatment. In the present study, 230 filamentous fungi isolates identified by [...] Read more.

Invasive infections caused by filamentous fungi constitute a leading cause of morbidity and mortality in immunocompromised patients. Rapid and reliable identification of filamentous fungi is essential for the early initiation of appropriate treatment. In the present study, 230 filamentous fungi isolates identified by conventional methods were investigated using MALDI-TOF MS (Bruker Daltonics, Bremen, Germany) in combination with the Filamentous Fungi Library 3.0 provided by the manufacturer. Three different sample preparation methods were applied as recommended by the manufacturer and identification rates were compared using the criteria provided by the manufacturer. Application of the more time-consuming sample preparation methods clearly improved identification at the species level. Thus, the identification rate increased from 48.9% using the simplest method to 76.1% with the most laborious procedure. Misidentifications did not occur. Furthermore, the reliability of an in-house threshold for species identification was investigated. The reduced threshold increased the rate of isolates correctly identified at the species level by up to 86.4%. As no misidentification was made at the genus level and only one misidentification of minor significance occurred at the species level, this threshold could be validated for routine use in our laboratory. In conclusion, regarding the high identification rates achieved, this commercial platform proved suitable for implementation in routine diagnosis. Full article

(This article belongs to the Topic Infectious Diseases)

8 pages, 1193 KiB

Open AccessArticle

The Presence of Exophiala dermatitidis in the Respiratory Tract of Cystic Fibrosis Patients Accelerates Lung Function Decline: A Retrospective Review of Lung Function

by Jonathan Ayling-Smith, Lorraine Speight, Rishi Dhillon, Matthijs Backx, Philip Lewis White, Kerenza Hood and Jamie Duckers

J. Fungi 2022, 8(4), 376; https://doi.org/10.3390/jof8040376 - 7 Apr 2022

Cited by 2 | Viewed by 1775

Abstract

Exophiala dermatitidis is increasingly isolated from cystic fibrosis (CF) respiratory samples. The decision to treat is hampered by limited evidence demonstrating the clinical significance of isolating E. dermatitidis. The objective was to assess the impact of E. dermatitidis isolation on the lung [...] Read more.

Exophiala dermatitidis is increasingly isolated from cystic fibrosis (CF) respiratory samples. The decision to treat is hampered by limited evidence demonstrating the clinical significance of isolating E. dermatitidis. The objective was to assess the impact of E. dermatitidis isolation on the lung function of CF patients. The rate of lung function decline in the local CF population was calculated using historic lung function data. A control population who had never had E. dermatitidis cultured from the respiratory tract was compared with the E. dermatitidis group, calculating their rate of lung function decline before and after the first isolation of the organism. A total of 1840 lung function measurements were reviewed between the 31 E. dermatitidis group patients and 62 control patients. Their demographics were similar. The control group declined at a rate of −0.824 FEV1%/year. The rate of decline in the E. dermatitidis group prior to infection was −0.337 FEV1%/year (p = 0.2). However, post infection with E. dermatitidis, there was a significant increase in the rate of decline in lung function (−1.824 FEV1%/year, p < 0.01). The results suggest E. dermatitidis has a temporal relationship with accelerated rate of lung function decline. It is not clear if this is a cause or effect, but this accelerated rate of decline indicates a need for further investigation. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 1902 KiB

Open AccessArticle

Restricted Activation of the NF-κB Pathway in Individuals with Latent Tuberculosis Infection after HIF-1α Blockade

by Aline de Oliveira Rezende, Rafaella Santos Sabóia, Adeliane Castro da Costa, Diana Messala Pinheiro da Silva Monteiro, Adrielle Zagmignan, Luis Ângelo Macedo Santiago, Rafael Cardoso Carvalho, Paulo Vitor Soeiro Pereira, Ana Paula Junqueira-Kipnis and Eduardo Martins de Sousa

Biomedicines 2022, 10(4), 817; https://doi.org/10.3390/biomedicines10040817 - 31 Mar 2022

Cited by 2 | Viewed by 2474

Abstract

Tuberculous granuloma formation is mediated by hypoxia-inducible factor 1 alpha (HIF-1α), and is essential for establishing latent tuberculosis infection (LTBI) and its progression to active tuberculosis (TB). Here, we investigated whether HIF-1α expression and adjacent mechanisms were associated with latent or active TB [...] Read more.

Tuberculous granuloma formation is mediated by hypoxia-inducible factor 1 alpha (HIF-1α), and is essential for establishing latent tuberculosis infection (LTBI) and its progression to active tuberculosis (TB). Here, we investigated whether HIF-1α expression and adjacent mechanisms were associated with latent or active TB infection. Patients with active TB, individuals with LTBI, and healthy controls were recruited, and the expression of cytokine genes IL15, IL18, TNFA, IL6, HIF1A, and A20 in peripheral blood mononuclear cells (PBMCs) and serum vitamin D (25(OH)D3) levels were evaluated. Additionally, nuclear factor kappa B (NF-κB) and tumor necrosis factor-alpha (TNF-α) levels were analyzed in PBMC lysates and culture supernatants, respectively, after HIF-1α blockade with 2-methoxyestradiol. We observed that IL-15 expression was higher in individuals with LTBI than in patients with active TB, while IL-18 and TNF-α expression was similar between LTBI and TB groups. Additionally, serum 25(OH)D3 levels and expression of IL-6, HIF1A, and A20 were higher in patients with active TB than in individuals with LTBI. Moreover, PBMCs from individuals with LTBI showed decreased NF-κB phosphorylation and increased TNF-α production after HIF-1α blockade. Together, these results suggest that under hypoxic conditions, TNF-α production and NF-κB pathway downregulation are associated with the LTBI phenotype. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 1511 KiB

Open AccessArticle

KI and WU Polyomaviruses: Seroprevalence Study and DNA Prevalence in SARS-CoV-2 RNA Positive and Negative Respiratory Samples

by Melinda Katona, Krisztina Jeles, Renátó Kovács and Eszter Csoma

Microorganisms 2022, 10(4), 752; https://doi.org/10.3390/microorganisms10040752 - 30 Mar 2022

Cited by 3 | Viewed by 1984

Abstract

The aim of this work was to study the possible co-infection of KI and WU polyomavirus (KIPyV and WUPyV, respectively) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory samples and to detect the seroprevalence of KIPyV and WUPyV. A total of [...] Read more.

The aim of this work was to study the possible co-infection of KI and WU polyomavirus (KIPyV and WUPyV, respectively) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in respiratory samples and to detect the seroprevalence of KIPyV and WUPyV. A total of 1030 nasopharyngeal samples were analyzed from SARS-CoV-2 RNA positive (n = 680) and negative (n = 350) adults and children (age: 1 day to 94.2 years) collected from August 2020 to October 2021. KIPyV DNA was detected in two SARS-CoV-2-positive samples (2/680, 0.29%) and in three SARS-CoV-2-negative samples (3/350, 0.86%). WUPyV DNA was observed in one-one samples from both groups (1/680, 0.15% vs. 1/350, 0.29%). We did not find an association between SARS-CoV-2 and KIPyV or WUPyV infection, and we found low DNA prevalence of polyomaviruses studied after a long-term lockdown in Hungary. To exclude a geographically different distribution of these polyomaviruses, we studied the seroprevalence of KIPyV and WUPyV by enzyme-linked immunosorbent assay among children and adults (n = 692 for KIPyV and n = 705 for WUPyV). Our data confirmed that primary infections by KIPyV and WUPyV occur mainly during childhood; the overall seropositivity of adults was 93.7% and 89.2% for KIPyV and WUPyV, respectively. Based on our data, we suggest that the spread of KIPyV and WUPyV might have been restricted in Hungary by the lockdown. Full article

(This article belongs to the Topic Infectious Diseases)

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9 pages, 1104 KiB

Open AccessArticle

Investigation of Clofazimine Resistance and Genetic Mutations in Drug-Resistant Mycobacterium tuberculosis Isolates

by Sanghee Park, Jihee Jung, Jiyeon Kim, Sang Bong Han and Sungweon Ryoo

J. Clin. Med. 2022, 11(7), 1927; https://doi.org/10.3390/jcm11071927 - 30 Mar 2022

Cited by 10 | Viewed by 2202

Abstract

Recently, as clofazimine (CFZ) showed a good therapeutic effect in treating multi-drug-resistant tuberculosis (MDR-TB), the anti-tuberculosis activity and resistance were re-focused. Here, we investigated the CFZ resistance and genetic mutations of drug-resistant Mycobacterium tuberculosis (DR-Mtb) isolates to improve the diagnosis and treatment of [...] Read more.

Recently, as clofazimine (CFZ) showed a good therapeutic effect in treating multi-drug-resistant tuberculosis (MDR-TB), the anti-tuberculosis activity and resistance were re-focused. Here, we investigated the CFZ resistance and genetic mutations of drug-resistant Mycobacterium tuberculosis (DR-Mtb) isolates to improve the diagnosis and treatment of drug-resistant TB patients. The minimal inhibitory concentration (MIC) of CFZ was examined by resazurin microtiter assay (REMA) with two reference strains and 122 clinical isolates from Korea. The cause of CFZ resistance was investigated in relation to the therapeutic history of patients. Mutations of Rv0678, Rv1979c and pepQ of CFZ resistant isolates were analyzed by PCR and DNA sequencing. The rate of CFZ resistance with MIC > 1 mg/L was 4.1% in drug-resistant Mtb isolates. The cause of CFZ resistance was not related to treatment with CFZ or bedaquiline. A CFZ susceptibility test should be conducted regardless of dugs use history. The four novel mutation sites were identified in the Rv0678 and pepQ genes related to CFZ resistance in this study. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 292 KiB

Open AccessArticle

Assessment of the Relationship between Clinical Manifestation and Pathogenic Potential of Streptococcus pyogenes Strains-Distribution of Genes and Genotypes of Toxins

by Tomasz Bogiel, Alicja Domian, Zuzanna Dobrzyńska, Agnieszka Mikucka and Eugenia Gospodarek-Komkowska

Biomedicines 2022, 10(4), 799; https://doi.org/10.3390/biomedicines10040799 - 29 Mar 2022

Cited by 3 | Viewed by 1892

Abstract

Streptococcus pyogenes is one of the most important species among beta-haemolytic streptococci, causing human infections of different localization. It is isolated from clinical specimens relatively frequently. In this study, the frequency and co-occurrence of toxin genes (speA, speB, speC, [...] Read more.

Streptococcus pyogenes is one of the most important species among beta-haemolytic streptococci, causing human infections of different localization. It is isolated from clinical specimens relatively frequently. In this study, the frequency and co-occurrence of toxin genes (speA, speB, speC, speH, speJ, speK) among 147 S. pyogenes strains were evaluated, using real-time PCR. In addition, the relationship between the occurrence of these genes and the origin of S. pyogenes strains from selected clinical material was assessed. The speB gene was present with the highest incidence (98.6%), while the speK gene was the least frequent (8.2%) among the tested strains. Based on the presence of the detected genes, the distribution of 17 genotypes was determined. The most common (21.8%), was speA (−) speB (+) speC (−) speH (−) speJ (−) speK (−) genotype. Furthermore, significant variation in the presence of some genes and genotypes of toxins in S. pyogenes strains isolated from different types of clinical material was found. There is a considerable variety and disproportion between the frequency of individual genes and genotypes of toxins in S. pyogenes strains. The relationship between the origin of S. pyogenes isolates and the presence of toxins genes indicates their pathogenic potential in the development of infections of selected localization. Full article

(This article belongs to the Topic Infectious Diseases)

11 pages, 1580 KiB

Open AccessSystematic Review

Consensus for the Treatment of Tinea Pedis: A Systematic Review of Randomised Controlled Trials

by Harry Ward, Nicholas Parkes, Carolyn Smith, Stefan Kluzek and Richard Pearson

J. Fungi 2022, 8(4), 351; https://doi.org/10.3390/jof8040351 - 29 Mar 2022

Cited by 8 | Viewed by 10393

Abstract

Objective: To systematically review literature enabling the comparison of the efficacy of pharmaceutical treatments for tinea pedis in adults. Design: Systematic review of randomised controlled trials (RCTs) with mycological cure as the primary outcome. Secondary outcomes did include the clinical assessment of resolving [...] Read more.

Objective: To systematically review literature enabling the comparison of the efficacy of pharmaceutical treatments for tinea pedis in adults. Design: Systematic review of randomised controlled trials (RCTs) with mycological cure as the primary outcome. Secondary outcomes did include the clinical assessment of resolving infection or symptoms, duration of treatment, adverse events, adherence, and recurrence. Eligibility Criteria: Study participants suffering from only tinea pedis that were treated with a pharmaceutical treatment. The study must have been conducted using an RCT study design and recording age of the participant > 16 years of age. Results: A total of seven studies met the inclusion criteria, involving 1042 participants. The likelihood of resolution in study participants treated with terbinafine was RR 3.9 (95% CI: 2.0–7.8) times those with a placebo. Similarly, the allylamine butenafine was effective by RR 5.3 (95% CI: 1.4–19.6) compared to a placebo. Butenafine was similarly efficacious to terbinafine RR 1.3 (95% CI: 0.4–4.4). Terbinafine was marginally more efficacious than itraconazole, RR 1.3 (95% CI: 1.1–1.5). Summary/Conclusion: Topical terbinafine and butenafine treatments of tinea pedis were more efficacious than placebo. Tableted terbinafine and itraconazole administered orally were efficacious in the drug treatment of tinea pedis fungal infection. We are concerned about how few studies were available that reported the baseline characteristics for each treatment arm and that did not suffer greater than 20% loss to follow-up. We would like to see improved reporting of clinical trials in academic literature. Registration name: Treatment’s for athlete’s foot—systematic review with meta-analysis [CRD42020162078]. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 23682 KiB

Open AccessArticle

Factors Influencing Immune Restoration in People Living with HIV/AIDS

by Bogusz Jan Aksak-Wąs, Anna Urbańska, Kaja Scheibe, Karol Serwin, Magdalena Leszczyszyn-Pynka, Milena Rafalska-Kosior, Joanna Gołąb, Daniel Chober and Miłosz Parczewski

J. Clin. Med. 2022, 11(7), 1887; https://doi.org/10.3390/jcm11071887 - 28 Mar 2022

Cited by 3 | Viewed by 2137

Abstract

Introduction: Immune restoration is a key clinical aspect that is pursued in the care of human immunodeficiency virus (HIV)-infected patients. Despite effective antiretroviral treatment and undetectable viremia, immune recovery is often incomplete. Materials and methods: Data from 311 Caucasian patients were collected. SNP [...] Read more.

Introduction: Immune restoration is a key clinical aspect that is pursued in the care of human immunodeficiency virus (HIV)-infected patients. Despite effective antiretroviral treatment and undetectable viremia, immune recovery is often incomplete. Materials and methods: Data from 311 Caucasian patients were collected. SNP in CCR2(rs1799864), CX3CR1(rs3732378), HLAC-35(rs9264942), and CCR5(promoter, rs1799988); a 32bp deletion(Δ32) in CCR5; and HLA-B*5701 genotypes were correlated with clinical data and selected endpoints. Kaplan–Meier and Cox proportional hazards models were used to analyze the effects of genetic factors over time. Results: For HLA-B*5701, the effect on the CD4+/CD8+ >0.8 cell ratio was lost within 48 months (HR = 2.04, 95% CI: 1.04–4.03), and the effect on the CD4+ cell count >500 cells/µL was lost within 12 months (HR = 2.12, CI: 1.11–4.04). The effect of CCR2 GG on the CD4+/CD8+ >0.8 cell ratio was lost within 36 months (HR = 1.7, CI: 1.05–2.75). For CCR5 wt/Δ32, the effect on the CD4+/CD8+ >1.0 cell ratio was lost within 24 months (HR = 2.0, CI: 1.08–3.69), and the effect on the CD4+ >800 cells/µL cell count was lost within 18 months (HR = 1.98, CI: 1.14–4.73). Conclusions: Selected genetic polymorphisms, namely CCR2 GG and CCR5 Δ32, and the presence of the HLA-B*5701 allele positively influenced immune restoration in cART-treated patients with HIV/AIDS. Full article

(This article belongs to the Topic Infectious Diseases)

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8 pages, 1478 KiB

Open AccessArticle

Pleural Peels Tissue Culture plus Pleural Fluid Culture Help to Improve Culture Rate for Empyema

by Ya-Fu Cheng, Ching-Yuan Cheng, Chang-Lun Huang, Wei-Heng Hung and Bing-Yen Wang

J. Clin. Med. 2022, 11(7), 1882; https://doi.org/10.3390/jcm11071882 - 28 Mar 2022

Cited by 4 | Viewed by 2013

Abstract

Background: Empyema is known as a serious infection, and outcomes of empyema cases remain poor. Pleural fluid culture and blood culture have been reported to give unsatisfactory results. We introduce a novel pleural peels tissue culture during surgery and aim to improve the [...] Read more.

Background: Empyema is known as a serious infection, and outcomes of empyema cases remain poor. Pleural fluid culture and blood culture have been reported to give unsatisfactory results. We introduce a novel pleural peels tissue culture during surgery and aim to improve the culture results of empyema. Methods: This was a retrospective study and was obtained from our institute. Patients with stage II or III empyema undergoing video-assisted thoracic surgery decortication from January 2019 to June 2021 were included in the study. Results: There were 239 patients that received a pleural peels tissue culture, a pleural fluid culture, and a blood culture concurrently during the perioperative period. Of these, 153 patients had at least one positive culture and 86 patients showed triple negative culture results. The positive culture rates were 46.9% for pleural peels tissue cultures, 46.0% for pleural fluid cultures, and 10% for blood cultures. The combination of pleural peels tissue culture and pleural fluid culture increased the positive rate to 62.7%. Streptococcus species and Staphylococcus species were the most common pathogens. Conclusion: The combination of pleural peels tissue culture and pleural fluid culture is an effective method to improve the positive culture rate in empyema. Full article

(This article belongs to the Topic Infectious Diseases)

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21 pages, 2812 KiB

Open AccessArticle

Mycobacterium tuberculosis Affects Protein and Lipid Content of Circulating Exosomes in Infected Patients Depending on Tuberculosis Disease State

by Fantahun Biadglegne, Johannes R. Schmidt, Kathrin M. Engel, Jörg Lehmann, Robert T. Lehmann, Anja Reinert, Brigitte König, Jürgen Schiller, Stefan Kalkhof and Ulrich Sack

Biomedicines 2022, 10(4), 783; https://doi.org/10.3390/biomedicines10040783 - 27 Mar 2022

Cited by 13 | Viewed by 3960

Abstract

Tuberculosis (TB), which is caused by the bacterium Mycobacterium tuberculosis (Mtb), is still one of the deadliest infectious diseases. Understanding how the host and pathogen interact in active TB will have a significant impact on global TB control efforts. Exosomes are [...] Read more.

Tuberculosis (TB), which is caused by the bacterium Mycobacterium tuberculosis (Mtb), is still one of the deadliest infectious diseases. Understanding how the host and pathogen interact in active TB will have a significant impact on global TB control efforts. Exosomes are increasingly recognized as a means of cell-to-cell contact and exchange of soluble mediators. In the case of TB, exosomes are released from the bacillus and infected cells. In the present study, a comprehensive lipidomics and proteomics analysis of size exclusion chromatography-isolated plasma-derived exosomes from patients with TB lymphadenitis (TBL) and treated as well as untreated pulmonary TB (PTB) was performed to elucidate the possibility to utilize exosomes in diagnostics and knowledge building. According to our findings, exosome-derived lipids and proteins originate from both the host and Mtb in the plasma of active TB patients. Exosomes from all patients are mostly composed of sphingomyelins (SM), phosphatidylcholines, phosphatidylinositols, free fatty acids, triacylglycerols (TAG), and cholesterylesters. Relative proportions of, e.g., SMs and TAGs, vary depending on the disease or treatment state and could be linked to Mtb pathogenesis and dormancy. We identified three proteins of Mtb origin: DNA-directed RNA polymerase subunit beta (RpoC), Diacyglycerol O-acyltransferase (Rv2285), and Formate hydrogenase (HycE), the latter of which was discovered to be differently expressed in TBL patients. Furthermore, we discovered that Mtb infection alters the host protein composition of circulating exosomes, significantly affecting a total of 37 proteins. All TB patients had low levels of apolipoproteins, as well as the antibacterial proteins cathelicidin, Scavenger Receptor Cysteine Rich Family Member (SSC5D), and Ficolin 3 (FCN3). When compared to healthy controls, the protein profiles of PTB and TBL were substantially linked, with 14 proteins being co-regulated. However, adhesion proteins (integrins, Intercellular adhesion molecule 2 (ICAM2), CD151, Proteoglycan 4 (PRG4)) were shown to be more prevalent in PTB patients, while immunoglobulins, Complement component 1r (C1R), and Glutamate receptor-interacting protein 1 (GRIP1) were found to be more abundant in TBL patients, respectively. This study could confirm findings from previous reports and uncover novel molecular profiles not previously in focus of TB research. However, we applied a minimally invasive sampling and analysis of circulating exosomes in TB patients. Based on the findings given here, future studies into host–pathogen interactions could pave the way for the development of new vaccines and therapies. Full article

(This article belongs to the Topic Infectious Diseases)

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Transmission electron microscopy images of exosome isolates from blood plasma of healthy individuals (A), pulmonary tuberculosis (B), tuberculous lymphadenitis (C), and after anti-TB drug treatment (D). One representative picture out of at least three independent experiments is shown for each group. Full article ">Figure 2
Flow cytometric MACSPlex exosome kit analysis of exosome surface protein markers. The x-axis represents selected proteins, whereas the y-axis shows the normalized APC-MFI. The median APC-signal intensity of each specific population of single beads was normalized to the average of the anti-CD9, anti-CD63, and anti-CD81 beads. MFI, median fluorescence intensity. Data sets are presented as mean ± SEM (n = 3). Complete data of all analyzed surface markers is provided in <a href="#app1-biomedicines-10-00783" class="html-app">Table S2</a>. Full article ">Figure 3
Composition of the sphingomyelin (SM) fraction of exosomes from TB patients. Organic extracts of exosome-derived lipids isolated from patients with pulmonary tuberculosis (PTB) and tuberculous lymphadenitis (TBL) as well as PTB-treated patients (Rx) were separated by high-performance thin layer chromatography. SM-containing spots were automatically eluted with methanol and directly analyzed by ESI-IT MS. The sum of SM species with up to 34, 36, 38, 40 and 42 C atoms (A) and the sum of SM species with one, two, three and four double bonds (db) (B) as well as the relative amounts of single SM species (C) were calculated from the sum of the signal intensities of all SM. Data sets in panels (A,B) are depicted as dot plots to show all single values, whereas data sets in panel (C) are depicted as bar graphs showing the mean and the positive standard deviation. Statistical significance was determined using the unpaired t test and the Holm–Sidak method to correct for multiple comparisons (alpha = 0.05). * p < 0.05. Full article ">Figure 4
Composition of the phosphatidylcholine (PC) fraction of exosomes from TB patients. Organic extracts of exosome-derived lipids isolated from patients with pulmonary tuberculosis (PTB) and tuberculous lymphadenitis (TBL) as well as PTB-treated patients (Rx) were separated by high-performance thin layer chromatography. PC-containing spots were automatically eluted with methanol and directly analyzed by ESI-IT MS. (A) The sum of PC species with 32, 34, 36, 38 and 40 C atoms (A) and the sum of PC species with a certain amount of double bonds (db) in their fatty acyl residues (B) as well as the relative amounts of single PC species (C) were calculated from the sum of the signal intensities of all PC. Data sets in (A,B) are depicted as dot plots to show all single values, data sets in (C) are depicted as bar graphs showing the mean and the positive standard deviation. Statistical significance was determined using the unpaired t test and the Holm–Sidak method to correct for multiple comparisons (alpha = 0.05). * p < 0.05. Full article ">Figure 5
Composition of the triacylglycerol (TAG) fraction of exosomes from TB patients. Organic extracts of exosome-derived lipids isolated from patients with pulmonary tuberculosis (PTB) and tuberculous lymphadenitis (TBL) as well as PTB-treated patients (Rx) were separated by high-performance thin layer chromatography. TAG-containing spots were automatically eluted with methanol and directly analyzed by ESI-IT MS. The sum of TAG species with 48, 50, 52, and 54 C atoms (A), the sum of TAG species with a certain amount of double bonds (db) in their fatty acyl residues, (B) as well as the relative amounts of single TAG species (C), were calculated from the sum of the signal intensities of all TAG. Data sets in (A,B) are depicted as dot plots to show all single values, data sets in (C) are depicted as bar graphs showing the mean and the positive standard deviation. Statistical significance was determined using the unpaired t test and the Holm–Sidak method to correct for multiple comparisons (alpha = 0.05). * p < 0.05. Full article ">Figure 6
Identification of exosomal proteins by mass spectrometry-based proteomics. (A) Proteins were isolated from circulating exosomes, proteolytically cleaved, and analyzed via mass spectrometry-based proteomics. Proteins were identified by MaxQuant (version 1.6.3.3). Protein abundances were estimated by the included MaxLFQ algorithm. Based on label-free quantification (LFQ), isolated proteins span about five orders of magnitude of abundance and include common populations of frequently observed vesicular proteins (blue) and proteins of M. tuberculosis origin (red). Identified proteins were used for gene ontology (GO) overrepresentation analysis, including the categories “cellular components” (B), “biological processes” (C), and “molecular functions” (D). Representative terms are illustrated by the number of included proteins (bars) and the significance of overrepresentation (as-log10 p value, red diamonds). Full article ">Figure 7
Disease and treatment state-specific protein composition. Comparative analyses of protein abundances at different disease and treatment stages were performed by tandem mass tag (TMT)-based quantification. Hierarchical clustering of ANOVA-revealed differentially abundant proteins (adjusted p < 0.01) resulted in a nearly perfect separation of the disease groups (columns) and grouping of proteins into three main branches (rows, branch 1 = green, branch 2 = brown, branch 3 = blue). Protein abundance values in heatmaps were scaled row-wise for visualization (A). Functional network analysis with STRING revealed significant protein–protein interaction (PPI) enrichments for proteins of main branch 1 (B) and main branch 2 (C). Stepwise pairwise analyses revealed 14 common, as well as eight and seven disease state-depending DAP as depicted in a Venn–Euler diagram (D). The Volcano plot represents treatment-affected DAP with log2-transformed ratios of protein abundances (Rx vs. PTB) and log10-transformed Benjamini–Hochberg-adjusted p values (E). HC—healthy controls, PTB—pulmonary tuberculosis, TBL—tuberculous lymphadenitis, and Rx—PTB after anti-TB drug treatment. Full article ">

14 pages, 3144 KiB

Open AccessArticle

Phage Therapy Potentiates Second-Line Antibiotic Treatment against Pneumonic Plague

by Yaron Vagima, David Gur, Moshe Aftalion, Sarit Moses, Yinon Levy, Arik Makovitzki, Tzvi Holtzman, Ziv Oren, Yaniv Segula, Ella Fatelevich, Avital Tidhar, Ayelet Zauberman, Shahar Rotem, Emanuelle Mamroud and Ida Steinberger-Levy

Viruses 2022, 14(4), 688; https://doi.org/10.3390/v14040688 - 26 Mar 2022

Cited by 7 | Viewed by 2954

Abstract

Plague pandemics and outbreaks have killed millions of people during the history of humankind. The disease, caused by the bacteria Yersinia pestis, is currently treated effectively with antibiotics. However, in the case of multidrug-resistant (MDR) bacteria, alternative treatments are required. Bacteriophage (phage) [...] Read more.

Plague pandemics and outbreaks have killed millions of people during the history of humankind. The disease, caused by the bacteria Yersinia pestis, is currently treated effectively with antibiotics. However, in the case of multidrug-resistant (MDR) bacteria, alternative treatments are required. Bacteriophage (phage) therapy has shown efficient antibacterial activity in various experimental animal models and in human patients infected with different MDR pathogens. Here, we evaluated the efficiency of фA1122 and PST phage therapy, alone or in combination with second-line antibiotics, using a well-established mouse model of pneumonic plague. Phage treatment significantly delayed mortality and limited bacterial proliferation in the lungs. However, the treatment did not prevent bacteremia, suggesting that phage efficiency may decrease in the circulation. Indeed, in vitro phage proliferation assays indicated that blood exerts inhibitory effects on lytic activity, which may be the major cause of treatment inefficiency. Combining phage therapy and second-line ceftriaxone treatment, which are individually insufficient, provided protection that led to the survival of all infected animals—a synergistic protective effect that represents a proof of concept for efficient combinatorial therapy in an emergency event of a plague outbreak involving MDR Y. pestis strains. Full article

(This article belongs to the Topic Infectious Diseases)

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Pharmacokinetic analysis of фA1122 in naive mice. A single dose of фA1122 phage suspension (1 × 109 PFU) was administered to naive C57BL/6J mice, either by (A) IP injection (0.5 mL) or (B) via the IN route (35 µL). For each administration route, n = 3 for each time point. Phage titration was performed using a spot assay test. Each dot represents the mean value in terms of PFU/organ (lung—blue dots, spleen—green dots, liver—black dots) or PFU/mL blood (red dots). Bars represent the standard deviations (SDs). Full article ">Figure 2
Intranasal administration of a single phage dose delayed disease progression. C57BL/6J mice were intranasally infected with 10 × LD50 Y. pestis Kim53 strain (A) or Kim53-lux luminescent strain (B–F). For phage treatment, one dose of 1 × 109 фA1122 PFU/mouse was IN administered at 5 hpi. Control mice were subjected to intranasal administration of PBS. (A) Survival curves of control mice (black line, n = 6) and phage-treated mice (blue line, n = 12). (B,C) Control (n = 3) and phage-treated mice (n = 4) were anesthetized at the indicated time points post Y. pestis infection. Lungs were harvested, and imaging was performed using IVIS as detailed in the <a href="#sec2-viruses-14-00688" class="html-sec">Section 2</a>. (D,E) The bacterial load in the lungs and blood was quantified by plating serial dilutions of tissue homogenate/blood on BHIA plates supplemented with 200 μg/mL ampicillin and counting the colonies. Black squares represent nontreated control mice and blue squares represent phage-treated mice. (F) Phage titration was performed by the spot assay technique described in the <a href="#sec2-viruses-14-00688" class="html-sec">Section 2</a>. Each point represents the phage load in the lungs (blue squares, total PFU/lung) or blood (black squares, PFU/mL) of an individual mouse. Horizontal bars represent median values. Dotted lines mark the limit of detection. Statistically significant differences between groups are denoted by asterisks (* p < 0.05; *** p < 0.0001; log-rank (Mantel–Cox) test). Bars indicate standard errors of the means. Full article ">Figure 3
Multiple-dose фA1122 phage treatments did not improve treatment efficacy. Schematic representation of mouse treatment regimens (A) and survival curves (B). C57BL/6J mice were IN infected with 10 × LD50 of Y. pestis Kim53. For IN phage treatment, mice were inoculated with 35 µL of 1 × 109 фA1122 PFU; IP injection included the administration of 0.5 mL of 1 × 109 фA1122 PFU. The treatment regimens were as follows: one dose of IN фA1122 at 5 hpi (n = 22; light blue line), two doses of IN фA1122 at 5 hpi and 24 hpi (n = 12, olive green line), one dose of IN фA1122 at 5 hpi + IP injections at 24 and 48 hpi (n = 17, green line) and one dose of IN фA1122 at 5 hpi + IP injections for 6 days, every 24 h (n = 10, purple line). Control mice: n = 17, black line. (B): Statistically significant differences between the control group and phage-treated groups are denoted by asterisks (*** p < 0.0001; log-rank (Mantel–Cox) test). Full article ">Figure 4
PST is more potent than фA1122 in the presence of blood. Phage-based lysis assays were performed with the bioluminescent Y. pestis strain EV76-lux (107 CFU/mL) suspended in BHI broth (blue and orange lines) or in mouse whole blood (gray and red lines). The Y. pestis strain was infected with фA1122 (A) or PST (B) phages (106 PFU/mL; multiplicity of infection (MOI) = 0.01). Bioluminescence (RLU) was measured at 37 °C in 15 min intervals for 24 h using a SPARK 10M plate reader. The experiment was performed in biological duplicates (using blood pooled from three mice for each experiment), and the results are representative of one experiment. Presented values are the average results from three wells in a single triplicate experiment, and the error bars represent the standard deviations (SD). The green line represents the background from BHI broth. G.C. = growth control. Full article ">Figure 5
Pharmacokinetic analysis of PST in naive mice. A single dose of PST phage suspension (1 × 109 PFU) was administered to naive C57BL/6J mice, either by (A) IP injection (0.5 mL) or (B) via the IN route (35 µL). For each administration route, n = 3 for each time point. Phage titration was performed using a spot assay test. Each dot represents the mean value in terms of PFU/organ (lung—blue dots, spleen—green dots, liver—black dots) or PFU/mL blood (red dots). Bars represent the standard deviations (SDs). Full article ">Figure 6
Treatment of pneumonic plague with фA1122 or PST results in similar outcomes. (A) Schematic presentation of the phage treatment regimen. C57BL/6J mice were IN infected with 10 × LD50 Y. pestis Kim53 (gray symbols), followed by PBS (control group) or phage administration. Each dose of PST (red phage symbol) or фA1122 (blue phage symbol) suspension contained 1 × 109 phages. (B) Survival curves. The mouse groups were as follows: no phage (n = 5, black line), IN phage administration at 5 hpi followed by IP injections every 24 h on days 1–7 post bacterial infection (n = 10; green line for фA1122 and red line for PST). Full article ">Figure 7
Effective rescue of infected mice by the phage–antibiotic combination treatment. Schematic presentation of the treatment regimens (A) and survival curves (B) Female C57BL/6J mice were IN infected with 100 × LD50 Y. pestis Kim53. Mouse groups included control nontreated (n = 4), phage-treated (n = 10), ceftriaxone-treated (n = 10) and phage–ceftriaxone combination-treated mice (n = 9). Phage treatment was performed using a phage cocktail composed of фA1122 and PST (1 × 109 each phage/dose; 35 µL for intranasal administration or 0.5 mL for IP injection). Treatment included IN administration at 5 hpi followed by IP injections at days 1–10, with 24 h intervals. Ceftriaxone was subcutaneously injected every 12 h on days 2–6 post bacterial infection. Mice were monitored for 22 days. Statistically significant differences are denoted by asterisks (*** p < 0.001; log rank (Mantel–Cox) test). Full article ">

15 pages, 719 KiB

Open AccessArticle

Peronosporales Species Associated with Strawberry Crown Rot in the Czech Republic

by Matěj Pánek, Marie Maňasová, Jana Wenzlová, Miloslav Zouhar and Jana Mazáková

J. Fungi 2022, 8(4), 346; https://doi.org/10.3390/jof8040346 - 26 Mar 2022

Cited by 2 | Viewed by 2241

Abstract

The symptoms of crown rot on strawberry plants are considered typical for the pathogen Phytophthora cactorum, which causes high losses of this crop. However, an unknown number of related species of pathogens of Peronosporales cause symptoms quite similar to those caused by [...] Read more.

The symptoms of crown rot on strawberry plants are considered typical for the pathogen Phytophthora cactorum, which causes high losses of this crop. However, an unknown number of related species of pathogens of Peronosporales cause symptoms quite similar to those caused by P. cactorum. To determine their spectrum and importance, strawberry plants were sampled from 41 farms in the Czech Republic. The cultures were isolated from the symptomatic plants using the baiting method, with subsequent cultivation on a semiselective medium. Isolates were identified to the species level using nuclear ribosomal internal transcribed spacer (ITS) barcoding after preliminary morphological determination. In total, 175 isolates of 24 species of Phytophthora, Phytopythium, Pythium, and Globisporangium were detected. The most represented was Phytophthora cactorum, with 113 (65%) isolates, which was recorded in 61% of farms, and the Pythium dissotocum complex with 20 (11%) isolates, which was recorded in 27% of farms. Other species were represented in units of percent. Large differences between farms in the species spectra were ascertained. The differences between species in cardinal growth temperatures and different management of the farms are discussed as a main reason for such a diversification. Regarding the dissimilar sensitivity of various species of Peronosporales against fungicides, the proper determination of the cause of disease is of crucial significance in plant protection. Full article

(This article belongs to the Topic Infectious Diseases)

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13 pages, 283 KiB

Open AccessArticle

Subclinical Left Ventricular Systolic Dysfunction in HIV Patients: Prevalence and Associations with Carotid Atherosclerosis and Increased Adiposity

by Eleni Athanasiadi, Maria Bonou, Dimitrios Basoulis, Chris J. Kapelios, Constantina Masoura, Marina Skouloudi, Sophie Mavrogeni, Constantina Aggeli, Mina Psichogiou and John Barbetseas

J. Clin. Med. 2022, 11(7), 1804; https://doi.org/10.3390/jcm11071804 - 24 Mar 2022

Cited by 3 | Viewed by 2009

Abstract

Background: Human immunodeficiency virus (HIV) is mainly detected in young, otherwise healthy, individuals. Cardiomyopathy and peripheral artery disease affecting these patients appears to be multifactorial. Prompt and potentially more effective implementation of therapeutic measures could be enabled by pre-symptomatic diagnosis of myocardial dysfunction [...] Read more.

Background: Human immunodeficiency virus (HIV) is mainly detected in young, otherwise healthy, individuals. Cardiomyopathy and peripheral artery disease affecting these patients appears to be multifactorial. Prompt and potentially more effective implementation of therapeutic measures could be enabled by pre-symptomatic diagnosis of myocardial dysfunction and peripheral artery damage. However, limited data is available to date on this specific topic. Μethods: We investigated the association between global longitudinal strain (GLS), an established index of subclinical left ventricular systolic dysfunction (LVSD) assessed by two-dimensional speckle-tracking echocardiography, and: (a) patient history; (b) demographic and clinical baseline characteristics; (c) carotid intima-media thickness (IMT) and the presence of carotid atherosclerotic plaque(s), measured by ultrasonography; (d) temperature difference (ΔT) along each carotid artery, measured by microwave radiometry; and (e) basic blood panel measurements, including high-sensitivity troponin-T (hsTnT) and NT-proBNP in people living with HIV (PLWH) and no history of cardiovascular disease. Results: We prospectively enrolled 103 consecutive PLWH (95% male, age 47 ± 11 years, anti-retroviral therapy 100%) and 52 age- and sex-matched controls. PLWH had a significantly higher relative wall thickness (0.38 ± 0.08 vs. 0.36 ± 0.04, p = 0.048), and higher rate of LVSD (34% vs. 15.4%, p = 0.015), and carotid artery atherosclerosis (28% vs. 6%, p = 0.001) compared with controls. Among PLWH, LVSD was independently associated with the presence of carotid atherosclerosis (adj. OR:3.09; 95%CI:1.10–8.67, p = 0.032) and BMI (1.15; 1.03–1.29, p = 0.017), while a trend for association between LVSD and left ventricular hypertrophy was also noted (3.12; 0.73–13.33, p = 0.124). No differences were seen in microwave radiometry parameters, NT-proBNP, hs-TnT and c-reactive protein between PLWH with and without LVSD. Conclusions: Subclinical LVSD and carotid atherosclerosis were significantly more frequent in PLWH compared to a group of healthy individuals, implying a possible link between HIV infection and these two pathological processes. Carotid atherosclerosis and increased adiposity were independently associated with impaired GLS in HIV-infected individuals. Full article

(This article belongs to the Topic Infectious Diseases)

21 pages, 8662 KiB

Open AccessArticle

Mycobacterium bovis PknG R242P Mutation Results in Structural Changes with Enhanced Virulence in the Mouse Model of Infection

by Fábio Muniz de Oliveira, Victor Oliveira Procopio, Gabriela de Lima Menezes, Roosevelt Alves da Silva, André Kipnis and Ana Paula Junqueira-Kipnis

Microorganisms 2022, 10(4), 673; https://doi.org/10.3390/microorganisms10040673 - 22 Mar 2022

Cited by 3 | Viewed by 2075

Abstract

Mycobacterium bovis is the causative agent of tuberculosis in domestic and wild animal species and sometimes in humans, presenting variable degrees of pathogenicity. It is known that PknG is involved in the first steps of Mycobacterium tuberculosis macrophage infection and immune evasion. We [...] Read more.

Mycobacterium bovis is the causative agent of tuberculosis in domestic and wild animal species and sometimes in humans, presenting variable degrees of pathogenicity. It is known that PknG is involved in the first steps of Mycobacterium tuberculosis macrophage infection and immune evasion. We questioned whether M. bovispknG genes were conserved among mycobacteria and if natural genetic modifications would affect its virulence. We discovered a single mutation at a catalytic domain (R242P) of one M. bovis isolate and established the relation between the presence of R242P mutation and enhanced M. bovis virulence. Here, we demonstrated that R242P mutation alters the PknG protein conformation to a more open ATP binding site cleft. It was observed that M. bovis with PknG mutation resulted in increased growth under stress conditions. In addition, infected macrophages by M. bovis (R242P) presented a higher bacterial load compared with M. bovis without the pknG mutation. Furthermore, using the mouse model of infection, animals infected with M. bovis (R242P) had a massive innate immune response migration to the lung that culminated with pneumonia, necrosis, and higher mortality. The PknG protein single point mutation in its catalytic domain did not reduce the bacterial fitness but rather increased its virulence. Full article

(This article belongs to the Topic Infectious Diseases)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Presence of non-synonymous SNPs in PknG protein of genes within M. bovis isolates. The protein sequence of PknG proteins from M. bovis genomes deposited in Gene Bank as well as that from M. tuberculosis H37Rv and a representative Beijing strain were aligned with ClustalX. * The mutation R242P is shown with an asterisk. Full article ">Figure 2
Molecular dynamics simulations analysis of PknG proteins. Molecular dynamics of the PknG protein from Mbb and Mbt isolates was performed in duplicates to evaluate protein structure and behavior in water. The main results suggest that PknG from Mbt has more opening conformation of substrate binding cleft than PknG from Mbb, which leads to higher kinase activity. (A) Average RMSD evolution of the PknG protein of Mbb (turquoise line) and Mbt (violet line) strains calculated from two independent 200 ns MD simulations for each strain. The individual RMSD values for each simulation can be seen in <a href="#app1-microorganisms-10-00673" class="html-app">Figure S2B</a>. (B) RMSF difference (Mbt − Mbb) of RMSF average calculated from two independent 200 ns MD simulations. Values above the red line (zero value) represent increased fluctuations in Mbt compared with Mbb isolates. Values below the red line represent decreased fluctuation in Mbt compared with Mbb isolates. Protein domains are delimited by a dashed rectangle according to the following colors: blue (NORS), red (RD), yellow (KD), and green (TPRD). (C) Structure of PknG showing open and closed cavity conformations. Protein domains are colored as previously described. (D) The distance of Cys109-Asn346 was calculated for each independent simulation (<a href="#app1-microorganisms-10-00673" class="html-app">Figure S3B,C</a>). The average for each isolate was obtained and the difference (Mbt − Mbb) resulted in the graph. Values above the red line represent a more open conformation of the PknG substrate binding site in the Mbt strain than in the Mbb strain. Values below the red line represent a less open conformation of the PknG substrate binding site in the Mbt strain than in the Mbb strain. Full article ">Figure 3
Mycobacterial growth under stressful conditions and pknG expression during macrophage infection. Bacteria were grown in 7H9 medium for 6 days under different conditions. (A) Cultures grown with 5 mM H2O2 (oxidative stress); (B) cultures grown under acid condition (pH 4.5); and (C) cultures grown in the presence of isoniazid (5 μg/mL). The results shown are the mean ± standard deviation of the different time points (*; significant difference, p < 0.05 between Mbt and Mbb). BMDM were infected at a MOI of 1:1 with Mtb, Mbb, or Mbt and three hours later extracellular mycobacteria were removed by replacing the supernatant media. (D) After 48 h of infection, macrophages were lysed, and intracellular mycobacteria were recovered. Expression of pknG gene was analyzed by quantitative RT-PCR with SybrGreen. The relative gene expression of pknG was determined by the delta delta Ct (2−ΔΔCt) method using the expression of the SigA gene as a normalizer. (E) After 48 h of infection, the supernatant (extracellular) and the attached macrophages were investigated for bacterial concentration by plating on agar 7H11 supplemented with OADC and pyruvate. Bacteria that extravasated from macrophages during infection were detected in the supernatant, while bacteria recovered from the lysed macrophages were considered as intracellular bacteria. Infected BMDM were supplemented with DFO (500 µM) or not to remove free iron when media was replenished 3 h after infection, and after 48 h of infection extravasated and intracellular mycobacteria were determined. Full article ">Figure 4
Evaluation of the mycobacterial load and survival of infected mice. C57BL/6 mice infected with 106 CFU of M. bovis Mbb, Mbt, or Mtb strains were euthanized at 5, 15, and 21 days p.i. and the number of CFU in lungs (A), spleen (B), and liver (C) were determined after plating on 7H11 agar supplemented with pyruvate and OADC. In (A), the CFU recovered from the lungs at one day post infection is also shown. The lines indicate the kinetics of the mean ± standard deviation of the number of CFU from each strain obtained with three animals per group, showing the statistically significant difference with an asterisk (*). This experiment is representative of 3 independent experiments. (D) Mice survival curve for each infected group accompanied for 30 days. Full article ">Figure 5
Kinetics of alveolar macrophages, monocytes, dendritic cells, neutrophils, and NK cells in the lungs of infected C57BL/6 mice. Lungs of mice not infected (non-infected) or infected with Mtb, Mbb, or Mbt euthanized at 5, 15, and 21 days p.i. were analyzed by flow cytometry. The results show the mean ± standard deviation (n = 6 per group) and significant differences (p < 0.05) between groups are shown as: * differences when compared with non-infected group; # differences between Mbt and Mbb groups. The kinetics of (A) total number of monocytes (small macrophages, F4/80lowCD11blowCD11clow), (B) neutrophils (F4/80+CD11bhighCD11c−Gr1+), (C) NK cells (CD3−NK1.1+), (D) alveolar macrophages (F4/80+CD11b+CD11c−), (E) dendritic cells (F4/80+CD11b+CD11c+), and (F) NKT (CD3+NK1.1+) are shown. Full article ">Figure 6
Subpopulations of T lymphocytes in the lungs of infected C57BL/6 mice. Lung cells from mice infected with Mtb, Mbb, or Mbt strains were euthanized at 21 days p.i. and analyzed by flow cytometry. The results show data from each mouse and the mean ± standard deviation per group (n = 6). (A) Total numbers of CD4+ T cells. (B) Total numbers of CD4+IFN-γ+ T cells. (C) Total numbers of CD4+IL17+ T cells. (D) Total numbers of CD8+ T cells. (E) Total numbers of CD8+IFN-γ+ T cells. (F) Total numbers of CD8+IL17+ T cells. Note that (A,D) are graphed as 104 cells. Significant differences (p < 0.05) to the non-infected group (*) or between Mbt and Mbb groups (#) are shown. Full article ">Figure 7
Lung histopathological analysis from C57BL/6 mice infected with Mtb and M. bovis isolates. C57BL/6 mice infected intravenously with 106 CFU of the Mtb, Mbb, or Mbt strains were euthanized at 5, 15, and 21 days p.i. and their lungs were processed and stained with H&E for analysis. As the control, a healthy lung from a non-infected mouse injected with PBS (NI) was analyzed. (A) Lung sections from representative mice are shown (100× magnification). (B) Four to six random fields from each lung were evaluated to determine the percentage of the affected area of each mouse. The bars on the graph show the mean ± standard deviation of each group (n = 6); asterisk (*) denotes significant differences (p < 0.05) between groups. Representative lung sections at low magnification from each group 21 days post infection are shown. (C) Characteristic cells present in the lung lesions of mice at 21 days p.i. observed at 400× magnification, evidencing mononuclear (red arrow) and polymorphonuclear cells (black arrow). Full article ">

13 pages, 1583 KiB

Open AccessArticle

The Effect of Natural-Based Formulation (NBF) on the Response of RAW264.7 Macrophages to LPS as an In Vitro Model of Inflammation

by Sheelu Monga, Basem Fares, Rami Yashaev, Dov Melamed, Meygal Kahana, Fuad Fares, Abraham Weizman and Moshe Gavish

J. Fungi 2022, 8(3), 321; https://doi.org/10.3390/jof8030321 - 21 Mar 2022

Cited by 5 | Viewed by 4295

Abstract

Macrophages are some of the most important immune cells in the organism and are responsible for creating an inflammatory immune response in order to inhibit the passage of microscopic foreign bodies into the blood stream. Sometimes, their activation can be responsible for chronic [...] Read more.

Macrophages are some of the most important immune cells in the organism and are responsible for creating an inflammatory immune response in order to inhibit the passage of microscopic foreign bodies into the blood stream. Sometimes, their activation can be responsible for chronic inflammatory diseases such as asthma, tuberculosis, hepatitis, sinusitis, inflammatory bowel disease, and viral infections. Prolonged inflammation can damage the organs or may lead to death in serious conditions. In the present study, RAW264.7 macrophages were exposed to lipopolysaccharide (LPS; 20 ng/mL) and simultaneously treated with 20 µg/mL of natural-based formulation (NBF), mushroom–cannabidiol extract). Pro-inflammatory cytokines, chemokines, and other inflammatory markers were analyzed. The elevations in the presence of interleukin-6 (IL-6), cycloxygenase-2 (COX-2), C-C motif ligand-5 (CCL5), and nitrite response, following exposure to LPS, were completely inhibited by NBF administration. IL-1β and tumor necrosis factor alpha (TNF-α) release were inhibited by 3.9-fold and 1.5-fold, respectively. No toxic effect of NBF, as assessed by lactate dehydrogenase (LDH) release, was observed. Treatment of the cells with NBF significantly increased the mRNA levels of TLR2, and TLR4, but not NF-κB. Thus, it appears that the NBF possesses anti-inflammatory and immunomodulatory effects which can attenuate the release of pro-inflammatory markers. NBF may be a candidate for the treatment of acute and chronic inflammatory diseases and deserves further investigation. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Cytotoxicity analysis as assessed by LDH release from RAW264.7 macrophages. LDH levels were measured by O.D. (arbitrary units) and are presented as the mean ± SD. At least 8 replicates were in each group (n = 8 for naïve, n = 16 for vehicle, and n = 14 for NBF). ANOVA with Bonferroni’s post hoc test was performed. p-value = 0.92. Full article ">Figure 2
NBF downregulates the release of pro-inflammatory cytokines induced by LPS in RAW264.7 macrophages. RAW 264.7 macrophages were exposed to 20 ng/mL LPS and simultaneously with the NBF, 20 µg/mL. IL-1β (A), IL-6 (B), and TNF-α (C) levels were measured using ELISA. The results are presented as the mean ± SD, (n = 4 in each group). ANOVA followed by Bonferroni’s post hoc test was performed. *** p < 0.001 compared to all other groups. Full article ">Figure 3
NBF downregulates the release of CCL5 (RANTES) in RAW264.7 macrophages following LPS stimulation. RAW 264.7 macrophages were exposed to 20 ng/mL LPS and simultaneously with the NBF, 20 µg/mL. CCL5 levels were measured (pg/mL) using standard calibration curves and are presented as the mean ± SD. Four replicates in each group (n = 4). ANOVA followed by Bonferroni’s post hoc test was performed. *** p < 0.001 compared to all other groups. Full article ">Figure 4
NBF affects COX-2 protein level in RAW264.7 macrophages following LPS stimulation. RAW 264.7 macrophages were exposed to 20 ng/mL LPS and simultaneously with the NBF, 20 µg/mL. COX-2 levels were measured by ELISA using standard calibration curve and are presented as the mean ± SD. Four replicates in each group (n = 4). ANOVA followed by Bonferroni’s post hoc test was performed. *** p < 0.001 compared to all other groups. Full article ">Figure 5
NBF downregulates the secretion of nitrite in RAW264.7 macrophages following LPS stimulation. RAW 264.7 macrophages were exposed to 20 ng/mL LPS and simultaneously with the NBF, 20 µg/mL. Nitrite levels were measured using standard calibration curve with sodium nitrite and are presented as the mean ± SD. Four replicates in each group (n = 4). ANOVA followed by Bonferroni’s post hoc test was performed. *** p < 0.001 compared to all other groups. Full article ">Figure 6
NBF upregulates mRNA expression levels of TLR2 and TLR4 but not NF-κB. RAW264.7 cells were treated with either Vehicle + LPS or NBF + LPS for 3 h. mRNA was extracted 3 h after treatment using an mRNA extraction kit and NF-κB, TLR2, and TLR4 mRNA were quantified and normalized to the glyceraldehyde 3-phosphate dehydrogenase (GAPDH)—mRNA expression levels are shown as the fold differences compared to untreated cells. Data are represented as the mean ± SEM of three independent experiments (three separate experiments in triplicates) and statistical analyses were performed using ANOVA followed by Bonferroni’s post hoc test. * p < 0.05, *** p < 0.001 vs. vehicle. Full article ">

12 pages, 472 KiB

Open AccessArticle

Risk of Seven-Day Worsening and Death: A New Clinically Derived COVID-19 Score

by Alessia Cruciata, Lorenzo Volpicelli, Silvia Di Bari, Giancarlo Iaiani, Bruno Cirillo, Francesco Pugliese, Daniela Pellegrino, Gioacchino Galardo and Gloria Taliani

Viruses 2022, 14(3), 642; https://doi.org/10.3390/v14030642 - 20 Mar 2022

Cited by 1 | Viewed by 2253

Abstract

This monocentric, retrospective, two-stage observational study aimed to recognize the risk factors for a poor outcome in patients hospitalized with SARS-CoV-2 infection, and to develop and validate a risk score that identifies subjects at risk of worsening, death, or both. The data of [...] Read more.

This monocentric, retrospective, two-stage observational study aimed to recognize the risk factors for a poor outcome in patients hospitalized with SARS-CoV-2 infection, and to develop and validate a risk score that identifies subjects at risk of worsening, death, or both. The data of patients with SARS-CoV-2 infection during the first wave of the pandemic were collected and analyzed as a derivation cohort. Variables with predictive properties were used to construct a prognostic score, which was tried out on a validation cohort enrolled during the second wave. The derivation cohort included 494 patients; the median age was 62 and the overall fatality rate was 22.3%. In a multivariable analysis, age, oxygen saturation, neutrophil-to-lymphocyte ratio, C-reactive protein and lactate dehydrogenase were independent predictors of death and composed the score. A cutoff value of 3 demonstrated a sensitivity (Se), specificity (Sp), positive predictive value (PPV) and negative predictive value (NPV) of 93.5%, 68.5%, 47.4% and 97.2% for death, and 84.9%, 84.5%, 79.6% and 87.9% for worsening, respectively. The validation cohort included 415 subjects. The score application showed a Se, Sp, PPV and NPV of 93.4%, 61.6%, 29.5% and 98.1% for death, and 81%, 76.3%, 72.1% and 84.1% for worsening, respectively. We propose a new clinical, easy and reliable score to predict the outcome in hospitalized SARS-CoV-2 patients. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 298 KiB

Open AccessArticle

Effect of Combined Antiretroviral Therapy on the Levels of Selected Parameters Reflecting Metabolic and Inflammatory Disturbances in HIV-Infected Patients

by Karolina Jurkowska, Beata Szymańska, Brygida Knysz and Agnieszka Piwowar

J. Clin. Med. 2022, 11(6), 1713; https://doi.org/10.3390/jcm11061713 - 19 Mar 2022

Cited by 1 | Viewed by 2595

Abstract

Subjects infected with human immunodeficiency virus (HIV) treated with combined antiretroviral therapy (cART) show a greater predisposition to metabolic disturbances compared to the general population. The aim of the study was to assess the effect of cART on the level of selected parameters [...] Read more.

Subjects infected with human immunodeficiency virus (HIV) treated with combined antiretroviral therapy (cART) show a greater predisposition to metabolic disturbances compared to the general population. The aim of the study was to assess the effect of cART on the level of selected parameters related to carbohydrate and lipid metabolism, cardiovascular diseases and inflammation in the plasma of HIV-infected patients against the uninfected. The levels of irisin (IRS), myostatin (MSTN), peptide YY (PYY), glucagon-like peptide-1 (GLP-1), dipeptidyl peptidase IV (DPP-4), fetuin A (FETU-A), pentraxin 3 (PTX 3), chemokine stromal cell-derived factor 1 (SDF-1), and regulated on activation normal T cell expressed and secreted (RANTES) in the plasma of HIV-infected patients and the control group were measured by immunoassay methods. HIV-infected patients were analyzed in terms of CD4+ T cells and CD8+ T cell count, HIV RNA viral load, and the type of therapeutic regimen containing either protease inhibitors (PIs) or integrase transfer inhibitors (INSTIs). The analysis of HIV-infected patients before and after cART against the control group showed statistically significant differences for the following parameters: IRS (p = 0.02), MSTN (p = 0.03), PYY (p = 0.03), GLP-1 (p = 0.03), PTX3 (p = 0.03), and RANTES (p = 0.02), but no significant differences were found for DPP-4, FETU-A, and SDF-1. Comparing the two applied therapeutic regimens, higher levels of all tested parameters were shown in HIV-infected patients treated with INSTIs compared to HIV-infected patients treated with PIs, but the differences were not statistically significant. The obtained results indicated significant changes in the expression of selected parameters in the course of HIV infection and cART. There is need for further research on the clinical usefulness of the selected parameters and for new information on the pathogenesis of HIV-related comorbidities to be provided. The obtained data may allow for better monitoring of the course of HIV infection and optimization of therapy in order to prevent the development of comorbidities as a result of long-term use of cART. Full article

(This article belongs to the Topic Infectious Diseases)

12 pages, 4209 KiB

Open AccessArticle

Distribution of Yeast Species and Risk Factors of Oral Colonization after Oral-Care Education among the Residents of Nursing Homes

by Ming-Gene Tu, Chih-Chao Lin, Ya-Ting Chiang, Zi-Li Zhou, Li-Yun Hsieh, Kai-Ting Chen, Yin-Zhi Chen, Wen-Chi Cheng and Hsiu-Jung Lo

J. Fungi 2022, 8(3), 310; https://doi.org/10.3390/jof8030310 - 17 Mar 2022

Viewed by 2482

Abstract

Most yeasts causing infections in humans are part of commensal microflora and etiological agents of different infections when hosts become susceptible, usually due to becoming immunocompromised. The colonization of potentially pathogenic microbes in the oral cavity is increased by poor oral hygiene. This [...] Read more.

Most yeasts causing infections in humans are part of commensal microflora and etiological agents of different infections when hosts become susceptible, usually due to becoming immunocompromised. The colonization of potentially pathogenic microbes in the oral cavity is increased by poor oral hygiene. This follow-up survey was conducted approximately two months after providing information on proper oral care at 10 nursing homes in Taiwan. Among the 117 of 165 residents colonized by yeasts, 67 were colonized by more than one yeast species. A total of 231 isolates comprising eight fungal genera and 25 species were identified. Candida albicans (44.6%) was the dominant species, followed by Candida glabrata (17.7%), Candida parapsilosis (8.7%), Candida tropicalis (7.8%), and Candida pararugosa (7.3%). Residents having a yeast colony-forming unit >10 (OR, 8.897; 95% CI 2.972–26.634; p < 0.001) or using a wheelchair (OR, 4.682; 95% CI 1.599–13.705; p = 0.005) were more likely to be colonized by multiple species. By comparing before and after oral-care education, dry mouth (OR, 3.199; 95% CI 1.448–7.068; p = 0.011) and having heart disease (OR, 2.681; 95% CI 1.068–6.732; p = 0.036) emerged as two independent risk factors for increased density of colonizing yeast. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 523 KiB

Open AccessArticle

Clinical Evaluation of a Fully-Automated High-Throughput Multiplex Screening-Assay to Detect and Differentiate the SARS-CoV-2 B.1.1.529 (Omicron) and B.1.617.2 (Delta) Lineage Variants

by Dominik Nörz, Moritz Grunwald, Hui Ting Tang, Celine Weinschenk, Thomas Günther, Alexis Robitaille, Katja Giersch, Nicole Fischer, Adam Grundhoff, Martin Aepfelbacher, Susanne Pfefferle and Marc Lütgehetmann

Viruses 2022, 14(3), 608; https://doi.org/10.3390/v14030608 - 15 Mar 2022

Cited by 5 | Viewed by 2627

Abstract

Background: The recently emerged SARS-CoV-2 B.1.1.529 lineage and its sublineages (Omicron variant) pose a new challenge to healthcare systems worldwide due to its ability to efficiently spread in immunized populations and its resistance to currently available monoclonal antibody therapies. RT-PCR-based variant tests can [...] Read more.

Background: The recently emerged SARS-CoV-2 B.1.1.529 lineage and its sublineages (Omicron variant) pose a new challenge to healthcare systems worldwide due to its ability to efficiently spread in immunized populations and its resistance to currently available monoclonal antibody therapies. RT-PCR-based variant tests can be used to screen large sample-sets rapidly and accurately for relevant variants of concern (VOC). The aim of this study was to establish and validate a multiplex assay on the cobas 6800/8800 systems to allow discrimination between the two currently circulating VOCs, Omicron and Delta, in clinical samples. Methods: Primers and probes were evaluated for multiplex compatibility. Analytic performance was assessed using cell culture supernatant of an Omicron variant isolate and a clinical Delta variant sample, normalized to WHO-Standard. Clinical performance of the multiplex assay was benchmarked against NGS results. Results: In silico testing of all oligos showed no interactions with a high risk of primer-dimer formation or amplification of human DNA/RNA. Over 99.9% of all currently available Omicron variant sequences are a perfect match for at least one of the three Omicron targets included in the multiplex. Analytic sensitivity was determined as 19.0 IU/mL (CI95%: 12.9–132.2 IU/mL) for the A67V + del-HV69-70 target, 193.9 IU/mL (CI95%: 144.7–334.7 IU/mL) for the E484A target, 35.5 IU/mL (CI95%: 23.3–158.0 IU/mL) for the N679K + P681H target and 105.0 IU/mL (CI95%: 80.7–129.3 IU/mL) for the P681R target. All sequence variances were correctly detected in the clinical sample set (225/225 Targets). Conclusion: RT-PCR-based variant screening compared to whole genome sequencing is both rapid and reliable in detecting relevant sequence variations in SARS-CoV-2 positive samples to exclude or verify relevant VOCs. This allows short-term decision-making, e.g., for patient treatment or public health measures. Full article

(This article belongs to the Topic Infectious Diseases)

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27 pages, 2332 KiB

Open AccessReview

Hallmarks of Metabolic Reprogramming and Their Role in Viral Pathogenesis

by Charles N. S. Allen, Sterling P. Arjona, Maryline Santerre and Bassel E. Sawaya

Viruses 2022, 14(3), 602; https://doi.org/10.3390/v14030602 - 14 Mar 2022

Cited by 26 | Viewed by 5745

Abstract

Metabolic reprogramming is a hallmark of cancer and has proven to be critical in viral infections. Metabolic reprogramming provides the cell with energy and biomass for large-scale biosynthesis. Based on studies of the cellular changes that contribute to metabolic reprogramming, seven main hallmarks [...] Read more.

Metabolic reprogramming is a hallmark of cancer and has proven to be critical in viral infections. Metabolic reprogramming provides the cell with energy and biomass for large-scale biosynthesis. Based on studies of the cellular changes that contribute to metabolic reprogramming, seven main hallmarks can be identified: (1) increased glycolysis and lactic acid, (2) increased glutaminolysis, (3) increased pentose phosphate pathway, (4) mitochondrial changes, (5) increased lipid metabolism, (6) changes in amino acid metabolism, and (7) changes in other biosynthetic and bioenergetic pathways. Viruses depend on metabolic reprogramming to increase biomass to fuel viral genome replication and production of new virions. Viruses take advantage of the non-metabolic effects of metabolic reprogramming, creating an anti-apoptotic environment and evading the immune system. Other non-metabolic effects can negatively affect cellular function. Understanding the role metabolic reprogramming plays in viral pathogenesis may provide better therapeutic targets for antivirals. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 1846 KiB

Open AccessArticle

Clinical and Immunological Predictors of Hemorrhagic Fever with Renal Syndrome Outcome during the Early Phase

by Geum-Young Lee, Won-Keun Kim, Jin Sun No, Yongjin Yi, Hayne Cho Park, Jaehun Jung, Seungchan Cho, Jingyeong Lee, Seung-Ho Lee, Kyungmin Park, Jongwoo Kim and Jin-Won Song

Viruses 2022, 14(3), 595; https://doi.org/10.3390/v14030595 - 14 Mar 2022

Cited by 3 | Viewed by 2831

Abstract

The ability to accurately predict the early progression of hemorrhagic fever with renal syndrome (HFRS) is crucial for reducing morbidity and mortality rates in severely affected patients. However, the utility of biomarkers for predicting clinical outcomes remains elusive in HFRS. The aims of [...] Read more.

The ability to accurately predict the early progression of hemorrhagic fever with renal syndrome (HFRS) is crucial for reducing morbidity and mortality rates in severely affected patients. However, the utility of biomarkers for predicting clinical outcomes remains elusive in HFRS. The aims of the current study were to analyze the serum levels of immune function-related proteins and identify novel biomarkers that may help ascertain clinical outcomes of HFRS. Enzyme-linked immunosorbent assay, Luminex, and bioanalyzer assays were used to quantitatively detect 15 biomarkers in 49 serum samples of 26 patients with HFRS. High hemoglobin (HGB) and low urine output (UO) levels were identified as potential biomarkers associated with the acute HFRS. The serum soluble urokinase plasminogen activator receptor (suPAR) and C-X-C motif chemokine ligand 10 (CXCL10) values increased in the early phase of diseases. Elevated suPAR, interleukin-10 (IL-10), CXCL10, and decreased transforming growth factor-beta 3 (TGF-β3) were representative predictors of the disease severity. Upregulation of the HGB showed a significant correlation with high levels of suPAR and CXCL10. Reduced UO positively correlated with increased suPAR, CXCL10, and TGF-β2, and decreased vascular endothelial growth factor and TGF-β3. The changing HGB and UO criteria, high suPAR, IL-10, CXCL10, and low TGF-β3 of HFRS raise significant awareness for physicians regarding prospective biomarkers for monitoring early warning signs of HFRS. This study provides critical insights into the clinical and immunological biomarkers for disease severity and progression in patients with HFRS to identify early predictions of fatal outcomes. Full article

(This article belongs to the Topic Infectious Diseases)

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Levels of clinical and laboratory parameters during early and late phases in patients with hemorrhagic fever with renal syndrome (HFRS). Full article ">Figure 2
Levels of inflammatory markers, cytokines, and chemokines during early and late phases in patients with hemorrhagic fever with renal syndrome (HFRS). * p < 0.05; ** p < 0.01; *** p < 0.0002; **** p < 0.0001. Full article ">Figure 3
Levels of inflammatory markers, cytokines, and chemokines for disease severity in the patients with hemorrhagic fever with renal syndrome (HFRS). * p < 0.05; ** p < 0.01; *** p < 0.0002; **** p < 0.0001. Full article ">Figure 4
Correlation of hemoglobin (HGB) and urine output (UO) with immunological biomarkers in patients with hemorrhagic fever with renal syndrome (HFRS). Full article ">Figure 5
Correlation of TGF-β3 with suPAR, IL-10, and CXCL10 in patients with hemorrhagic fever with renal syndrome. Full article ">Figure 6
A schematic model summarizing the predictors of clinical progression and outcome in patients with hemorrhagic fever with renal syndrome (HFRS). Full article ">

62 pages, 13513 KiB

Open AccessReview

Viral Shrimp Diseases Listed by the OIE: A Review

by Dain Lee, Young-Bin Yu, Jae-Ho Choi, A-Hyun Jo, Su-Min Hong, Ju-Chan Kang and Jun-Hwan Kim

Viruses 2022, 14(3), 585; https://doi.org/10.3390/v14030585 - 12 Mar 2022

Cited by 48 | Viewed by 15474

Abstract

Shrimp is one of the most valuable aquaculture species globally, and the most internationally traded seafood product. Consequently, shrimp aquaculture practices have received increasing attention due to their high value and levels of demand, and this has contributed to economic growth in many [...] Read more.

Shrimp is one of the most valuable aquaculture species globally, and the most internationally traded seafood product. Consequently, shrimp aquaculture practices have received increasing attention due to their high value and levels of demand, and this has contributed to economic growth in many developing countries. The global production of shrimp reached approximately 6.5 million t in 2019 and the shrimp aquaculture industry has consequently become a large-scale operation. However, the expansion of shrimp aquaculture has also been accompanied by various disease outbreaks, leading to large losses in shrimp production. Among the diseases, there are various viral diseases which can cause serious damage when compared to bacterial and fungi-based illness. In addition, new viral diseases occur rapidly, and existing diseases can evolve into new types. To address this, the review presented here will provide information on the DNA and RNA of shrimp viral diseases that have been designated by the World Organization for Animal Health and identify the latest shrimp disease trends. Full article

(This article belongs to the Topic Infectious Diseases)

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28 pages, 1336 KiB

Open AccessReview

Expression Profile and Biological Role of Immune Checkpoints in Disease Progression of HIV/SIV Infection

by Yuting Sun and Jing Xue

Viruses 2022, 14(3), 581; https://doi.org/10.3390/v14030581 - 11 Mar 2022

Cited by 8 | Viewed by 3428

Abstract

During HIV/SIV infection, the upregulation of immune checkpoint (IC) markers, programmed cell death protein-1 (PD-1), cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4), T cell immunoglobulin and ITIM domain (TIGIT), lymphocyte-activation gene-3 (LAG-3), T cell immunoglobulin and mucin domain-3 (Tim-3), CD160, 2B4 (CD244), and V-domain Ig suppressor [...] Read more.

During HIV/SIV infection, the upregulation of immune checkpoint (IC) markers, programmed cell death protein-1 (PD-1), cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4), T cell immunoglobulin and ITIM domain (TIGIT), lymphocyte-activation gene-3 (LAG-3), T cell immunoglobulin and mucin domain-3 (Tim-3), CD160, 2B4 (CD244), and V-domain Ig suppressor of T cell activation (VISTA), can lead to chronic T cell exhaustion. These ICs play predominant roles in regulating the progression of HIV/SIV infection by mediating T cell responses as well as enriching latent viral reservoirs. It has been demonstrated that enhanced expression of ICs on CD4⁺ and CD8⁺ T cells could inhibit cell proliferation and cytokine production. Overexpression of ICs on CD4⁺ T cells could also format and prolong HIV/SIV persistence. IC blockers have shown promising clinical results in HIV therapy, implying that targeting ICs may optimize antiretroviral therapy in the context of HIV suppression. Here, we systematically review the expression profile, biological regulation, and therapeutic efficacy of targeted immune checkpoints in HIV/SIV infection. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 989 KiB

Open AccessArticle

Epidemiological and Clinical Characteristics, Antifungal Susceptibility, and MLST-Based Genetic Analysis of Cryptococcus Isolates in Southern Taiwan in 2013–2020

by Yi-Chun Chen, Shu-Fang Kuo, Shang-Yi Lin, Yin-Shiou Lin and Chen-Hsiang Lee

J. Fungi 2022, 8(3), 287; https://doi.org/10.3390/jof8030287 - 11 Mar 2022

Cited by 6 | Viewed by 2296

Abstract

Cryptococcal meningoencephalitis (CM) is a treatable condition, but it leads to excessive morbidity and mortality. We collected 115 non-duplicated Cryptococcus clinical isolates during 2013–2020 in southern Taiwan to perform antifungal susceptibility testing. Multi-locus sequence typing was performed on 96 strains from patients with [...] Read more.

Cryptococcal meningoencephalitis (CM) is a treatable condition, but it leads to excessive morbidity and mortality. We collected 115 non-duplicated Cryptococcus clinical isolates during 2013–2020 in southern Taiwan to perform antifungal susceptibility testing. Multi-locus sequence typing was performed on 96 strains from patients with CM (n = 47) or cryptococcemia (n = 49). In addition, the epidemiological and clinical characteristics of patients with CM during 2013–2020 (n = 47) were compared with those during 2000–2010 (n = 46). During 2013–2020, only one C. neoformans isolate (0.9%) had a fluconazole minimum inhibitory concentration of >8 μg/mL. Amphotericin B (AMB), flucytosine (5FC), and voriconazole were highly active against all C. neoformans/C. gattii isolates. The most common sequence type was ST5. Among these 47 patients with CM, cerebrospinal fluid cryptococcal antigen (CSF CrAg) titer >1024 was a significant predictor of death (odds ratio, 48.33; 95% CI, 5.17–452.06). A standard induction therapy regimen with AMB and 5FC was used for all patients during 2013–2020, but only for 2.2% of patients in 2000–2010. The in-hospital CM mortality rate declined from 39.1% during 2000–2010 to 25.5% during 2013–2020, despite there being significantly younger patients with less CSF CrAg >1024 during 2000–2010. The study provides insight into the genetic epidemiology and antifungal susceptibility of Cryptococcus strains in southern Taiwan. The recommended antifungal drugs, AMB, 5FC, and FCZ, remained active against most of the Cryptococcus strains. Early diagnosis of patients with CM and adherence to the clinical practice guidelines cannot be overemphasized to improve the outcomes of patients with CM. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 789 KiB

Open AccessArticle

Clinical Outcomes of an Innovative Cefazolin Delivery Program for MSSA Infections in OPAT

by Laura Herrera-Hidalgo, Rafael Luque-Márquez, Aristides de Alarcon, Ana Belén Guisado-Gil, Belen Gutierrez-Gutierrez, Maria Dolores Navarro-Amuedo, Julia Praena-Segovia, Juan Manuel Carmona-Caballero, Elena Fraile-Ramos, Alicia Gutierrez-Valencia, Luis Eduardo Lopez-Cortes and Maria Victoria Gil-Navarro

J. Clin. Med. 2022, 11(6), 1551; https://doi.org/10.3390/jcm11061551 - 11 Mar 2022

Cited by 3 | Viewed by 2218

Abstract

Cefazolin is a recommended treatment for methicillin-susceptible Staphylococcus aureus (MSSA) infections that has been successfully used in outpatient parenteral antibiotic therapy (OPAT) programs. The aim of this study was to assess the clinical outcomes of cefazolin delivered each day (Group 24) vs. every [...] Read more.

Cefazolin is a recommended treatment for methicillin-susceptible Staphylococcus aureus (MSSA) infections that has been successfully used in outpatient parenteral antibiotic therapy (OPAT) programs. The aim of this study was to assess the clinical outcomes of cefazolin delivered each day (Group 24) vs. every two days (Group 48) for MSSA infections in OPAT programs. It was a prospective observational study with retrospective analysis of a cohort of MSSA infections attended in OPAT. The primary outcome was treatment success, defined as completing the antimicrobial regimen without death, treatment discontinuation, or readmission during treatment and follow-up. A univariate and multivariate logistic regression model was built. A two-sided p < 0.05 was considered statistically significant. Of the 149 MSSA infections treated with cefazolin 2 g/8 h in OPATs, 94 and 55 patients were included in the delivery Group 24 and Group 48, respectively. Treatment failure and unplanned readmission rates were similar in both groups (11.7% vs. 7.3% p = 0.752 and 8.5% vs. 5.5% p = 0.491). There was a significant increase in vascular access complications in Group 24 (33.0%) with respect to Group 48 (7.3%) (p < 0.001). Treating uncomplicated MSSA infection with cefazolin home-delivered every two days through an OPAT program is not associated with an increased risk of treatment failure and entails a significant reduction in resource consumption compared to daily delivery. Full article

(This article belongs to the Topic Infectious Diseases)

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6 pages, 1766 KiB

Open AccessBrief Report

COVID-19 Vaccination Limits Systemic Danger Signals in SARS-CoV-2 Infected Patients

by Roberta Angioni, Lolita Sasset, Chiara Cioccarelli, Ricardo Sánchez-Rodríguez, Nicole Bertoldi, Cristina C. Putaggio, Antonella Viola, Annamaria Cattelan and Barbara Molon

Viruses 2022, 14(3), 565; https://doi.org/10.3390/v14030565 - 9 Mar 2022

Cited by 3 | Viewed by 2268

Abstract

Vaccination with an mRNA COVID-19 vaccine determines not only a consistent reduction in the risk of SARS-CoV-2 infection but also contributes to disease attenuation in infected people. Of note, hyperinflammation and damage-associated molecular patterns (DAMPs) have been clearly associated with severe illness and [...] Read more.

Vaccination with an mRNA COVID-19 vaccine determines not only a consistent reduction in the risk of SARS-CoV-2 infection but also contributes to disease attenuation in infected people. Of note, hyperinflammation and damage-associated molecular patterns (DAMPs) have been clearly associated with severe illness and poor prognosis in COVID-19 patients. In this report, we revealed a significant reduction in the levels of IL-1ß and DAMPs molecules, as S100A8 and High Mobility Group Protein B1 (HMGB1), in vaccinated patients as compared to non-vaccinated ones. COVID-19 vaccination indeed prevents severe clinical manifestations in patients and limits the release of systemic danger signals in SARS-CoV-2 infected people. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 7879 KiB

Open AccessArticle

Inanimate Surfaces and Air Contamination with Multidrug Resistant Species of Staphylococcus in the Neonatal Intensive Care Unit Environment

by Ralciane de Paula Menezes, Lara de Andrade Marques, Felipe Flávio Silva, Nagela Bernadelli Sousa Silva, Priscila Guerino Vilela Alves, Meliza Arantes de Souza Bessa, Lúcio Borges de Araújo, Mário Paulo Amante Penatti, Reginaldo dos Santos Pedroso and Denise Von Dolinger de Brito Röder

Microorganisms 2022, 10(3), 567; https://doi.org/10.3390/microorganisms10030567 - 5 Mar 2022

Cited by 2 | Viewed by 2343

Abstract

Background: Contamination of the hospital environment with multi-resistant (MDR) Staphylococcus increases the risk of infection. The aim of this study is to identify the MDR species of Staphylococcus on inanimate surfaces, in air, and in clinical samples, and analyze the risk factors that [...] Read more.

Background: Contamination of the hospital environment with multi-resistant (MDR) Staphylococcus increases the risk of infection. The aim of this study is to identify the MDR species of Staphylococcus on inanimate surfaces, in air, and in clinical samples, and analyze the risk factors that correlate with the occurrence of infections in a Neonatal Intensive Care Unit. Methods: Samples of inanimate surfaces and air were taken using a premoistened swab (0.9% sodium chloride) and spontaneous air sedimentation, respectively. The clinical isolates were recovered from infected neonates. The isolates (environmental and clinical) were identified by matrix-assisted laser desorption ionization-time of flight and the resistance profile was calculated using the disk diffusion agar technique. Results: In total, 181 isolates were obtained, 93 from (surfaces), 18 from the air, and 70 clinical samples. S. epidermidis was the most frequent species (66.8%), and the failure rate in air cleaning was 100%. More than 60% of the isolates were MDR, and the majority of clinical isolates (60.4%) had a resistance profile identical to that of the environmental isolates. Conclusion: Staphylococcus spp. were found in most of the analyzed samples, with a high frequency of MDR isolates, demonstrating the importance of the hospital environment as a reservoir, and the need for infection control measures, and rational use of antimicrobials. Full article

(This article belongs to the Topic Infectious Diseases)

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8 pages, 817 KiB

Open AccessBrief Report

Genetic Diversity Does Not Contribute to Attenuation of HeLa Passaged Wild-Type Yellow Fever Virus Strain French Viscerotropic Virus

by Ashley E. Strother, Jill K. Thompson, Steven G. Widen and Alan D. T. Barrett

Viruses 2022, 14(3), 527; https://doi.org/10.3390/v14030527 - 4 Mar 2022

Viewed by 1576

Abstract

The disease yellow fever was prevented by two live attenuated vaccines, strains 17D and French neurotropic vaccine (FNV), derived by serial passage of wild-type (WT) strains Asibi and French Viscerotropic virus (FVV), respectively. Both 17D and FNV displayed decreased genetic diversity and resistance [...] Read more.

The disease yellow fever was prevented by two live attenuated vaccines, strains 17D and French neurotropic vaccine (FNV), derived by serial passage of wild-type (WT) strains Asibi and French Viscerotropic virus (FVV), respectively. Both 17D and FNV displayed decreased genetic diversity and resistance to the antiviral Ribavirin compared to their WT parental strains, which are thought to contribute to their attenuated phenotypes. Subsequent studies found that only a few passages of WT strain FVV in HeLa cells resulted in an attenuated virus. In the current study, the genome sequence of FVV following five passages in HeLa cells (FVV HeLa p5) was determined through Next Generation Sequencing (NGS) with the aim to investigate the molecular basis of viral attenuation. It was found that WT FVV and FVV HeLa p5 virus differed by five amino acid substitutions: E-D155A, E-K331R, E-I412V, NS2A-T105A, and NS4B-V98I. Surprisingly, the genetic diversity and Ribavirin resistance of the FVV HeLa p5 virus were not statistically different to WT parent FVV. These findings suggest that while FVV HeLa p5 is attenuated, this is not dependent on a high-fidelity replication complex, characterized by reduced genetic diversity or increased Ribavirin stability, as seen with FNV and 17D vaccines. Full article

(This article belongs to the Topic Infectious Diseases)

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14 pages, 2602 KiB

Open AccessArticle

Evaluating the Mode of Antifungal Action of Heat-Stable Antifungal Factor (HSAF) in Neurospora crassa

by Xiaodong Liu, Xianzhang Jiang, Haowen Sun, Jiawen Du, Yuhang Luo, Jianzhong Huang and Lina Qin

J. Fungi 2022, 8(3), 252; https://doi.org/10.3390/jof8030252 - 1 Mar 2022

Cited by 6 | Viewed by 2437

Abstract

Heat-stable antifungal factor (HSAF) isolated from Lysobacter enzymogenes has shown a broad-spectrum of antifungal activities. However, little is known about its mode of action. In this study, we used the model filamentous fungus Neurospora crassa to investigate the antifungal mechanism of HSAF. [...] Read more.

Heat-stable antifungal factor (HSAF) isolated from Lysobacter enzymogenes has shown a broad-spectrum of antifungal activities. However, little is known about its mode of action. In this study, we used the model filamentous fungus Neurospora crassa to investigate the antifungal mechanism of HSAF. We first used HSAF to treat the N. crassa strain at different time points. Spore germination, growth phenotype and differential gene expression analysis were conducted by utilizing global transcriptional profiling combined with genetic and physiological analyses. Our data showed that HSAF could significantly inhibit the germination and aerial hyphae growth of N. crassa. RNA-seq analysis showed that a group of genes, associated with cell wall formation and remodeling, were highly activated. Screening of N. crassa gene deletion mutants combined with scanning electron microscopic observation revealed that three fungal cell wall integrity-related genes played an important role in the interaction between N. crassa and L. enzymogens. In addition, Weighted Gene Co-Expression Network Analysis (WGCNA), accompanied by confocal microscopy observation revealed that HSAF could trigger autophagy-mediated degradation and eventually result in cell death in N. crassa. The findings of this work provided new insights into the interactions between the predatory Lysobacter and its fungal prey. Full article

(This article belongs to the Topic Infectious Diseases)

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HSAF caused growth defect in N. crassa. (A) Chemical structure of HSAF; (B) Growth of N. crassa on Vogel’s plates supplemented with HSAF (0, 20, 30, 40, 50, 60 µM) for 36 h. Images show the results of one out of three experiments, and the statistical analysis of colony diameter is shown in (C); (D) Germination rate of N. crassa under HSAF treatment. Asterisks indicate significant differences (*, p < 0.05; ***, p < 0.001); (E) Microscopic morphology of N. crassa grown on Vogel’s media without (CK) or with 30 µM HSAF treatment (HSAF) for 6 h. The black arrow indicates the hyper-branch. Full article ">Figure 2
The effect of HSAF treatment on the formation and remodeling of cell wall. (A) The heat map of DEGs related to fungal-type cell wall organization. The heat map was constructed by R software pheatmap package with the original FPKM value of each gene; (B) Microscopic morphological characteristics and cell wall staining by CFW at different time of spore germination (1 h, 3 h, 5 h). The arrows indicate the regions with the thickened cell wall. Images show the results of one out of three replicates. Full article ">Figure 3
HSAF does not affect protoplast regeneration. (A) Protoplasting of N. crassa; (B) Protoplast regeneration tests with protoplasts suspended in sorbitol or distilled water. 106/mL protoplasts were inoculated into Vogel’s media supplemented with 1 M sorbitol and 30 μM HSAF. Full article ">Figure 4
Deletion of gene chs-9, gh16-5, or chs-1 in N. crassa increased the HSAF resistance. (A) Growth phenotype of the indicated mutants and wildtype of N. crassa on Vogel’s media with 50 μM HSAF; (B) CFW staining of cell wall of wildtype and the indicated mutants of N. crassa. Images show the results of one out of three replicates. Full article ">Figure 5
Physical interactions between different L. enzymogenes mutants and N. crassa mutants. (A) N. crassa WT; (B) N. crassa Δchs-9 mutant; (C) N. crassa Δchs-1 mutant; (D) N. crassa Δgh16-5 mutant interacted with L. enzymogenes strains. Control indicates growth of N. crassa alone, WT indicates L. enzymogenes wildtype strain and (-)HSAF indicates no-producing HSAF L. enzymogenes strain. Images show the results of one out of three replicates. Full article ">Figure 6
HSAF treatment may trigger autophagy-mediated degradation in N. crassa. (A) Correlation heat map of Modules and HSAF; (B) Functional category of DEGs in different modules; (C) Confocal microscopy of cellular morphology from germlings containing sGFP-tagged NCA-1 (ER marker); (D) Confocal microscopy of cellular morphology from germlings containing sGFP-tagged VRG-4 (Golgi marker); (E) Confocal microscopy of cellular morphology from germlings stained with DAPI. The germlings were grown in Vogel’s medium supplemented with 30 μM HSAF for 5 h. Images show the results of one out of three replicates. Full article ">

12 pages, 1495 KiB

Open AccessArticle

Surveillance of Antifungal Resistance in Candidemia Fails to Inform Antifungal Stewardship in European Countries

by Liliana Galia, Maria Diletta Pezzani, Monica Compri, Astrid Callegari, Nithya Babu Rajendran, Elena Carrara, Evelina Tacconelli and the COMBACTE MAGNET EPI-Net Network

J. Fungi 2022, 8(3), 249; https://doi.org/10.3390/jof8030249 - 28 Feb 2022

Cited by 13 | Viewed by 3517

Abstract

Background: The increasing burden of candidemia and the emergence of resistance, especially among non-Candida albicans strains, represent a new threat for public health. We aimed to assess the status of surveillance and to identify publicly accessible resistance data in Candida spp. blood [...] Read more.

Background: The increasing burden of candidemia and the emergence of resistance, especially among non-Candida albicans strains, represent a new threat for public health. We aimed to assess the status of surveillance and to identify publicly accessible resistance data in Candida spp. blood isolates from surveillance systems and epidemiological studies in 28 European and 4 European Free Trade Association member states. Methods: A systematic review of national and international surveillance networks, from 2015 to 2020, and peer-reviewed epidemiological surveillance studies, from 2005 to 2020, lasting for at least 12 consecutive months and with at least two centers involved, was completed to assess reporting of resistance to amphotericin B, azoles, and echinocandins in C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, C. krusei, and C. auris. Results: Only 5 (Austria, Italy, Norway, Spain, and United Kingdom) of 32 countries provided resistance data for Candida spp blood isolates. Among 322 surveillance studies identified, 19 were included from Belgium, Denmark, Iceland, Italy, Portugal, Spain, Sweden, Switzerland, and United Kingdom. C. albicans and C. glabrata were the most monitored species, followed by C. parapsilosis and C. tropicalis. C. krusei was not included in any national surveillance system; 13 studies assessed resistance. No surveillance system or study reported resistance for C. auris. Fluconazole, voriconazole, caspofungin, and amphotericin B resistance in C. albicans, C. glabrata, and C. parapsilosis were the most common drug–species combination monitored. Quality of surveillance data was poor, with only two surveillance systems reporting microbiological methods and clinical data. High heterogeneity was observed in modalities of reporting, data collection, and definitions. Conclusion: Surveillance of antifungal resistance in Candida spp blood-isolates is fragmented and heterogeneous, delaying the application of a translational approach to the threat of antifungal resistance and the identification of proper targets for antifungal stewardship activities. International efforts are needed to implement antifungal resistance surveillance programs in order to adequately monitor antifungal resistance. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 1351 KiB

Open AccessArticle

Comparative Evaluation of Rapid Isothermal Amplification and Antigen Assays for Screening Testing of SARS-CoV-2

by Nol Salcedo, Brena F. Sena, Xiying Qu and Bobby Brooke Herrera

Viruses 2022, 14(3), 468; https://doi.org/10.3390/v14030468 - 25 Feb 2022

Cited by 4 | Viewed by 2029

Abstract

Human transmission of SARS-CoV-2 and emergent variants of concern continue to occur globally, despite mass vaccination campaigns. Public health strategies to reduce virus spread should therefore rely, in part, on frequent screening with rapid, inexpensive, and sensitive tests. We evaluated two digitally integrated [...] Read more.

Human transmission of SARS-CoV-2 and emergent variants of concern continue to occur globally, despite mass vaccination campaigns. Public health strategies to reduce virus spread should therefore rely, in part, on frequent screening with rapid, inexpensive, and sensitive tests. We evaluated two digitally integrated rapid tests and assessed their performance using stored nasal swab specimens collected from individuals with or without COVID-19. An isothermal amplification assay combined with a lateral flow test had a limit of detection of 10 RNA copies per reaction, and a positive percent agreement (PPA)/negative percent agreement (NPA) during the asymptomatic and symptomatic phases of 100%/100% and 95.83/100%, respectively. Comparatively, an antigen-based lateral flow test had a limit of detection of 30,000 copies and a PPA/NPA during the asymptomatic and symptomatic phases of 82.86%/98.68% and 91.67/100%, respectively. Both the isothermal amplification and antigen-based lateral flow tests had optimized detection of SARS-CoV-2 during the peak period of transmission; however, the antigen-based test had reduced sensitivity in clinical samples with qPCR Ct values greater than 29.8. Low-cost, high-throughput screening enabled by isothermal amplification or antigen-based techniques have value for outbreak control. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Schematic of RT-RPA assay versus antigen-based test. (A) In RT-RTPA, viral RNA is coped to cDNA by reverse transcriptase, then degraded by RNase H. Using a forward and a FAM-labeled reverse pair of primers specific to a target sequence, the cDNA product is amplified by RPA, then denatured and hybridized to a biotinylated probe. FAM-labeled and biotin-labeled products are detected on a lateral flow strip using molecules specific for FAM and biotin and nanoparticles. (B) In an antigen test, protein targets are detected by a lateral flow strip using protein-specific antibodies and nanoparticles. (C) A mobile phone application was used to image capture, machine-read, and quantify test results. The average pixel intensity is quantified at the test line, control line, and background areas. The background-subtracted test line signal is then normalized to the background-subtracted control line and expressed at % of control. − (red), test signal below the limit of detection; + (orange), low test signal; ++ (blue), medium test signal; +++ (green), high test signal. Full article ">Figure 2
Analytical sensitivity of the RT-RPA assay and the antigen test using nasal swab dilution specimens. (A) Lateral flow strips for the RT-RPA reactions with dilution specimens containing RNA copies ranging from 0 to 1000. (B) Plot from the RT-RPA assay results quantified by the mobile phone application. The x-axis corresponds to dilutions’ specimens with known input copies of SARS-CoV-2 RNA. The y-axis corresponds to background subtracted test signal normalized to the control line for each lateral flow strip. Test results (purple dots) less than 10% of control are considered negative results, which is indicated by the black dashed line. (C) Lateral flow strips for the antigen tests with dilution specimens containing RNA copies ranging from 0 to 200,000. (D) Plot from the antigen tests results quantified by the mobile phone application. The x-axis corresponds to dilutions’ specimens with known input copies of SARS-CoV-2 RNA. The y-axis corresponds to background subtracted test signal normalized to the control line for each lateral flow strip. Test results (blue dots) less than 10% of control are considered negative results, which is indicated by the black dashed line. Full article ">Figure 3
Clinical performance of the RT-RPA assay and the antigen test using nasal swab specimens collected from individuals with or without COVID-19. (A) Comparative evaluation of the RT-RPA assay (purple) and the antigen test (blue) using nasal swab specimens from asymptomatic cases. Comparative performance between the tests was plotted according to qPCR positive (Ct values between <20 to <40) and negative results. (B) Comparative evaluation of the RT-RPA assay (purple) and the antigen test (blue) using nasal swab specimens from symptomatic cases. Comparative performance between the tests was plotted according to qPCR positive (Ct values between <20 to <40) and negative results. Full article ">

10 pages, 709 KiB

Open AccessArticle

The Impact of SARS-CoV-2 Primary Vaccination in a Cohort of Patients Hospitalized for Acute COVID-19 during Delta Variant Predominance

by Daša Stupica, Stefan Collinet-Adler, Nataša Kejžar, Zala Jagodic, Mario Poljak and Mirijam Nahtigal Klevišar

J. Clin. Med. 2022, 11(5), 1191; https://doi.org/10.3390/jcm11051191 - 23 Feb 2022

Cited by 7 | Viewed by 2672

Abstract

Vaccine breakthrough SARS-CoV-2 infections necessitating hospitalization have emerged as a relevant problem with longer time interval since vaccination and the predominance of the Delta variant. The aim of this study was to evaluate the association between primary vaccination with four SARS-CoV-2 vaccines authorized [...] Read more.

Vaccine breakthrough SARS-CoV-2 infections necessitating hospitalization have emerged as a relevant problem with longer time interval since vaccination and the predominance of the Delta variant. The aim of this study was to evaluate the association between primary vaccination with four SARS-CoV-2 vaccines authorized for use in the European Union—BNT162b2, ChAdOx-1S, mRNA-1273 or Ad.26.COV2.S—and progression to critically severe disease (mechanical ventilation or death) and duration of hospitalization among adult patients with PCR-confirmed acute COVID-19 hospitalized during the Delta variant predominance (October–November 2021) in Slovenia. Among the 529 enrolled patients hospitalized with COVID-19 (median age, 65 years; 58.2% men), 175 (33.1%) were fully vaccinated at the time of symptom onset. Compared with 345 unvaccinated patients, fully vaccinated patients with breakthrough infections were older, more often immunocompromised, and had higher Charlson comorbidity index scores. After adjusting for sex, age, and comorbidities, fully vaccinated patients had lower odds for progressing to critically severe disease and were discharged from the hospital earlier than unvaccinated patients. Vaccination against SARS-CoV-2 remains an extremely effective intervention to alleviate morbidity and mortality in COVID-19 patients. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 546 KiB

Open AccessArticle

Incidence and Risk Factors of Reinfection with HCV after Treatment in People Living with HIV

by Chien-Yu Cheng, Shin-Yen Ku, Yi-Chun Lin, Cheng-Pin Chen, Shu-Hsing Cheng and I-Feng Lin

Viruses 2022, 14(2), 439; https://doi.org/10.3390/v14020439 - 21 Feb 2022

Cited by 6 | Viewed by 2308

Abstract

Infection with hepatitis C virus (HCV) does not induce protective immunity, and re-exposure to HCV can reinfect the population engaging in high-risk behavior. An increasing incidence of acute hepatitis C infection in people living with HIV (PLWH) has been described in recent years. [...] Read more.

Infection with hepatitis C virus (HCV) does not induce protective immunity, and re-exposure to HCV can reinfect the population engaging in high-risk behavior. An increasing incidence of acute hepatitis C infection in people living with HIV (PLWH) has been described in recent years. This retrospective cohort study was conducted in PLWH who completed HCV therapy between June 2009 and June 2020 at an HIV care hospital, to analyze their basic characteristics and risky behavior. Of 2419 patients, 639 were diagnosed with HCV infection and 516 completed the HCV therapy with a sustained virologic response. In total, 59 patients (11.4%) were reinfected with acute hepatitis C, and the median time to reinfection was 85.3 weeks (IQR: 57–150). The incidence of reinfection was 6.7 cases/100 person-years. The factors associated with reinfection were being male (AHR, 8.02; 95% CI 1.08–59.49), DAA (direct-acting antiviral) treatment (AHR, 2.23; 95% CI 1.04–4.79), liver cirrhosis (AHR, 3.94; 95% CI 1.09–14.22), heroin dependency (AHR: 7.41; 95% CI 3.37–14.3), and HIV viral loads <50 copies/mL at the follow-up (AHR: 0.47, 95% CI 0.24–0.93) in the subgroup of people who inject drugs (PWID). Amphetamine abuse (AHR: 20.17; 95% CI 2.36–172.52) was the dominant factor in the subgroup of men who have sex with men (MSM). Our study suggests that education and behavioral interventions are needed in this population to prevent reinfection. Full article

(This article belongs to the Topic Infectious Diseases)

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21 pages, 1053 KiB

Open AccessReview

Tinea Imbricata among the Indigenous Communities: Current Global Epidemiology and Research Gaps Associated with Host Genetics and Skin Microbiota

by Yi Xian Er, Soo Ching Lee, Leslie Thian-Lung Than, Azdayanti Muslim, Kin Fon Leong, Zhenli Kwan, Izandis Mohd Sayed and Yvonne Ai-Lian Lim

J. Fungi 2022, 8(2), 202; https://doi.org/10.3390/jof8020202 - 20 Feb 2022

Cited by 3 | Viewed by 4386

Abstract

Tinea imbricata is a unique fungal skin disease that mostly affects indigenous populations in Southeast Asia, Oceania, and Central and South America. The control and management of this disease among these communities are challenging given their remote locations, certain traditional practices, and severe [...] Read more.

Tinea imbricata is a unique fungal skin disease that mostly affects indigenous populations in Southeast Asia, Oceania, and Central and South America. The control and management of this disease among these communities are challenging given their remote locations, certain traditional practices, and severe malnutrition status. To date, there are only a handful of reports published globally, which highlights the need for a more holistic approach in addressing this skin disease. Several bodies of evidence and reports have shown that host genetic factors have a profound influence on the pathogenesis of tinea imbricata, while skin microbiota is touted to have a role in the pathogenesis of the disease. However, there are limited studies of how host genetics and skin microbiota impact disease susceptibility in the host. To improve the understanding of this disease and to find possible long-term effective treatment among the affected indigenous communities, a comprehensive literature review is needed. Hence, this review paper aims to present the current status of tinea imbricata among the indigenous communities, together with published findings on the possible underlying reasons for its specific distribution among these communities, particularly on the ways in which host skin microbiota and host genetics affect occurrence and disease patterns. This information provides valuable insights for future research by highlighting the current knowledge gaps in these areas. Full article

(This article belongs to the Topic Infectious Diseases)

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13 pages, 803 KiB

Open AccessArticle

A Multicenter Retrospective Study on Clinical Characteristics and Outcome of Pyogenic Liver Abscess Focusing Multidrug-Resistant Organisms

by Ji-Won Park, Jung-Hee Kim, Jang-Han Jung, Sung-Eun Kim, Hyoung-Su Kim, Haemin Jeong, Ki Tae Suk, Myoung-Kuk Jang, Dong-Joon Kim, Myung-Seok Lee and Sang-Hoon Park

J. Clin. Med. 2022, 11(4), 1114; https://doi.org/10.3390/jcm11041114 - 19 Feb 2022

Cited by 3 | Viewed by 2101

Abstract

The emergence of multidrug-resistant organisms (MDROs) is a growing problem worldwide. However, little is known about the incidence, clinical features and outcomes of pyogenic liver abscesses (PLAs) caused by MDROs. A retrospective study of 833 patients with PLA admitted from 2008 to 2017 [...] Read more.

The emergence of multidrug-resistant organisms (MDROs) is a growing problem worldwide. However, little is known about the incidence, clinical features and outcomes of pyogenic liver abscesses (PLAs) caused by MDROs. A retrospective study of 833 patients with PLA admitted from 2008 to 2017 was performed. MDROs were found in 55 (6.6%) patients, and extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae was the most common causative microorganism. To evaluate the clinical features of and risk factors for MDRO-induced PLAs, propensity score matching (PSM) was performed in a 1:3 ratio (55 patients with MDROs and 165 patients without MDROs). After PSM, previous hepatobiliary procedure, preadmission exposure to antibiotics and elevated alkaline phosphatase levels were independent risk factors for MDRO-induced PLA. Sixteen patients (7.3%) died during hospitalization. Admission to intensive care unit (ICU), inadequate initial antibiotic treatment and use of inotropic agents were factors predictive of mortality. Although the presence of MDROs was not associated with in-hospital mortality, inadequate initial antibiotic treatment was prescribed to a large portion of the patients with MDRO-induced PLAs. We conclude that initial empirical antibiotic therapy for PLA should be based on the possibility of infection with MDROs, and close monitoring is necessary for patients with risk factors for in-hospital mortality. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 706 KiB

Open AccessArticle

The Burden of Vertebral Osteomyelitis—An Analysis of the Workforce before and after Treatment

by Ayla Yagdiran, Jan Bredow, Carolyn Weber, Ghaith Mousa Basha, Peer Eysel, Julia Fischer and Norma Jung

J. Clin. Med. 2022, 11(4), 1095; https://doi.org/10.3390/jcm11041095 - 18 Feb 2022

Cited by 5 | Viewed by 1517

Abstract

Although vertebral osteomyelitis (VO) has a major impact on morbidity, functional status, and quality of life, data concerning the influence on the patient’s ability to work (ATW) are lacking. Therefore, the aim of this study was to analyze the work status after VO-treatment [...] Read more.

Although vertebral osteomyelitis (VO) has a major impact on morbidity, functional status, and quality of life, data concerning the influence on the patient’s ability to work (ATW) are lacking. Therefore, the aim of this study was to analyze the work status after VO-treatment as well as risk factors associated with loss of the ATW. We conducted a post-hoc analysis of data from a prospective VO-registry (2008–2019) supplemented by workforce data. Primary endpoint was the work status after one year (T1). Univariate analysis comparing patients’ characteristics “at-work” versus “not-at-work” at T1 was performed. Of a total of 335 VO-patients, n = 52 (16%) were part of the workforce at time of diagnosis (T0), of which 22 (42%) failed to be part of the workforce at T1. A higher number of comorbidities and a body mass index (BMI) < 25 kg/m² were associated with a reduced ATW. VO in working age patients is a debilitating condition and associated with reduced patients’ ATW. Patients engaged in heavy physical work mostly had a BMI < 25 kg/m² and therefore were more severely affected and no longer able to keep their workforce. More support in retraining should be offered after successful treatment to maintain ATW and reduce the socio-economic burden. Full article

(This article belongs to the Topic Infectious Diseases)

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14 pages, 470 KiB

Open AccessReview

Pancreatic Stone Protein: Review of a New Biomarker in Sepsis

by Pedro Fidalgo, David Nora, Luis Coelho and Pedro Povoa

J. Clin. Med. 2022, 11(4), 1085; https://doi.org/10.3390/jcm11041085 - 18 Feb 2022

Cited by 16 | Viewed by 5175

Abstract

Sepsis is a life-threatening syndrome characterized by a dysregulated host response to an infection that may evolve rapidly into septic shock and multiple organ failure. Management of sepsis relies on the early recognition and diagnosis of infection and the providing of adequate and [...] Read more.

Sepsis is a life-threatening syndrome characterized by a dysregulated host response to an infection that may evolve rapidly into septic shock and multiple organ failure. Management of sepsis relies on the early recognition and diagnosis of infection and the providing of adequate and prompt antibiotic therapy and organ support. A novel protein biomarker, the pancreatic stone protein (PSP), has recently been studied as a biomarker of sepsis and the available evidence suggests that it has a higher diagnostic performance for the identification of infection than the most used available biomarkers and adds prognostic value. This review summarizes the clinical evidence available for PSP in the diagnosis and prognosis of sepsis. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 2726 KiB

Open AccessArticle

Influenza A Virus Causes Histopathological Changes and Impairment in Functional Activity of Blood Vessels in Different Vascular Beds

by Vladimir Marchenko, Irina Zelinskaya, Yana Toropova, Tatyana Shmakova, Ekaterina Podyacheva, Dmitry Lioznov and Irina N. Zhilinskaya

Viruses 2022, 14(2), 396; https://doi.org/10.3390/v14020396 - 15 Feb 2022

Cited by 5 | Viewed by 2343

Abstract

It has been established that blood vessels are a target for influenza virus; however, the mechanism by which virus affects the cardiovascular system remains unknown. The aim of the study is the identification of histological changes and changes in the functional activity of [...] Read more.

It has been established that blood vessels are a target for influenza virus; however, the mechanism by which virus affects the cardiovascular system remains unknown. The aim of the study is the identification of histological changes and changes in the functional activity of the pulmonary and mesenteric blood vessels of Wistar rats. Wistar rats were intranasally infected with the influenza A(H1N1)pdm09 virus. At 24 and 96 h post infection (hpi), histopathological changes were observed in lung tissues with the absence of histological changes in mesenteric tissues. The functional activity of pulmonary and mesenteric arteries was determined using wire myography. In pulmonary arteries, there was a tendency towards an increase in integral response to the vasodilator and a decrease in the integral response to the vasoconstrictor at 24 hpi (compared with control). At 96 hpi, a tendency towards a decrease in the integral response to the vasoconstrictor persisted, while the response to acetylcholine was slightly increased. The functional activity of the mesenteric blood vessels was inverted: a significant decrease in the integral response to the vasodilator and an increase in the response to the vasoconstrictor at 24 hpi were observed; at 96 hpi, the integral response to the vasoconstrictor persisted, while the response to the vasodilator remained significantly reduced. Obtained data indicate the development of endothelial dysfunction in non-lethal and clinically non-severe experimental influenza virus infection. Full article

(This article belongs to the Topic Infectious Diseases)

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Histological examination of pulmonary tissues and blood vessels of rats in the control group (A) and at 24 (B) and 96 h post infection (C) with influenza A/St. Petersburg/48/16 (H1N1)pdm09 virus. Magnification ×200 (A,B); ×400 (C); H&E staining. (1) Stratification of adventitia; (2) stratification of media into separate muscle bundles; (3) thinning of the media; (4) thinning of the endothelium; (5) foci of erythrocyte extravasation; (6) endothelium in the form of stockade. Full article ">Figure 2
Histological examination of tissues and blood vessels of the lungs and mesentery of rats in the control group (A) and 24 (B) and 96 h after infection (C) with influenza A/St. Petersburg/48/16 (H1N1)pdm09 virus. Magnification ×400; H&E staining. Full article ">Figure 3
Immunohistochemical assay of pulmonary tissues and blood vessels of rats in the control group (A) and at 24 (B) and 96 h post infection (C) with influenza A/St. Petersburg/48/16 (H1N1)pdm09 virus using anti-NP Mabs (clone 6D11). Magnification ×200; DAB chromogen staining. Full article ">Figure 4
Immunohistochemical assay of mesenteric tissues and blood vessels of rats in the control group (A) and at 24 (B) and 96 h post infection (C) with influenza A/St. Petersburg/48/16 (H1N1)pdm09 virus using anti-NP Mabs (clone 6D11). Magnification ×400; DAB chromogen staining. Full article ">Figure 5
Functional activity of pulmonary arteries in the control group and at 24 and 96 h post infection with influenza A/St. Petersburg/48/16 (H1N1)pdm09 virus. (A): Dose-dependent response curves to serotonin (5-HT). (B): dose–response curves of concentration response to acetylcholine (Ach). (C): Maximum response of pulmonary arteries to serotonin and acetylcholine. Values represent mean ± standard error mean from 30 arteries of 10 rats in every group. * p < 0.05 versus control group (Dunnett’s test). Full article ">Figure 6
Functional activity of mesenteric arteries in the control group and at 24 and 96 h post infection with influenza A/St. Petersburg/48/16 (H1N1)pdm09 virus. (A): Dose-dependent response curves to phenylephrine (PE). (B): dose–response curves to acetylcholine (ACh). (C): Maximum response of pulmonary arteries to serotonin and acetylcholine. Values represent mean ± standard error mean from 30 arteries of 10 rats in every group. * p < 0.05, *** p < 0.001, **** p < 0.0001 versus control group (Dunnett’s test). Full article ">

12 pages, 1463 KiB

Open AccessArticle

Usefulness of Selected Peripheral Blood Counts in Predicting Death in Patients with Severe and Critical COVID-19

by Michał P. Pluta, Mateusz N. Zachura, Katarzyna Winiarska, Alicja Kalemba, Cezary Kapłan, Anna J. Szczepańska and Łukasz J. Krzych

J. Clin. Med. 2022, 11(4), 1011; https://doi.org/10.3390/jcm11041011 - 15 Feb 2022

Cited by 6 | Viewed by 1867

Abstract

Background. Immune dysregulation and hypoxemia are two important pathophysiological problems in patients with COVID-19 that affect peripheral blood count parameters. We hypothesized that assessment of the neutrophil–lymphocyte ratio (NLR) and red blood cell distribution width index (RDW-SD) could predict death in patients with [...] Read more.

Background. Immune dysregulation and hypoxemia are two important pathophysiological problems in patients with COVID-19 that affect peripheral blood count parameters. We hypothesized that assessment of the neutrophil–lymphocyte ratio (NLR) and red blood cell distribution width index (RDW-SD) could predict death in patients with severe and critical COVID-19. Methods. Seventy patients admitted to the intensive care unit (ICU) for COVID-19 acute respiratory failure were included in the study. RDW-SD and NLR on the day of ICU admission and peak values during the entire hospitalization were assessed. The primary endpoint was death before ICU discharge. Results. Patients who died had higher NLR on admission (20.3, IQR 15.3–30.2 vs. 11.0, IQR 6.8–16.9; p = 0.003) and higher RDW-SD (48.1 fL; IQR 43.1–50.5 vs. 43.9 fL; IQR 40.9–47.3, p = 0.01) than patients discharged from the ICU. NLR and RDW-SD values on ICU admission accurately predicted death in 76% (AUC = 0.76; 95%CI 0.65–0.86; p = 0.001; cut-off > 14.38) and 72% of cases (AUC = 0.72; 95%CI 0.60–0.82; p = 0.003; cut-off > 44.7 fL), respectively. Multivariable analysis confirmed that NLR > 14.38 on the day of ICU admission was associated with a 12-fold increased risk of death (logOR 12.43; 95%CI 1.61–96.29, p = 0.02), independent of other blood counts, clinical and demographic parameters. Conclusions. Neutrophil–lymphocyte ratio determined on the day of ICU admission may be a useful biomarker predicting death in patients with severe and critical COVID-19. Full article

(This article belongs to the Topic Infectious Diseases)

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NLR values on admission to the ICU, and survival by the discharge from the ICU. The length of the rectangle represents the interquartile range (IQR), comprising the middle 50% of observations. The box is separated by a horizontal line that marks the median value (Me). It divides the quartile interval (Q) into two areas containing 25% of the observations. The whiskers connect the box with the largest and smallest values of the studied variable from the interval (Q1 − 1.5 × IQR; Q1) and (Q3; Q3 + 1.5 IQR), respectively. Dots indicate outliers. Full article ">Figure 2
Final outcome of ICU treatment by systemic stress severity group (based on NLR index [<a href="#B14-jcm-11-01011" class="html-bibr">14</a>]). Full article ">Figure 3
Comparison of ROC curves for selected leukocyte parameters measured on admission to the ICU. Full article ">Figure 4
RDW-SD values at ICU admission and survival to ICU discharge. The length of the rectangle represents the interquartile range (IQR), comprising the middle 50% of observations. The box is separated by a horizontal line that marks the median value (Me). It divides the quartile interval (Q) into two areas containing 25% of the observations. The whiskers connect the box with the largest and smallest values of the studied variable from the interval (Q1 − 1.5 × IQR; Q1) and (Q3; Q3 + 1.5 IQR), respectively. Dots indicate outliers. Full article ">Figure 5
Survival probability in terms of NLR on admission. Full article ">

10 pages, 895 KiB

Open AccessArticle

Sputum Galactomannan Has Utility in the Diagnosis of Chronic Pulmonary Aspergillosis

by Ali Nuh, Newara Ramadan, Anand Shah and Darius Armstrong-James

J. Fungi 2022, 8(2), 188; https://doi.org/10.3390/jof8020188 - 14 Feb 2022

Cited by 5 | Viewed by 3618

Abstract

Diagnosis of pulmonary aspergillosis (PA), a fungal disease caused by Aspergillus species, is challenging since symptoms are unspecific. The galactomannan (antigen secreted by Aspergillus species) test in bronchoalveolar lavage (BAL) fluid is a valuable diagnostic adjunct test in the diagnosis of PA. [...] Read more.

Diagnosis of pulmonary aspergillosis (PA), a fungal disease caused by Aspergillus species, is challenging since symptoms are unspecific. The galactomannan (antigen secreted by Aspergillus species) test in bronchoalveolar lavage (BAL) fluid is a valuable diagnostic adjunct test in the diagnosis of PA. However, BAL collection is invasive and may not be suitable to severely ill patients. Sputum is non-invasive, easily collected, and lung specific and may be an alternative to BAL. The aim of this research was to retrospectively evaluate the utility of sputum galactomannan in the diagnosis of pulmonary aspergillosis in patients with chronic respiratory diseases and to estimate the sputum galactomannan cut-off value. We collected data from patients with clinical suspicion of pulmonary aspergillosis who had sputum galactomannan, culture, and Aspergillus IgG tests performed within four weeks. Sputum galactomannan was validated against the clinical diagnosis of aspergillosis, Aspergillus culture, and Aspergillus IgG tests. In total, 218 patients met inclusion criteria. Overall, sputum GM showed satisfactory agreement with clinical diagnosis of aspergillosis, Aspergillus culture, and Aspergillus IgG. When a receiver operating characteristic curve was constructed using Aspergillus culture/IgG and clinical diagnosis, the same cut-off (CO) of 0.71 (AUC: 0.83; CI: 0.69–0.86, p < 0.001) was determined. Against clinical diagnosis, sputum GM gave sensitivity and specificity of 70% and 71%, respectively. Sensitivity of 77% and specificity of 78% were found when sputum GM was evaluated against Aspergillus culture/IgG. In conclusion, this study showed that sputum galactomannan antigen testing has utility in the diagnosis of chronic forms of pulmonary aspergillosis and further prospective validation is indicated. Full article

(This article belongs to the Topic Infectious Diseases)

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Galactomannan index (GMI) values box plot for control group and combined clinical groups (CPA, ABPA and colonisation). Control group has significantly lower median GMI compared with the clinical groups (p < 0.001). Full article ">Figure 2
Galactomannan index (GMI) values box plot for control group, chronic pulmonary aspergillosis (CPA), allergic bronchopulmonary aspergillosis (ABPA), colonization, and Aspergillus IgG positive (AspIgG positive). Medians GMI of the control and the other groups were compared using Kruskal-Wallis test. Control group had significantly lower median GMI value compared with CPA (p < 0.001), ABPA (p = 0.018), and colonisation (p = 0.002). Full article ">Figure 3
Galactomannan index (GMI) values box plot for Aspergillus IgG/culture positive and negative groups. Groups were compared by using Mann-Whitney U test. Control group had significantly lower GMI value compared with Aspergillus IgG or culture positive group. (p < 0.001). Full article ">Figure 4
Receiver operating characteristic curve (ROC) for sputum galactomannan index value using Aspergillosis clinical diagnosis as comparator. The area under the curve (AUC) was 0.74 (95% CI: 0.65–0.83, p < 0.001). Optimal cut-off (CO) was 0.71 with Younden’s J index of 0.4. At this CO, sensitivity and specificity were 71% and 70%, respectively. Full article ">Figure 5
Receiver operating characteristic curve (ROC) for sputum galactomannan index value using mycological evidence as comparator. The area under the curve (AUC) was 0.79 (95% CI: 0.0.71–0.86, p < 0.001). Optimal cut-off (CO) was 0.71 with Younden’s J index of 0.6. At this CO point, sensitivity and specificity were 77% and 78%, respectively. Full article ">

7 pages, 237 KiB

Open AccessArticle

Low Serum Levels of Interferon Alpha in COVID-19 Patients Are Associated with Older Age

by Enagnon Kazali Alidjinou, Mickael Hirabidian, Anthony Rabat, Mahdi Ouafi, Magloire Pandoua Nekoua, Famara Sane, Julien Poissy, Didier Hober and The Lille COVID Research Network (LICORNE)

J. Clin. Med. 2022, 11(4), 961; https://doi.org/10.3390/jcm11040961 - 12 Feb 2022

Cited by 1 | Viewed by 1787

Abstract

Innate immune response, especially type 1 interferon (IFN) response is considered to play a substantial role in the outcome of SARS-CoV-2 infection. A reduced and delayed IFN response has been associated with progression to severe COVID-19. In this study, we investigated levels of [...] Read more.

Innate immune response, especially type 1 interferon (IFN) response is considered to play a substantial role in the outcome of SARS-CoV-2 infection. A reduced and delayed IFN response has been associated with progression to severe COVID-19. In this study, we investigated levels of circulating IFNα and serum neutralizing activity in COVID-19 patients admitted to the intensive care unit. We found a significant association of levels of IFNα with age (p = 0.007). This association has also been observed in a cohort of COVID-19 outpatients with mild infection (p = 0.02). The impact of senescence on IFN response can explain the higher susceptibility of the elderly to severe COVID-19. Full article

(This article belongs to the Topic Infectious Diseases)

13 pages, 1137 KiB

Open AccessArticle

Prognostic Value of Decreased High-Density Lipoprotein Cholesterol Levels in Infective Endocarditis

by Rosa Zampino, Fabian Patauner, Arta Karruli, Domenico Iossa, Maria Paola Ursi, Lorenzo Bertolino, Anna Maria Peluso, Fabiana D’Amico, Giusi Cavezza and Emanuele Durante-Mangoni

J. Clin. Med. 2022, 11(4), 957; https://doi.org/10.3390/jcm11040957 - 12 Feb 2022

Cited by 4 | Viewed by 1612

Abstract

(1) Background: Simple parameters to be used as early predictors of prognosis in infective endocarditis (IE) are lacking. The aim of this study was to evaluate the prognostic role of high-density-lipoprotein cholesterol (HDL-C) and also of total-cholesterol (TC), low-density-lipoprotein cholesterol (LDL-C), and triglycerides, [...] Read more.

(1) Background: Simple parameters to be used as early predictors of prognosis in infective endocarditis (IE) are lacking. The aim of this study was to evaluate the prognostic role of high-density-lipoprotein cholesterol (HDL-C) and also of total-cholesterol (TC), low-density-lipoprotein cholesterol (LDL-C), and triglycerides, in relation to clinical features and mortality, in IE. (2) Methods: Retrospective analysis of observational data from 127 consecutive patients with a definite diagnosis of IE between 2016 and 2019. Clinical, laboratory and echocardiography data, mortality, and co-morbidities were analyzed in relation to HDL-C and lipid profile. (3) Results: Lower HDL-C levels (p = 0.035) were independently associated with in-hospital mortality. HDL-C levels were also significantly lower in IE patients with embolic events (p = 0.036). Based on ROC curve analysis, a cut-off value was identified for HDL-C equal to 24.5 mg/dL for in-hospital mortality. HDL-C values below this cut-off were associated with higher triglyceride counts (p = 0.008), higher prevalence of S. aureus etiology (p = 0.046) and a higher in-hospital mortality rate (p = 0.004). Kaplan–Meier survival analysis showed higher 90-day mortality in patients with HDL-C ≤ 24.5 mg/dL (p = 0.001). (4) Conclusions: Low HDL-C levels could be used as an easy and low-cost marker of severity in IE, particularly to predict complications, in-hospital and 90-day mortality. Full article

(This article belongs to the Topic Infectious Diseases)

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8 pages, 621 KiB

Open AccessCase Report

The Continuing Emergence of Candida blankii as a Pathogenic Fungus: A New Case of Fungemia in a Patient Infected with SARS-CoV-2

by Ryan Mirchin, Jonathan M. Czeresnia, Erika P. Orner, Sudha Chaturvedi, Kerry Murphy and Joshua D. Nosanchuk

J. Fungi 2022, 8(2), 166; https://doi.org/10.3390/jof8020166 - 9 Feb 2022

Cited by 8 | Viewed by 2689

Abstract

Candida blankii is a recently recognized human pathogen, with most cases of the infection being reported in the immunocompromised. We here describe the case of a critically ill elderly woman with COVID-19 who developed a C. blankii bloodstream infection from a femoral central [...] Read more.

Candida blankii is a recently recognized human pathogen, with most cases of the infection being reported in the immunocompromised. We here describe the case of a critically ill elderly woman with COVID-19 who developed a C. blankii bloodstream infection from a femoral central venous catheter. Aspergillus niger was also isolated from her respiratory secretions. The patient was started on voriconazole for empiric coverage of both A. niger, and at that time, unidentified yeast was found in the blood. Fevers persisted, and the patient expired six days after the yeast was first isolated. Almost one month after her death, C. blankii was identified as the cause of fungemia by sequencing of the internal transcribed spacer (ITS) region of the ribosomal gene and BLAST searching against two databases (performed by a reference laboratory). The isolate demonstrated high minimum inhibitory concentrations (MICs) to azoles and low MICs to amphotericin B, similar to previously described isolates. Timely identification of C. blankii would have prompted different empiric antifungal choices and possibly changed the final outcome. Clinicians should be aware of the pathological potential of C. blankii, the challenges of correctly identifying the organism, and its susceptibility patterns to common antifungals. There is an urgent need to improve assays for C. blankii identification, which will aid in accurate and timely pathogen identification, and appropriate therapeutic management. Full article

(This article belongs to the Topic Infectious Diseases)

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9 pages, 231 KiB

Open AccessArticle

Factors Associated with Hepatitis B Medication Adherence and Persistence among Underserved Chinese and Vietnamese Americans

by Aisha Bhimla, Lin Zhu, Wenyue Lu, Sarit Golub, Chibuzo Enemchukwu, Elizabeth Handorf, Yin Tan, Ming-Chin Yeh, Minhhuyen T. Nguyen, Min Qi Wang and Grace X. Ma

J. Clin. Med. 2022, 11(3), 870; https://doi.org/10.3390/jcm11030870 - 7 Feb 2022

Cited by 5 | Viewed by 2268

Abstract

Background: Hepatitis B virus (HBV) infection disproportionately affects Asian Americans in the United States, while this population faces low adherence to HBV treatment. Using the information–motivation–behavioral skills model (IMB), the study aims to examine medication adherence and persistence among Chinese and Vietnamese people [...] Read more.

Background: Hepatitis B virus (HBV) infection disproportionately affects Asian Americans in the United States, while this population faces low adherence to HBV treatment. Using the information–motivation–behavioral skills model (IMB), the study aims to examine medication adherence and persistence among Chinese and Vietnamese people with HBV. Methodology: Study participants were recruited between March 2019 and March 2020 and were enrolled through multiple recruitment approaches in the Greater Philadelphia Area and New York City. The study is an assessment of the baseline data on medication adherence, HBV-related knowledge, motivation of HBV medication treatment, self-efficacy about HBV medication treatment, and socioeconomic status. Results: Among 165 participants, 77.6% were Chinese and 22.4% were Vietnamese Americans. HBV-related knowledge/information, motivation, and self-efficacy were all positively associated with having medium/high medication adherence. Multilevel mixed-effects generalized linear regression revealed that living more than 10 years in the U.S. (OR = 4.24; p = 0.028) and greater information–knowledge about HBV (OR = 1.46; p = 0.004) were statistically associated with higher odds of medium/high medication adherence. Moreover, greater HBV-related knowledge/information (OR = 1.49; p = 0.023) and greater motivation towards HBV treatment adherence (OR = 1.10; p = 0.036) were both associated with a higher likelihood of medication persistence. Conclusion: Our findings provided significant implications in designing behavioral interventions focused on self-efficacy, information, and motivation to promote better medication adherence among Asian Americans living with HBV. Full article

(This article belongs to the Topic Infectious Diseases)

17 pages, 2222 KiB

Open AccessArticle

In Vitro Inhibition of Replication of Dengue Virus Serotypes 1–4 by siRNAs Bound to Non-Toxic Liposomes

by Carlos Andrés Rodriguez-Salazar, Delia Piedad Recalde-Reyes, Juan Pablo Bedoya, Leonardo Padilla-Sanabria, Jhon Carlos Castaño-Osorio and Maria Isabel Giraldo

Viruses 2022, 14(2), 339; https://doi.org/10.3390/v14020339 - 7 Feb 2022

Cited by 3 | Viewed by 2525

Abstract

Dengue virus is a ssRNA+ flavivirus, which produces the dengue disease in humans. Currently, no specific treatment exists. siRNAs regulate gene expression and have been used systematically to silence viral genomes; however, they require controlled release. Liposomes show favorable results encapsulating siRNA for [...] Read more.

Dengue virus is a ssRNA+ flavivirus, which produces the dengue disease in humans. Currently, no specific treatment exists. siRNAs regulate gene expression and have been used systematically to silence viral genomes; however, they require controlled release. Liposomes show favorable results encapsulating siRNA for gene silencing. The objective herein was to design and evaluate in vitro siRNAs bound to liposomes that inhibit DENV replication. siRNAs were designed against DENV1–4 from conserved regions using siDirect2.0 and Web-BLOCK-iT™ RNAiDesigner; the initial in vitro evaluation was carried out through transfection into HepG2 cells. siRNA with silencing capacity was encapsulated in liposomes composed of D-Lin-MC3-DMA, DSPC, Chol. Cytotoxicity, hemolysis, pro-inflammatory cytokine release and antiviral activity were evaluated using plaque assay and RT-qPCR. A working concentration of siRNA was established at 40 nM. siRNA1, siRNA2, siRNA3.1, and siRNA4 were encapsulated in liposomes, and their siRNA delivery through liposomes led to a statistically significant decrease in viral titers, yielded no cytotoxicity or hemolysis and did not stimulate release of pro-inflammatory cytokines. Finally, liposomes were designed with siRNA against DENV, which proved to be safe in vitro. Full article

(This article belongs to the Topic Infectious Diseases)

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siRNA shows a decrease in the viral titers and relative quantification of viral genome of the DENV1–4 by plaque assay and RT-qPCR, respectively. Upper row. Effect of siRNA on the production of infectious viral particles (a) DENV1. (b) DENV2 (c) DENV3 (d) DENV4. Lower row. Expression level through relative quantification via RT-qPCR 2−ΔΔCt normalized by GAPDH. e. DENV1. f. DENV2 g. DENV3 h. DENV4. Infection control (CCI), Negative control (CN) Tukey’s multiple comparisons test * p < 0.05 ** p < 0.001 *** p < 0.0001 **** p < 0.00001. Graphic and analysis constructed in GraphPad-Prism 9. Full article ">Figure 2
Characteristic sizes of liposomes with siRNA were obtained by fluorescent microscopy and dynamic light scattering (DLS). (a) liposomes with siRNA without reduction in multilamellar size. Upper left row liposomes fluorescing in green due to the L-siRNA (FITC Conjugate)-A. Right L-siRNA (CN). Lower row liposomes with siRNA against each DENV serotype treated with Hoechst. (b) The mean size distribution of the L-siRNA is given in diameter values in nanometers (d.nm) through DLS. Full article ">Figure 3
L-siRNAs did not increase the interleukins levels evaluated. (a) L-1β. (b) TNF-α. (c) IFN-γ. (d) IL-6. The stimuli are given by: LPS (Lipopolysaccharide 100 ng/mL), RPMI 1640, liposomes-siRNA (L-siRNA1, L-siRNA2, L-siRNA3.1, L-siRNA4. As negative control, blood was used without stimulus (blood). Data are expressed as Mean + SEM of the three independent assays in triplicate. The measurement is given by the intensity in grayscale in an equivalent area in all the samples (911 square pixels). ** p < 0.001 *** p < 0.0001 **** p < 0.00001. The measurement was performed with Fiji and was represented as Log10 through GraphPad Prism 9. Full article ">Figure 4
Liposomes-siRNAs inhibit the DENV 1–4 replication. The evaluation was performed through: (a,d,g,l) Plaque assay, (b,e,h,k) relative expression of viral RNA through RT-qPCR, and (c,f,i,l) production of the NS1 protein via dot blot; the last was measured through intensity in grayscale in an equivalent area in all the samples (911 square pixels), analysis was performed with Fiji and was represented as Log10. Infection control (CCI DV), Negative control (L-siRNA (CN)). Data are expressed as Mean + SEM of the three independent assays in triplicate. Tukey’s multiple comparisons test. ** p < 0.001 *** p < 0.0001 **** p < 0.00001. Graphics and analysis constructed through GraphPad Prism 9. Full article ">

16 pages, 2528 KiB

Open AccessArticle

Strong SARS-CoV-2 N-Specific CD8⁺ T Immunity Induced by Engineered Extracellular Vesicles Associates with Protection from Lethal Infection in Mice

by Flavia Ferrantelli, Chiara Chiozzini, Francesco Manfredi, Patrizia Leone, Massimo Spada, Antonio Di Virgilio, Andrea Giovannelli, Massimo Sanchez, Andrea Cara, Zuleika Michelini and Maurizio Federico

Viruses 2022, 14(2), 329; https://doi.org/10.3390/v14020329 - 6 Feb 2022

Cited by 13 | Viewed by 3925

Abstract

SARS-CoV-2-specific CD8⁺ T cell immunity is expected to counteract viral variants in both efficient and durable ways. We recently described a way to induce a potent SARS-CoV-2 CD8⁺ T immune response through the generation of engineered extracellular vesicles (EVs) emerging from [...] Read more.

SARS-CoV-2-specific CD8⁺ T cell immunity is expected to counteract viral variants in both efficient and durable ways. We recently described a way to induce a potent SARS-CoV-2 CD8⁺ T immune response through the generation of engineered extracellular vesicles (EVs) emerging from muscle cells. This method relies on intramuscular injection of DNA vectors expressing different SARS-CoV-2 antigens fused at their N-terminus with the Nef^mut protein, i.e., a very efficient EV-anchoring protein. However, quality, tissue distribution, and efficacy of these SARS-CoV-2-specific CD8⁺ T cells remained uninvestigated. To fill the gaps, antigen-specific CD8⁺ T lymphocytes induced by the immunization through the Nef^mut-based method were characterized in terms of their polyfunctionality and localization at lung airways, i.e., the primary targets of SARS-CoV-2 infection. We found that injection of vectors expressing Nef^mut/S1 and Nef^mut/N generated polyfunctional CD8⁺ T lymphocytes in both spleens and bronchoalveolar lavage fluids (BALFs). When immunized mice were infected with 4.4 lethal doses of 50% of SARS-CoV-2, all S1-immunized mice succumbed, whereas those developing the highest percentages of N-specific CD8⁺ T lymphocytes resisted the lethal challenge. We also provide evidence that the N-specific immunization coupled with the development of antigen-specific CD8⁺ T-resident memory cells in lungs, supporting the idea that the Nef^mut-based immunization can confer a long-lasting, lung-specific immune memory. In view of the limitations of current anti-SARS-CoV-2 vaccines in terms of antibody waning and efficiency against variants, our CD8⁺ T cell-based platform could be considered for a new combination prophylactic strategy. Full article

(This article belongs to the Topic Infectious Diseases)

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14 pages, 1257 KiB

Open AccessArticle

Secondary Structure of Subgenomic RNA M of SARS-CoV-2

by Marta Soszynska-Jozwiak, Agnieszka Ruszkowska, Ryszard Kierzek, Collin A. O’Leary, Walter N. Moss and Elzbieta Kierzek

Viruses 2022, 14(2), 322; https://doi.org/10.3390/v14020322 - 4 Feb 2022

Cited by 5 | Viewed by 2903

Abstract

SARS-CoV-2 belongs to the Coronavirinae family. Like other coronaviruses, SARS-CoV-2 is enveloped and possesses a positive-sense, single-stranded RNA genome of ~30 kb. Genomic RNA is used as the template for replication and transcription. During these processes, positive-sense genomic RNA (gRNA) and subgenomic RNAs [...] Read more.

SARS-CoV-2 belongs to the Coronavirinae family. Like other coronaviruses, SARS-CoV-2 is enveloped and possesses a positive-sense, single-stranded RNA genome of ~30 kb. Genomic RNA is used as the template for replication and transcription. During these processes, positive-sense genomic RNA (gRNA) and subgenomic RNAs (sgRNAs) are created. Several studies presented the importance of the genomic RNA secondary structure in SARS-CoV-2 replication. However, the structure of sgRNAs has remained largely unsolved so far. In this study, we probed the sgRNA M model of SARS-CoV-2 in vitro. The presented model molecule includes 5′UTR and a coding sequence of gene M. This is the first experimentally informed secondary structure model of sgRNA M, which presents features likely to be important in sgRNA M function. The knowledge of sgRNA M structure provides insights to better understand virus biology and could be used for designing new therapeutics. Full article

(This article belongs to the Topic Infectious Diseases)

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14 pages, 1969 KiB

Open AccessReview

Cell-Free DNA: Potential Application in COVID-19 Diagnostics and Management

by Robert Stawski, Dariusz Nowak and Ewelina Perdas

Viruses 2022, 14(2), 321; https://doi.org/10.3390/v14020321 - 4 Feb 2022

Cited by 11 | Viewed by 3279

Abstract

WHO has declared COVID-19 as a worldwide, public health emergency. The elderly, pregnant women, and people with associated co-morbidities, including pulmonary disease, heart failure, diabetes, and cancer are the most predisposed population groups to infection. Cell-free DNA is a very commonly applied marker, [...] Read more.

WHO has declared COVID-19 as a worldwide, public health emergency. The elderly, pregnant women, and people with associated co-morbidities, including pulmonary disease, heart failure, diabetes, and cancer are the most predisposed population groups to infection. Cell-free DNA is a very commonly applied marker, which is elevated in various pathological conditions. However, it has a much higher sensitivity than standard biochemical markers. cfDNA appears to be an effective marker of COVID-19 complications, and also serves as a marker of certain underlying health conditions and risk factors of severe illness during COVID-19 infection. We aimed to present the possible mechanisms and sources of cfDNA released during moderate and severe infections. Moreover, we attempt to verify how efficiently cfDNA increase could be applied in COVID-19 risk assessment and how it corresponds with epidemiological data. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 3779 KiB

Open AccessArticle

Repurposing Based Identification of Novel Inhibitors against MmpS5-MmpL5 Efflux Pump of Mycobacterium smegmatis: A Combined In Silico and In Vitro Study

by Mohd Shahbaaz, Dmitry A. Maslov, Aleksey A. Vatlin, Valery N. Danilenko, Maria Grishina and Alan Christoffels

Biomedicines 2022, 10(2), 333; https://doi.org/10.3390/biomedicines10020333 - 31 Jan 2022

Cited by 2 | Viewed by 3524

Abstract

In the current era of a pandemic, infections of COVID-19 and Tuberculosis (TB) enhance the detrimental effects of both diseases in suffering individuals. The resistance mechanisms evolving in Mycobacterium tuberculosis are limiting the efficiency of current therapeutic measures and pressurizing the stressed medical [...] Read more.

In the current era of a pandemic, infections of COVID-19 and Tuberculosis (TB) enhance the detrimental effects of both diseases in suffering individuals. The resistance mechanisms evolving in Mycobacterium tuberculosis are limiting the efficiency of current therapeutic measures and pressurizing the stressed medical infrastructures. The bacterial efflux pumps enable the development of resistance against recently approved drugs such as bedaquiline and clofazimine. Consequently, the MmpS5-MmpL5 protein system was selected because of its role in efflux pumping of anti-TB drugs. The MmpS5-MmpL5 systems of Mycobacterium smegmatis were modelled and the virtual screening was performed using an ASINEX library of 5968 anti-bacterial compounds. The inhibitors with the highest binding affinities and QSAR based highest predicted inhibitory concentration were selected. The MmpS5-MmpL5 associated systems with BDE_26593610 and BDD_27860195 showed highest inhibitory parameters. These were subjected to 100 ns Molecular Dynamics simulations and provided the validation regarding the interaction studies. The in vitro studies demonstrated that the BDE_26593610 and BDD_27860195 can be considered as active inhibitors for M. smegmatis MmpS5-MmpL5. The outcomes of this study can be utilized in other experimentation aimed at drug design and discovery against the drug resistance strains of M. tuberculosis. Full article

(This article belongs to the Topic Infectious Diseases)

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The graphical representation of the MmpS5-MmpL5 docked complexes with (A) BDD_27860195 and (B) BDE_26593610. Full article ">Figure 2
The graphical representation of assembled mmpS5-mmpL5 with compounds BDD_27869195 and BDE_26593610. (A) shows MmpS5-MmpL5 with compound BDD_27869195 (Blue). (B) shows MmpS5-MmpL5 with compound BDE_26593610 (Blue). Full article ">Figure 3
The outcomes of 100 ns MD simulations showing (A) Changes in the RMSD values reflecting the variations in the topologies for both the systems (Standard Deviation (SD), BDD_27869195 = 0.035 nm, BDE_26593610 = 0.05 nm). (B) Fluctuation in the Rg values shows the changes in the compactness of the studied systems (SD, BDD_27869195 = 0.029 nm, BDE_26593610 = 0.07 nm). (C) Dynamics of the H-bond patterns were observed for both systems (SD, BDD_27869195 = 0.89, BDE_26593610 = 0.29). (D) Differences in the calculated distance values for both the studied systems (SD, BDD_27869195 = 0.02 nm, BDE_26593610 = 0.03 nm). Full article ">Figure 4
The calculated free energy landscapes showing the changes in the conformational stability (PC1 is RMSD and PC2 is Rg). Full article ">Figure 5
Growth inhibition halos, produced by 3a and its combination with MmpS5-MmpL5inhibitors: (A) at 10 nmol/disc, and (B) at 50 nmol/disc. The error bars represent the SDs. Full article ">Figure 6
Growth inhibition halos, produced by the combination of 50 nmol/disc MmpS5-MmpL5inhibitors (25 nmol/disc for LAS_52157603) with (A) TRP and (B) PK31. The error bars represent the SDs. Full article ">

12 pages, 723 KiB

Open AccessArticle

Increasing Terbinafine Resistance in Danish Trichophyton Isolates 2019–2020

by Karen Marie Thyssen Astvad, Rasmus Krøger Hare, Karin Meinike Jørgensen, Ditte Marie Lindhardt Saunte, Philip Kjettinge Thomsen and Maiken Cavling Arendrup

J. Fungi 2022, 8(2), 150; https://doi.org/10.3390/jof8020150 - 31 Jan 2022

Cited by 47 | Viewed by 4410 | Correction

Abstract

Terbinafine resistance in Trichophyton species has emerged and appears to be increasing. A new EUCAST susceptibility testing method and tentative ECOFFs were recently proposed for Trichophyton. Terbinafine resistance and target gene mutations were detected in 16 Danish isolates in 2013–2018. In this [...] Read more.

Terbinafine resistance in Trichophyton species has emerged and appears to be increasing. A new EUCAST susceptibility testing method and tentative ECOFFs were recently proposed for Trichophyton. Terbinafine resistance and target gene mutations were detected in 16 Danish isolates in 2013–2018. In this study, samples/isolates submitted for dermatophyte susceptibility testing 2019–2020 were examined. Species identification (ITS sequencing for T. mentagrophytes/T. interdigitale species complex (SC) isolates), EUCAST MICs and squalene epoxidase (SQLE) profiles were obtained. Sixty-three isolates from 59 patients were included. T. rubrum accounted for 81% and T. mentagrophytes/T. interdigitale SC for 19%. Approximately 60% of T. rubrum and T. mentagrophytes/interdigitale SC isolates were terbinafine non-wildtype and/or had known/novel SQLE mutations with possible implications for terbinafine MICs. All infections with terbinafine-resistant T. mentagrophytes/interdigitale SC isolates were caused by Trichophyton indotineae. Compared to 2013–2018, the number of patients with terbinafine-resistant Trichophyton isolates increased. For T. rubrum, this is partly explained by an increase in number of requests for susceptibility testing. Terbinafine-resistant T. indotineae was first detected in 2018, but accounted for 19% of resistance (4 of 21 patients) in 2020. In conclusion, terbinafine resistance is an emerging problem in Denmark. Population based studies are warranted and susceptibility testing is highly relevant in non-responding cases. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 1153 KiB

Open AccessArticle

Impact of COVID-19-Related Lockdown on Delivery and Perinatal Outcomes: A Retrospective Cohort Study

by Thibaud Quibel, Norbert Winer, Laurence Bussières, Christophe Vayssière, Philippe Deruelle, Manon Defrance, Patrick Rozenberg, Jean Bouyer, Ninon Dupuis, Benoit Renaudin, Louise Dugave, Nathalie Banaszkiewicz, Charles Garabedian and Yves Ville

J. Clin. Med. 2022, 11(3), 756; https://doi.org/10.3390/jcm11030756 - 30 Jan 2022

Cited by 2 | Viewed by 2740

Abstract

Objective: The magnitude and direction of effects on pregnancy outcomes of the lockdown imposed during COVID-19 have been uncertain and debated. Therefore, we aimed to quantify delivery and perinatal outcomes during the first nationwide lockdown due to the COVID-19 pandemic compared with the [...] Read more.

Objective: The magnitude and direction of effects on pregnancy outcomes of the lockdown imposed during COVID-19 have been uncertain and debated. Therefore, we aimed to quantify delivery and perinatal outcomes during the first nationwide lockdown due to the COVID-19 pandemic compared with the same durations of time for the pre- and post-lockdown periods. Study design: This was a retrospective cohort study of six university hospital maternity units distributed across France, each of which serves as the obstetric care referral unit within its respective perinatal network. Maternal and perinatal outcomes were compared between the lockdown period and same-duration (i.e., 55-day) periods before and after the 2020 lockdown (pre-lockdown: 22 January–16 March; lockdown: 17 March–10 May; post-lockdown: 11 May–4 July). We compared the overall rates of Caesarean delivery (CD), pre-labor CD, labor induction, operative vaginal delivery, severe postpartum hemorrhage (≥1 L), severe perineal tear, maternal transfusion, and neonatal mortality and morbidity (1- and 5-min Apgar scores < 7), hypoxia and anoxia (umbilical arterial pH < 7.20 or <7.10, respectively), and admission to a neonatal intensive care unit before discharge. Adjusted odds ratios were estimated using logistic regression, controlling for region of birth, maternal age category, multiparity, multiple pregnancies, diabetes, and hypertensive disorders. Results: The study sample consisted of 11,929 women who delivered consecutively at one of the six maternity units studied (4093 pre-lockdown, 3829 during lockdown, and 4007 post-lockdown) and their 12,179 neonates (4169 pre-lockdown, 3905 during lockdown, and 4105 post-lockdown). The maternal and obstetric characteristics of the women delivering during the lockdown period were alike those delivering pre- and post-lockdown on maternal age, parity, body mass index, rate of complication by hypertensive disorders or insulin-treated diabetes, and gestational age at delivery. Overall CD rates were similar during the three periods (23.6%, 24.8%, and 24.3% pre-lockdown, lockdown, and post-lockdown, respectively) and no outcome differed significantly during lockdown compared to pre- and post-lockdown. These findings were consistent across maternity units. Conclusion: The maternal and perinatal outcomes are reassuring regarding the performance of the health-care system during the COVID-19 lockdown studied. Such information is crucial, because additional COVID-19-related lockdowns might still be needed. They are also instructive regarding potential future pandemics. Full article

(This article belongs to the Topic Infectious Diseases)

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18 pages, 4125 KiB

Open AccessArticle

Identification, Structure and Characterization of Bacillus tequilensis Biofilm with the Use of Electrophoresis and Complementary Approaches

by Katarzyna Pauter, Viorica Railean-Plugaru, Michał Złoch, Paweł Pomastowski, Małgorzata Szultka-Młyńska and Bogusław Buszewski

J. Clin. Med. 2022, 11(3), 722; https://doi.org/10.3390/jcm11030722 - 29 Jan 2022

Cited by 6 | Viewed by 2220

Abstract

Biofilm is a complex structure formed as a result of the accumulation of bacterial cell clusters on a surface, surrounded by extracellular polysaccharide substances (EPSs). Biofilm-related bacterial infections are a significant challenge for clinical treatment. Therefore, the main goal of our study was [...] Read more.

Biofilm is a complex structure formed as a result of the accumulation of bacterial cell clusters on a surface, surrounded by extracellular polysaccharide substances (EPSs). Biofilm-related bacterial infections are a significant challenge for clinical treatment. Therefore, the main goal of our study was to design a complementary approach in biofilm characterization before and after the antibiotic treatment. The 16S rRNA gene sequencing allowed for the identification of Bacillus tequilensis, as a microbial model of the biofilm formation. Capillary electrophoresis demonstrates the capability to characterize and show the differences of the electrophoretic mobility between biofilms untreated and treated with antibiotics: amoxicillin, gentamicin and metronidazole. Electrophoretic results show the clumping phenomenon (amoxicillin and gentamicin) as a result of a significant change on the surface electric charge of the cells. The stability of the dispersion study, the molecular profile analysis, the viability of bacterial cells and the scanning morphology imaging were also investigated. The microscopic and spectrometry study pointed out the degradation/remodeling of the EPSs matrix, the inhibition of the cell wall synthesis and blocking the ribosomal protein synthesis by amoxicillin and gentamicin. However, untreated and treated bacterial cells show a high stability for the biofilm formation system. Moreover, on the basis of the type of the antibiotic treatment, the mechanism of used antibiotics in cell clumping and degradation were proposed. Full article

(This article belongs to the Topic Infectious Diseases)

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The evolutionary timeline of the study bacteria as a phylogenetic tree. *—indicate the isolated strain and used in present study. Full article ">Figure 2
Electropherograms of the B. tequilensis treated antibiotics. Electrophoretic conditions: inlet buffer TB (pH 7.3), outlet buffer TBH (pH 8.0), U—20 kV, T—25 °C, injection—8 psi/10 s, λ = 214 nm, capillary—Ltot = 70 cm; Leff = 50 cm; and i.d. 75 μm. ΣSAS—sum of surface area signal. Full article ">Figure 3
MALDI-TOF MS mass spectra of bacteria—Bacillus tequilenis after influence of antibiotic drugs. (A) main MS spectra, (B,C) represent the zooms MS spectra. Full article ">Figure 4
Comparison of signals noticed on MALDI-TOF mass spectra for Bacillus tequilensis (control) and under antibiotics treatment: (A) control, (B) B. tequilensis/metronidazole, (C) B. tequilensis/amoxicillin, (D) B. tequilensis/gentamicin. #1—3711 m/z, #2—5190 m/z, #3—5248, #4—5294 m/z, #5—6184 m/z, #6—6435 m/z, #7–6720 m/z, #8—9552 m/z, #9—9722 m/z, #10—9878 m/z. Full article ">Figure 5
Fluorescence images of the biofilm formed by B. tequilensis bacteria treated with antibiotics, at magnifications of 100×. Full article ">Figure 6
SEM images of the biofilm formed by B. tequilensis bacteria treated with antibiotics, before capillary electrophoresis at magnifications of 10.000×; 25.000× and 50.000× respectively. Full article ">Figure 7
SEM images of the biofilm formed by B. tequilensis bacteria treated with antibiotics, after capillary electrophoresis, at magnifications of 1.000×; 2.500×; 10.000×; 25.000× and 50.000× respectively. Full article ">Figure 8
Scheme of mechanism of bacterial biofilm response—B. tequilensis. Full article ">

12 pages, 981 KiB

Open AccessArticle

Female Reproductive Factors and the Risk of Bronchiectasis: A Nationwide Population-Based Longitudinal Study

by Bumhee Yang, Dong-Hwa Lee, Kyungdo Han, Hayoung Choi, Hyung Koo Kang, Dong Wook Shin and Hyun Lee

Biomedicines 2022, 10(2), 303; https://doi.org/10.3390/biomedicines10020303 - 28 Jan 2022

Cited by 3 | Viewed by 2448

Abstract

Although the oestrogen level is thought to be involved in the occurrence of bronchiectasis, limited data are available on the relationship between female reproductive factors and the risk of bronchiectasis. We performed a population-based retrospective cohort study of 959,523 premenopausal women and 1,362,401 [...] Read more.

Although the oestrogen level is thought to be involved in the occurrence of bronchiectasis, limited data are available on the relationship between female reproductive factors and the risk of bronchiectasis. We performed a population-based retrospective cohort study of 959,523 premenopausal women and 1,362,401 postmenopausal women without a previous history of bronchiectasis who participated in a health screening exam in 2009 in South Korea. In premenopausal women, compared with a later age at menarche (≥16 years), an earlier menarche (<12 years) was associated with a reduced risk of bronchiectasis with an adjusted hazard ratio (aHR) (95% confidence interval (CI)) of 0.74 (0.67–0.81). However, there were no significant associations between other reproductive factors (breastfeeding, parity, or oral contraceptive use) and the risk of bronchiectasis. In postmenopausal women, the risk of bronchiectasis (aHR (95% CI)) was lower in those with an earlier menarche (0.79 (0.72–0.87) for <12 years vs. ≥16 years), a later menopause (0.90 (0.84–0.96) ≥55 years vs. <40 years), and a longer reproductive period (0.90 (0.86–0.94) for ≥40 years vs. <30 years). There was no significant relationship between parity and the risk of bronchiectasis. Although breastfeeding <1 year (aHR (95% CI) = 0.92 (0.87–0.97) for <0.5 years and 0.93 (0.88–0.97) for 0.5–1 years) and oral contraceptive use <1 year (0.97 (0.94–0.99)) reduced the risk of bronchiectasis, hormone replacement therapy ≥5 years increased the risk of bronchiectasis (1.24 (1.18–1.30)). Female reproductive factors are risk factors for developing bronchiectasis, showing a higher risk associated with shorter endogenous oestrogen exposure regardless of the menopausal status. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 7713 KiB

Open AccessArticle

Serological Changes in Anti-Aspergillus IgG Antibody and Development of Chronic Pulmonary Aspergillosis in Patients Treated for Pulmonary Tuberculosis

by Changwhan Kim, Jin-Wook Moon, Yong-Bum Park and Yousang Ko

J. Fungi 2022, 8(2), 130; https://doi.org/10.3390/jof8020130 - 28 Jan 2022

Cited by 9 | Viewed by 2789

Abstract

Chronic pulmonary aspergillosis (CPA) is an important infection to understand in survivors of pulmonary tuberculosis (PTB). However, limited data are available regarding CPA development and its predisposing factors following PTB. We investigated the development of, and the predisposing factors for, CPA following the [...] Read more.

Chronic pulmonary aspergillosis (CPA) is an important infection to understand in survivors of pulmonary tuberculosis (PTB). However, limited data are available regarding CPA development and its predisposing factors following PTB. We investigated the development of, and the predisposing factors for, CPA following the completion of PTB treatment. A total of 345 patients, with newly diagnosed culture-positive PTB (between January 2015 and December 2018), were included. Enrolled cases were categorized into four groups (persistently seronegative, seroconversion, seroreversion, and persistently seropositive) according to serological changes in their anti-Aspergillus IgG antibodies before and after PTB treatment. The patients were followed up for a median of 25.8 months. Ten (10/345, 2.9%) patients developed CPA at a median of 13.5 months after treatment completion, including seven (7/24, 29.2%) and three (3/73, 4.1%) in the seroconversion and persistently seropositive groups, respectively. Upon multivariate analysis, seroconversion of anti-Aspergillus IgG antibody (adjusted hazard ratio [HR], 25.21; 95% confidence interval [CI], 6.11–103.99; p < 0.001) and diabetic status (adjusted HR, 7.54; 95% CI, 1.93–29.50; p = 0.004) were independently associated with CPA development. The development of CPA in patients with PTB was observed in 2.9% of patients during post-treatment follow-up, and this was significantly associated with both the seroconversion of anti-Aspergillus IgG antibody and diabetes characteristics. Full article

(This article belongs to the Topic Infectious Diseases)

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The study population according to results of anti-Aspergillus IgG antibody investigations. Full article ">Figure 2
Seropositivity rates for anti-Aspergillus IgG antibody. (a) Change in levels according to serological group (b) before and after anti-TB treatment. In <a href="#jof-08-00130-f002" class="html-fig">Figure 2</a>b, anti-Aspergillus antibody levels are presented according to serotype as the mean with standard error of the mean. Full article ">Figure 3
Chest images of patients with chronic pulmonary aspergillosis (CPA) after pulmonary tuberculosis (PTB). (a–e) A 53-year-old man was diagnosed with CPA after PTB in the seroconversion group. A chest image from September 2018 showed residual lung damage in both upper lungs. Approximately 11 months later, the patient had respiratory symptoms, including cough and productive sputum with hemoptysis. (c,e) display a new possible fungal infiltration in the scar in the left upper lung. (f–k) A 33-year-old man who was previously treated for PTB (five years prior) was diagnosed with CPA after a second instance of PTB in the persistently seropositive group. Serial chest images showed that primary PTB lesions resolved with anti-PTB treatment and aggravated with new fungal infection. Abbreviations: CPA, chronic pulmonary aspergillosis; and PTB, pulmonary tuberculosis. Full article ">Figure 4
Cumulative development rate of chronic pulmonary aspergillosis (CPA) according to serological results for anti-Aspergillus IgG antibody. Abbreviations: CPA, chronic pulmonary aspergillosis; and PTB, pulmonary tuberculosis. Full article ">Figure 5
Changes in anti-Aspergillus IgG levels at different time points in patients diagnosed with CPA. Abbreviations: CPA, chronic pulmonary aspergillosis; and PTB, pulmonary tuberculosis. Full article ">

9 pages, 8156 KiB

Open AccessArticle

Kinetics of Glycoprotein-Specific Antibody Response in Patients with Severe Fever with Thrombocytopenia Syndrome

by Hyemin Chung, Eunsil Kim, Bomin Kwon, Yeong-Geon Cho, Seongman Bae, Jiwon Jung, Min-Jae Kim, Yong-Pil Chong, Sung-Han Kim, Sang-Oh Lee, Sang-Ho Choi, Yang-Soo Kim and Korea SFTS Study Group

Viruses 2022, 14(2), 256; https://doi.org/10.3390/v14020256 - 27 Jan 2022

Cited by 1 | Viewed by 2697

Abstract

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tickborne disease in East Asia that is causing high mortality. The Gn glycoprotein of the SFTS virus (SFTSV) has been considered to be an essential target for virus neutralization. However, data on anti-Gn glycoprotein [...] Read more.

Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tickborne disease in East Asia that is causing high mortality. The Gn glycoprotein of the SFTS virus (SFTSV) has been considered to be an essential target for virus neutralization. However, data on anti-Gn glycoprotein antibody kinetics are limited. Therefore, we investigated the kinetics of Gn-specific antibodies compared to those of nucleocapsid protein (NP)-specific antibodies. A multicenter prospective study was performed in South Korea from January 2018 to September 2021. Adult patients with SFTS were enrolled. Anti-Gn-specific IgM and IgG were measured using an enzyme-linked immunosorbent assay. A total of 111 samples from 34 patients with confirmed SFTS were analyzed. Anti-Gn-specific IgM was detected at days 5–9 and peaked at day 15–19 from symptom onset, whereas the anti-NP-specific IgM titers peaked at days 5–9. Median seroconversion times of both anti-Gn- and NP-specific IgG were 7.0 days. High anti-Gn-specific IgG titers were maintained until 35–39 months after symptom onset. Only one patient lost their anti-Gn-specific antibodies at 41 days after symptom onset. Our data suggested that the anti-Gn-specific IgM titer peaked later than anti-NP-specific IgM, and that anti-Gn-specific IgG remain for at least 3 years from symptom onset. Full article

(This article belongs to the Topic Infectious Diseases)

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24 pages, 1059 KiB

Open AccessReview

Aspirin and Infection: A Narrative Review

by Stefano Di Bella, Roberto Luzzati, Luigi Principe, Verena Zerbato, Elisa Meroni, Mauro Giuffrè, Lory Saveria Crocè, Marco Merlo, Maria Perotto, Elisabetta Dolso, Cristina Maurel, Antonio Lovecchio, Eugenia Dal Bo, Cristina Lagatolla, Bruna Marini, Rudy Ippodrino and Gianfranco Sanson

Biomedicines 2022, 10(2), 263; https://doi.org/10.3390/biomedicines10020263 - 25 Jan 2022

Cited by 12 | Viewed by 10292

Abstract

Acetylsalicylic acid (ASA) is one of the most commonly used drugs in the world. It derives from the extract of white willow bark, whose therapeutic potential was known in Egypt since 1534 BC. ASA’s pharmacological effects are historically considered secondary to its anti-inflammatory, [...] Read more.

Acetylsalicylic acid (ASA) is one of the most commonly used drugs in the world. It derives from the extract of white willow bark, whose therapeutic potential was known in Egypt since 1534 BC. ASA’s pharmacological effects are historically considered secondary to its anti-inflammatory, platelet-inhibiting properties; however, human studies demonstrating a pro-inflammatory effect of ASA exist. It is likely that we are aware of only part of ASA’s mechanisms of action; moreover, the clinical effect is largely dependent on dosages. During the past few decades, evidence of the anti-infective properties of ASA has emerged. We performed a review of such research in order to provide a comprehensive overview of ASA and viral, bacterial, fungal and parasitic infections, as well as ASA’s antibiofilm properties. Full article

(This article belongs to the Topic Infectious Diseases)

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13 pages, 2786 KiB

Open AccessArticle

Hyperendemic Dengue and Possible Zika Circulation in the Westernmost Region of the Indonesian Archipelago

by Harapan Harapan, Kritu Panta, Alice Michie, Timo Ernst, Suzi McCarthy, Muhsin Muhsin, Safarianti Safarianti, Tjut Mariam Zanaria, Mudatsir Mudatsir, R. Tedjo Sasmono and Allison Imrie

Viruses 2022, 14(2), 219; https://doi.org/10.3390/v14020219 - 24 Jan 2022

Cited by 2 | Viewed by 3653

Abstract

The transmission of dengue and other medically important mosquito-borne viruses in the westernmost region of Indonesia is not well described. We assessed dengue and Zika virus seroprevalence in Aceh province, the westernmost area of the Indonesian archipelago. Serum samples collected from 199 randomly [...] Read more.

The transmission of dengue and other medically important mosquito-borne viruses in the westernmost region of Indonesia is not well described. We assessed dengue and Zika virus seroprevalence in Aceh province, the westernmost area of the Indonesian archipelago. Serum samples collected from 199 randomly sampled healthy residents of Aceh Jaya in 2017 were analyzed for neutralizing antibodies by plaque reduction neutralization test (PRNT). Almost all study participants (198/199; 99.5%) presented with multitypic profiles of neutralizing antibodies to two or more DENV serotypes, indicating transmission of multiple DENV in the region prior to 2017. All residents were exposed to one or more DENV serotypes by the age of 30 years. The highest geometric mean titers were measured for DENV-4, followed by DENV-1, DENV-2 and DENV-3. Among a subset of 116 sera, 27 neutralized ZIKV with a high stringency (20 with PRNT₉₀ > 10 and 7 with PRNT₉₀ > 40). This study showed that DENV is hyperendemic in the westernmost region of the Indonesian archipelago and suggested that ZIKV may have circulated prior to 2017. Full article

(This article belongs to the Topic Infectious Diseases)

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Number of participants based on age and gender (n = 199). Full article ">Figure 2
Status of DENV infection by age group (n = 199). Status of individuals with naïve, monotypic, or multitypic infections classified using two thresholds (PRNT50 and PRNT90 at >10). For each threshold, all monotypic infections were observed in individuals younger than 30 years old. Full article ">Figure 3
Geometric mean titers (GMT) of DENV NAb at two different thresholds: PRNT50 (A) and PRNT90 (B) (n = 199). Neutralizing antibody (NAb) GMTs were interpolated using non-linear regression. Full article ">Figure 4
Stratification of geometric mean titer (GMT) of DENV neutralizing antibody (NAb) titers by age (n = 199). DENV NAb GMTs for each age group for all serotypes were calculated based on two thresholds PRNT50 (blue), and PRNT90 (red). Full article ">Figure 5
Geometric mean titer (GMT) of ZIKV neutralizing antibody (NAb) and the distribution of ZIKV NAb-positive sera at different thresholds (n = 116). (A) GMT of ZIKV NAb using two thresholds (PRNT50 and PRNT90). (B) ZIKV seropositive sera were classified using a combination of four cut-offs (two thresholds of plaque reductions percentage and two cut-offs for serum dilutions). Full article ">Figure 6
Geometric mean titers (GMTs) of ZIKV neutralizing antibody (NAb) at two thresholds (PRNT50 and PRNT90). Full article ">Figure 7
Neutralizing antibody (NAb) titers for ZIKV and DENV at PRNT90 (n = 116). (A) ZIKV NAb titers and corresponding DENV NAb titers were plotted to show dengue infection background. (B) For seven serum samples that had ZIKV NAb titers > 40, the DENV NAb titers were plotted individually and the GMTs were calculated. Using criteria developed in the Indonesian context [<a href="#B34-viruses-14-00219" class="html-bibr">34</a>] none of the samples can be classified as ZIKV-seropositive. One dot indicates an individual sample; grey dots indicate samples that have ZIKV NAb titers < 40 at PRNT90, while colored dots represent samples that had ZIKV NAb titers > 40 at PRNT90. Full article ">

16 pages, 8253 KiB

Open AccessArticle

Borrelia burgdorferi Outer Membrane Vesicles Contain Antigenic Proteins, but Do Not Induce Cell Death in Human Cells

by Kati Karvonen, Hanna Tammisto, Jonna Nykky and Leona Gilbert

Microorganisms 2022, 10(2), 212; https://doi.org/10.3390/microorganisms10020212 - 19 Jan 2022

Cited by 6 | Viewed by 3331

Abstract

Like many bacterial species, Borrelia burgdorferi, the pleomorphic bacterium that causes Lyme borreliosis, produces outer membrane vesicles (OMVs). Borrelial OMVs (BbOMVs) have been identified as containing virulence factors, such as outer surface proteins (Osps) A, B, and C, as well as DNA. [...] Read more.

Like many bacterial species, Borrelia burgdorferi, the pleomorphic bacterium that causes Lyme borreliosis, produces outer membrane vesicles (OMVs). Borrelial OMVs (BbOMVs) have been identified as containing virulence factors, such as outer surface proteins (Osps) A, B, and C, as well as DNA. However, the pathogenicity of BbOMVs in disease development is still unclear. In this study, we characterized purified BbOMVs by analyzing their size and immunolabeling for known antigenic markers: OspA, OspC, p39, and peptidoglycan. In addition, BbOMVs were cocultured with human non-immune cells for cytotoxicity analysis. The results demonstrated that, on average, the vesicles were small, ranging between 11 and 108 nm in diameter. In addition, both OspA and OspC, as well as Lyme arthritis markers p39 and peptidoglycan, were detected from BbOMVs. Furthermore, BbOMVs were cocultured with non-immune cells, which did not result in cell death. Combined, these results suggested that BbOMVs could participate in the induction of infection by functioning as a decoy for the host immune system. Furthermore, BbOMVs might serve as a means for persistent antigens to remain in the host for prolonged periods of time. Full article

(This article belongs to the Topic Infectious Diseases)

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B. burgdorferi outer membrane vesicles (BbOMVs) were, on average, 33 nm in diameter. Purified BbOMVs were numerated (n = 600) and their diameters measured from negatively stained transmission electron micrographs, and were then divided into four size categories: 0–20, 20.1–60, 60.1–100, and 100.1–140 nm. The average diameters in each category are presented. The combined average diameter of a BbOMV was 33 nm. Full article ">Figure 2
BbOMVs could be successfully and reproducibly purified from Borrelia cultures. (A) Transmission electron micrographs of epon embedded samples of purified BbOMVs demonstrating spherical shapes with single bilayer membranes. (B) As a control for purification, epon embedded B. burgdorferi spirochetes with a zoomed image (black box) of blebbing and BbOMVs directly originating from the bacterial cells are presented. White arrows indicate both clusters and separate BbOMVs in the purified vesicle and spirochete samples. Scale bars: A: 100 nm, B: 500 nm. Full article ">Figure 3
B. burgdorferi outer membrane vesicles contained several antigenic markers. (A) BbOMVs contained double stranded DNA, which was measured using a Qubit 2.0 fluorometer with a broad-range stain. Standard deviations from triplicate experiments. (B) Proteins were resolved with SDS-PAGE and stained with Coomassie Blue, while a Pierce Glycoprotein staining kit (Thermo scientific) was used for visualizing glycoproteins (C). Western blot analysis demonstrated known borrelial antigens OspA (D), OspC (E), peptidoglycan (F), and p39 (G). Anti-B. burgdorferi whole cell antibody was examined as a control (H). For the protein analysis, H2O was used as a negative control, and albumin (lane 2) as a positive control, for the staining. The negative (−, soybean trypsin inhibitor) and positive (+, horseradish peroxidase) controls provided by the glycoprotein staining kit were employed in the analysis. In the Western blots, albumin was utilized as a negative control for the immunolabel. B. burgdorferi strains GCBC (lane 1) and B31 (lane 6) bacterial cell lysates were used as positive controls for the labels in each experiment. Lanes 3 and 4 demonstrate BbOMVs purified from CGBC culture, while lane 5 has B31 purified BbOMVs. In order to obtain the full range of signals, the intensity values were analyzed from each lane in the Coomassie Blue and glycoprotein gels, as well as in the peptidoglycan and anti-B. burgdorferi labeled blots. Whereas the signals from specific bands representing each expected protein (black box) in OspA, OspC, and p39 blots were examined. Values were normalized to the positive controls: borrelial cell lysates in Coomassie Blue stained gel and western blots, and the kit provided positive control (horseradish peroxidase) in the glycoprotein gel. GCBC BbOMVs and albumin were normalized to GCBC lysates, and the B31 BbOMVs to the B31 lysate. Representative images from three separate experiments. Full article ">Figure 4
BbOMVs did not induce cell death in human cells. In order to detect different stages of cellular viability after infection, SW1353 (A) and BJ (B) cells were infected with B. burgdorferi spirochetes (MOI 40), RBs (MOI 40) and BbOMVs (50 µg/mL), respectively, for 72 h and double labelled with DNA (7-AAD) and pan-caspase inhibitor-fluorochrome complex (FAM-VAD-FMK) markers. Untreated cells were used as negative control and 1 µM staurosporine treated (2 h) cells were a positive control for apoptosis (cell death). The samples were analyzed with Guava easyCyte 8HT flow cytometer. Standard deviations from triplicate experiments. Statistical significance was compared to both negative and positive controls. * p ≤ 0.05; ** p ≤ 0.01; *** p ≤ 0.001. (C) Representative dot plots of SW1353 (top row) and BJ (bottom row) cells from the abovementioned experiment. In the graphs, viable cells are located at the bottom left corner, early apoptotic at the bottom right corner, late apoptotic/ necrotic cells at the top right corner, and dead cells at the top left corner. Full article ">

16 pages, 276 KiB

Open AccessArticle

Real-World Use of Isavuconazole as Primary Therapy for Invasive Fungal Infections in High-Risk Patients with Hematologic Malignancy or Stem Cell Transplant

by Hiba Dagher, Ray Hachem, Anne-Marie Chaftari, Ying Jiang, Shahnoor Ali, Rita Deeba, Shivan Shah and Issam Raad

J. Fungi 2022, 8(1), 74; https://doi.org/10.3390/jof8010074 - 13 Jan 2022

Cited by 9 | Viewed by 3667

Abstract

(1) Introduction: Invasive fungal infections (IFIs) are a major cause of morbidity and mortality among immunocompromised patients with hematologic malignancies (HM) and stem cell transplants (SCT). Isavuconazole was approved by FDA as a primary therapy for Invasive Aspergillosis (IA) and Mucormycosis. The aim [...] Read more.

(1) Introduction: Invasive fungal infections (IFIs) are a major cause of morbidity and mortality among immunocompromised patients with hematologic malignancies (HM) and stem cell transplants (SCT). Isavuconazole was approved by FDA as a primary therapy for Invasive Aspergillosis (IA) and Mucormycosis. The aim of this study is to look at the real-world use of Isavuconazole in patients with HM and evaluate their clinical outcomes and safety. (2) Methods: We conducted a retrospective study of HM patients at MD Anderson Cancer Center who had definite, probable or possible mold infections between 1 April 2016 and 31 January 2020 and were treated with Isavuconazole for a period of at least 7 days. Clinical and radiological findings were assessed at baseline and at 6 and 12 weeks of follow up. (3) Results: We included 200 HM patients with IFIs that were classified as definite (11), probable (63) and possible (126). Aspergillus spp was the most commonly isolated pathogen. The majority of patients (59%) received prophylaxis with anti-mold therapy and Isavuconazole was used as a primary therapy in 43% of patients, and as salvage therapy in 58%. The switch to Isavuconazole was driven by the failure of the primary therapy in 66% of the cases and by adverse effects in 29%. Isavuconazole was used as monotherapy in 30% of the cases and in combination in 70%. Adverse events possibly related to Isavuconazole were reported in eight patients (4%) leading to drug discontinuation. Moreover, a favorable response with Isavuconazole was observed in 40% at 6 weeks and in 60% at 12 weeks. There was no significant difference between isavuconazole monotherapy and combination therapy (p = 0.16 at 6 weeks and p = 0.06 at 12 weeks). Finally, there was no significant difference in outcome when Isavuconazole was used after failure of other anti-mold prophylaxis or treatment versus when used de novo as an anti-mold therapy (p = 0.68 at 6 weeks and p = 0.25 at 12 weeks). (4) Conclusions: Whether used as first-line therapy or after the failure of other azole and non-azole prophylaxis or therapies, isavuconazole seems to have a promising clinical response and a good safety profile as an antifungal therapy in high-risk cancer patients with hematologic malignancies. Moreover, combination therapy did not improve the outcome compared to Isavuconazole therapy. Full article

(This article belongs to the Topic Infectious Diseases)

15 pages, 458 KiB

Open AccessArticle

Molecular Epidemiology of Rotavirus Strains in Symptomatic and Asymptomatic Children in Manhiça District, Southern Mozambique 2008–2019

by Filomena Manjate, Eva D. João, Percina Chirinda, Marcelino Garrine, Delfino Vubil, Nélio Nobela, Karen Kotloff, James P. Nataro, Tacilta Nhampossa, Sozinho Acácio, Jacqueline E. Tate, Umesh Parashar, Jason M. Mwenda, Pedro L. Alonso, Martin Nyaga, Celso Cunha and Inácio Mandomando

Viruses 2022, 14(1), 134; https://doi.org/10.3390/v14010134 - 12 Jan 2022

Cited by 8 | Viewed by 2879

Abstract

Group A rotaviruses remain the leading cause of diarrhoea in children aged <5 years. Mozambique introduced rotavirus vaccine (Rotarix^®) in September 2015. We report rotavirus genotypes circulating among symptomatic and asymptomatic children in Manhiça District, Mozambique, pre- and post-vaccine introduction. Stool [...] Read more.

Group A rotaviruses remain the leading cause of diarrhoea in children aged <5 years. Mozambique introduced rotavirus vaccine (Rotarix^®) in September 2015. We report rotavirus genotypes circulating among symptomatic and asymptomatic children in Manhiça District, Mozambique, pre- and post-vaccine introduction. Stool was collected from enrolled children and screened for rotavirus by enzyme-immuno-sorbent assay. Positive specimens were genotyped for VP7 (G genotypes) and VP4 (P genotypes) by the conventional reverse transcriptase polymerase chain reaction. The combination G12P[8] was more frequently observed in pre-vaccine than in post-vaccine introduction, in moderate to severe diarrhoea (34%, 61/177 vs. 0, p < 0.0001) and controls (23%, 26/113 vs. 0, p = 0.0013) and mixed genotypes (36%, 24/67 vs. 7% 4/58, p = 0.0003) in less severe diarrhoea. We observed changes in post-vaccine compared to pre-vaccine introduction, where G3P[4] and G3P[8] were prevalent in moderate to severe diarrhoea (10%, 5/49 vs. 0, p = 0.0002; and 14%, 7/49 vs. 1%, 1/177, p < 0.0001; respectively), and in less severe diarrhoea (21%, 12/58 vs. 0, p = 0.003; and 24%, 14/58 vs. 0, p < 0.0001; respectively). Our surveillance demonstrated the circulation of similar genotypes contemporaneously among cases and controls, as well as switching from pre- to post-vaccine introduction. Continuous surveillance is needed to evaluate the dynamics of the changes in genotypes following vaccine introduction. Full article

(This article belongs to the Topic Infectious Diseases)

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19 pages, 7281 KiB

Open AccessArticle

Characterization of the In Vitro and In Vivo Efficacy of Baloxavir Marboxil against H5 Highly Pathogenic Avian Influenza Virus Infection

by Keiichi Taniguchi, Yoshinori Ando, Masanori Kobayashi, Shinsuke Toba, Haruaki Nobori, Takao Sanaki, Takeshi Noshi, Makoto Kawai, Ryu Yoshida, Akihiko Sato, Takao Shishido, Akira Naito, Keita Matsuno, Masatoshi Okamatsu, Yoshihiro Sakoda and Hiroshi Kida

Viruses 2022, 14(1), 111; https://doi.org/10.3390/v14010111 - 8 Jan 2022

Cited by 9 | Viewed by 3393

Abstract

Human infections caused by the H5 highly pathogenic avian influenza virus (HPAIV) sporadically threaten public health. The susceptibility of HPAIVs to baloxavir acid (BXA), a new class of inhibitors for the influenza virus cap-dependent endonuclease, has been confirmed in vitro, but it has [...] Read more.

Human infections caused by the H5 highly pathogenic avian influenza virus (HPAIV) sporadically threaten public health. The susceptibility of HPAIVs to baloxavir acid (BXA), a new class of inhibitors for the influenza virus cap-dependent endonuclease, has been confirmed in vitro, but it has not yet been fully characterized. Here, the efficacy of BXA against HPAIVs, including recent H5N8 variants, was assessed in vitro. The antiviral efficacy of baloxavir marboxil (BXM) in H5N1 virus-infected mice was also investigated. BXA exhibited similar in vitro activities against H5N1, H5N6, and H5N8 variants tested in comparison with seasonal and other zoonotic strains. Compared with oseltamivir phosphate (OSP), BXM monotherapy in mice infected with the H5N1 HPAIV clinical isolate, the A/Hong Kong/483/1997 strain, also caused a significant reduction in viral titers in the lungs, brains, and kidneys, thereby preventing acute lung inflammation and reducing mortality. Furthermore, compared with BXM or OSP monotherapy, combination treatments with BXM and OSP using a 48-h delayed treatment model showed a more potent effect on viral replication in the organs, accompanied by improved survival. In conclusion, BXM has a potent antiviral efficacy against H5 HPAIV infections. Full article

(This article belongs to the Topic Infectious Diseases)

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21 pages, 9647 KiB

Open AccessArticle

Short ‘1.2× Genome’ Infectious Clone Initiates Kolmiovirid Replication in Boa constrictor Cells

by Leonora Szirovicza, Udo Hetzel, Anja Kipar and Jussi Hepojoki

Viruses 2022, 14(1), 107; https://doi.org/10.3390/v14010107 - 8 Jan 2022

Cited by 3 | Viewed by 2189

Abstract

Human hepatitis D virus (HDV) depends on hepatitis B virus co-infection and its glycoproteins for infectious particle formation. HDV was the sole known deltavirus for decades and believed to be a human-only pathogen. However, since 2018, several groups reported finding HDV-like agents from [...] Read more.

Human hepatitis D virus (HDV) depends on hepatitis B virus co-infection and its glycoproteins for infectious particle formation. HDV was the sole known deltavirus for decades and believed to be a human-only pathogen. However, since 2018, several groups reported finding HDV-like agents from various hosts but without co-infecting hepadnaviruses. In vitro systems enabling helper virus-independent replication are key for studying the newly discovered deltaviruses. Others and we have successfully used constructs containing multimers of the deltavirus genome for the replication of various deltaviruses via transfection in cell culture. Here, we report the establishment of deltavirus infectious clones with 1.2× genome inserts bearing two copies of the genomic and antigenomic ribozymes. We used Swiss snake colony virus 1 as the model to compare the ability of the previously reported “2× genome” and the “1.2× genome” infectious clones to initiate replication in cell culture. Using immunofluorescence, qRT-PCR, immuno- and northern blotting, we found the 2× and 1.2× genome clones to similarly initiate deltavirus replication in vitro and both induced a persistent infection of snake cells. The 1.2× genome constructs enable easier introduction of modifications required for studying deltavirus replication and cellular interactions. Full article

(This article belongs to the Topic Infectious Diseases)

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14 pages, 1176 KiB

Open AccessArticle

A Large Gap in Patients’ Characteristics and Outcomes between the Real-World and Clinical Trial Settings in Community-Acquired Pneumonia and Healthcare-Associated Pneumonia

by Nobuhiro Asai, Yuichi Shibata, Daisuke Sakanashi, Hideo Kato, Mao Hagihara, Yuka Yamagishi, Hiroyuki Suematsu and Hiroshige Mikamo

J. Clin. Med. 2022, 11(2), 297; https://doi.org/10.3390/jcm11020297 - 7 Jan 2022

Cited by 1 | Viewed by 1585

Abstract

(1) Introduction: Evidence-based medicine (EBM) is necessary to standardize treatments for infections because EBM has been established based on the results of clinical trials. Since entry criteria for clinical trials are very strict, it may cause skepticism or questions on whether the results [...] Read more.

(1) Introduction: Evidence-based medicine (EBM) is necessary to standardize treatments for infections because EBM has been established based on the results of clinical trials. Since entry criteria for clinical trials are very strict, it may cause skepticism or questions on whether the results of clinical trials reflect the real world of medical practice. (2) Methods: To examine how many patients could join any randomized clinical trials for the treatment of community-acquired pneumonia (CAP) and healthcare-associated pneumonia (HCAP). We reviewed all the pneumonia patients in our institute during 2014–2017. The patients were divided into two groups: patients who were eligible for clinical trials (participation-possible group), and those who were not (participation-impossible group). Exclusion criteria for clinical trials were set based on previous clinical trials. (3) Results: A total of 406 patients were enrolled in the present study. Fifty-seven (14%) patients were categorized into the participation-possible group, while 86% of patients belonged to the participation-impossible group. Patients in the participation-possible group had less comorbidities and more favorable outcomes than those with the participation-impossible group. As for the outcomes, there were significant differences in the 30-day and in-hospital mortality rates between the two groups. In addition, the participation-possible group showed a longer overall survival time than the participation-impossible group (p < 0.001 by Log-Rank test). (4) Conclusion: There is a difference in patients’ profile and outcomes between clinical trials and the real world. Though EBM is essential to advance medicine, we should acknowledge the facts and the limits of the clinical trials. Full article

(This article belongs to the Topic Infectious Diseases)

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15 pages, 3077 KiB

Open AccessArticle

Co-Circulation of Chikungunya and Multiple DENV Serotypes and Genotypes, Western Indonesia 2015–2016

by Harapan Harapan, Alice Michie, Timo Ernst, Kritu Panta, Mudatsir Mudatsir, Benediktus Yohan, Sotianingsih Haryanto, Suzi McCarthy, R. Tedjo Sasmono and Allison Imrie

Viruses 2022, 14(1), 99; https://doi.org/10.3390/v14010099 - 6 Jan 2022

Cited by 3 | Viewed by 2202

Abstract

Dengue is a mosquito-borne disease of public health concern affecting tropical and subtropical countries, including Indonesia. Although studies on dengue epidemiology have been undertaken in Indonesia, data are lacking in many areas of the country. The aim of this study was to determine [...] Read more.

Dengue is a mosquito-borne disease of public health concern affecting tropical and subtropical countries, including Indonesia. Although studies on dengue epidemiology have been undertaken in Indonesia, data are lacking in many areas of the country. The aim of this study was to determine dengue virus (DENV) and chikungunya virus (CHIKV) molecular epidemiology in western regions of the Indonesian archipelago. A one-year prospective study was conducted in Aceh and Jambi in 2015 and 2016, respectively, where patients with dengue-like illness were enrolled. Of 205 patients recruited, 29 and 27 were confirmed with dengue in Aceh and Jambi, respectively, and three from Jambi were confirmed with chikungunya. DENV-1 was the predominant serotype identified in Aceh while DENV-2 was predominant in Jambi. All DENV-1 and DENV-2 from both regions were classified as Genotype I and Cosmopolitan genotype, respectively, and all DENV-3 viruses from Jambi were Genotype I. Some viruses, in particular DENV-1, displayed a distinct lineage distribution, where two DENV-1 lineages from Aceh were more closely related to viruses from China instead of Jambi highlighting the role of travel and flight patterns on DENV transmission in the region. DENV-2 from both Aceh and Jambi and DENV-3 from Jambi were all closely related to Indonesian local strains. All three CHIKV belonged to Asian genotype and clustered closely with Indonesian CHIKV strains including those previously circulating in Jambi in 2015, confirming continuous and sustainable transmission of CHIKV in the region. The study results emphasize the importance of continuous epidemiological surveillance of arboviruses in Indonesia and simultaneous testing for CHIKV among dengue-suspected patients. Full article

(This article belongs to the Topic Infectious Diseases)

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Serotype distribution of DENV isolated from Aceh (2015) and Jambi (2016). In Aceh, there was one co-infection of two serotypes (DENV-2 and DENV-3). Full article ">Figure 2
Phylogenetic tree of DENV-1 isolated from Aceh and Jambi showing Lineages 1–5. The phylogenetic tree was generated using the maximum likelihood method using RAxML with a GTR+Γ model with 4268 sequences from NCBI. Some phylogenetic clusters have been collapsed to reveal the positions of isolated viruses in more detail. Pink indicates viruses isolated from Aceh and blue indicates viruses isolated from Jambi in this study. G: genotype, L: lineage. CHN: China, IDN: Indonesia, SGP: Singapore, THA: Thailand. Asterix (*) indicates virus isolated from travelers returning from Indonesia. Full article ">Figure 3
Phylogenetic tree of DENV-2 isolated from Aceh and Jambi showing two lineages (L1 and 2). The tree was generated using the maximum likelihood method using RAxML with a GTR+Γ model of an alignment including three viruses from Aceh, eight viruses from Jambi, and 3469 sequences from NCBI. Some phylogenetic clusters have been collapsed to reveal the positions of isolated viruses in more detail. All identified viruses belong to the Cosmopolitan genotype and clustered into two lineages (L1 and L2). Blue indicates viruses from Jambi and pink indicates viruses isolated from Aceh. Green box indicates the lineage that consists of viruses isolated both from Aceh and Jambi. L: lineage. AUS: Australia, CHN: China, IDN: Indonesia, PNG: Papua New Guinea, MYS: Malaysia, SGP: Singapore, THA: Thailand. Asterix (*) indicates virus isolated from travelers returning from Indonesia. Full article ">Figure 4
Phylogenetic tree of DENV-3 isolated from Jambi, 2016. The phylogenetic tree was generated using the maximum likelihood method using RAxML with a GTR+Γ model of an alignment including four viruses from Jambi and 2032 sequences from NCBI. Some phylogenetic clusters have been collapsed to reveal the positions of isolated viruses in more detail. All identified viruses belong to Genotype I and clustered into one lineage (L1). Blue indicates viruses isolated from Jambi. G: genotype, L: lineage. CHN: China, IDN: Indonesia, MYS: Malaysia. Asterix (*) indicates virus isolated from travelers returning from Indonesia. Full article ">Figure 5
Genome-based phylogeny of CHIKV isolated from Jambi, 2016. The phylogenetic tree was generated using the maximum likelihood method employing RAxML with a GTR+Γ model of an alignment of three CHIKV isolated in Jambi in 2016, 560 sequences from NCBI. Some phylogenetic clusters have been collapsed (indicated as green) to reveal the positions of the viruses from Jambi. CHIKVs sampled from Jambi are colored in blue. CHN: China, FSM: Federated States of Micronesia, IDN: Indonesia, PHL: the Philippine, MYS: Malaysia, NCL: New Caledonia, TON: Tonga, THA: Thailand. Full article ">Figure 6
Flight patterns between Aceh and Jambi. The arrows indicate the main flight routes between Aceh, Jambi and neighbor localities. Red dot indicates location of Medan, the capital of North Sumatra Province. Medan is the largest city in Sumatra Island and has major international flight routes connected to neighboring dengue endemic areas, especially Malaysia and Singapore. There is no direct flight between Aceh and Jambi Province. Full article ">

22 pages, 25576 KiB

Open AccessArticle

Gammaherpesvirus Alters Alveolar Macrophages According to the Host Genetic Background and Promotes Beneficial Inflammatory Control over Pneumovirus Infection

by Gautier Gilliaux and Daniel Desmecht

Viruses 2022, 14(1), 98; https://doi.org/10.3390/v14010098 - 6 Jan 2022

Cited by 6 | Viewed by 2052

Abstract

Human respiratory syncytial virus (hRSV) infection brings a wide spectrum of clinical outcomes, from a mild cold to severe bronchiolitis or even acute interstitial pneumonia. Among the known factors influencing this clinical diversity, genetic background has often been mentioned. In parallel, recent evidence [...] Read more.

Human respiratory syncytial virus (hRSV) infection brings a wide spectrum of clinical outcomes, from a mild cold to severe bronchiolitis or even acute interstitial pneumonia. Among the known factors influencing this clinical diversity, genetic background has often been mentioned. In parallel, recent evidence has also pointed out that an early infectious experience affects heterologous infections severity. Here, we analyzed the importance of these two host-related factors in shaping the immune response in pneumoviral disease. We show that a prior gammaherpesvirus infection improves, in a genetic background-dependent manner, the immune system response against a subsequent lethal dose of pneumovirus primary infection notably by inducing a systematic expansion of the CD8⁺ bystander cell pool and by modifying the resident alveolar macrophages (AMs) phenotype to induce immediate cyto/chemokinic responses upon pneumovirus exposure, thereby drastically attenuating the host inflammatory response without affecting viral replication. Moreover, we show that these AMs present similar rapid and increased production of neutrophil chemokines both in front of pneumoviral or bacterial challenge, confirming recent studies attributing a critical antibacterial role of primed AMs. These results corroborate other recent studies suggesting that the innate immunity cells are themselves capable of memory, a capacity hitherto reserved for acquired immunity. Full article

(This article belongs to the Topic Infectious Diseases)

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Past MuHV-4 infection provides protection against subsequent pneumoviral disease. (A) Schematic of the survival study. On day -28, CD-1, BALB/c, and C57BL/6 mice were inoculated intranasally with 1.4 × 104 TCID50 units of MuHV-4, hiMuHV-4, or PBS. On day 0, mice were intranasally inoculated with 4, 10, or 25 TCID50 units of PVM, and the survivability of each mice strain was monitored. (B) Survival study enrolling each mice strains given either MuHV-4, hiMuHV-4, or PBS intranasally 28 days prior to 4 TCID50 units of PVM infection (n = 6 mice/mouse strain/priming condition; representative of three independent experiments). (C) Schematic of experimental protocol. On day −28, CD-1, BALB/c, and C57BL/6 mice were inoculated intranasally with 1.4 × 104 TCID50 units of MuHV-4, hiMuHV-4, or PBS. On day 0, mice were intranasally inoculated with PVM (4 TCID50 units for BALB/c mice and 10 TCID50 units for CD-1 and C57BL/6 mice). Finally, on day 6, lungs were removed for further examinations. (D) Macroscopic aspect of lungs excised from each mouse strain on day 6 after PVM infection (scale bar = 1 cm). (E) Representative sections of BALB/c mice H&E-stained lung tissues on day 6 after PVM infection (4 TCID50 units) (histopathological reactions are similar among each mice strain). Conspicuous alveolar (blue arrows), peribronchiolar (yellow arrows), and perivascular (white arrows) inflammatory infiltrations were constant among PBS- and hiMuHV-4-primed mice, while occasional in MuHV-4-primed mice. Scale bar = 200 µm for left panels, 50 µm for right panels. Full article ">Figure 2
MuHV-4 priming adjusts lung lymphoid subpopulations both before and 6 days after exposure to PVM. (A) Schematic of experimental protocol. On day −28, CD-1, BALB/c, and C57BL/6 mice were inoculated intranasally (i.n.) with 1.4 × 104 TCID50 units of MuHV-4, hiMuHV-4, or PBS. Each cohort was then divided into two sub-cohorts based on whether euthanasia was performed just before (day 0) or 6 days after intranasal inoculation of PVM. On day 0, the lungs of the first half of the mice were removed for flow cytometry analysis, while the other half of the mice were infected with PVM. On day 6, the lungs were removed and analyzed by flow cytometry. (B) Enumeration of absolute lung lymphoid subpopulations in mock-primed (hiMuHV-4 and PBS) and MuHV-4-primed mice on days 0 (primed lungs) and 6 (primed and infected lungs) following PVM inoculation. (C) Absolute number of activated (CD69+) and inactivated (CD69−) lungs CD8+ T-cell subsets in mock- or MuHV-4 primed mice measured on days 0 and 6 following PVM inoculation (mean ± SD, with n = 6 mice/mouse strain/priming condition; representative of three independent experiments). Mock lungs, primed lungs (day 0), and primed/infected lungs (day 6) are considered separately from each other for statistical analysis. Significantly different means are highlighted, with * p < 0.05, ** p < 0.01, or *** p < 0.001. n.s., not significant (one-way ANOVA and Bonferroni post-tests). Full article ">Figure 3
MuHV-4 priming adjusts lung myeloid subpopulations both before and 6 days after exposure to PVM. (A) Schematic of experimental protocol. On day −28, CD-1, BALB/c, and C57BL/6 mice were inoculated intranasally (i.n.) with MuHV-4, hiMuHV-4, or PBS. Each cohort was then divided into two sub-cohorts based on whether euthanasia was performed just before (day 0) or 6 days after intranasal inoculation of PVM. On day 0, the lungs of the first half of the mice were removed for flow cytometry analysis, while the other half of the mice were infected with PVM. On day 6, the lungs of the remaining mice were removed and analyzed by flow cytometry. (B) Enumeration of absolute lung myeloid subpopulations in mock-primed (hiMuHV-4 and PBS) and MuHV-4-primed mice on days 0 (primed lungs) and 6 (primed and infected lungs) following PVM inoculation. (C) Mean fluorescence intensity (MFI) of MHC II, CD64, and SiglecF expression on AMs 28 days after priming either with MuHV-4 or PBS (mean ± SD, with n = 6 mice/mouse strain/priming condition; representative of three independent experiments). Mock lungs, primed lungs (day 0), and primed/infected lungs (day 6) are considered separately from each other for statistical analysis. Significantly different means are highlighted, with * p < 0.05, ** p < 0.01, or *** p < 0.001. n.s., not significant (one-way ANOVA and Bonferroni post-tests). Full article ">Figure 4
MuHV-4 priming results in strain-dependent virus recovery modification and reduced lung pro-inflammatory cyto- and chemokine contents during pneumoviral disease. (A) Schematic of experimental protocol. On day −28, CD-1, BALB/c, and C57BL/6 mice were inoculated intranasally with MuHV-4, hiMuHV-4, or PBS. On day 6 after PVM inoculation, lungs were prepared for virus titration and chemokine/cytokine assays. (B) PVM titer determined by quantitative RT-qPCR applied on whole-lung homogenate. Results are expressed as PVM sh copies per 104 ywhaz copies. (C) Lung cyto- and chemokine concentrations normalized to sample total protein content. All results are reported as mean ± SD, with n = 6 mice/mouse strain/priming condition, representative of three independent experiments. Significantly different means are highlighted, with * p < 0.05, ** p < 0.01, or *** p < 0.001. n.s., not significant (one-way ANOVA and Bonferroni post-tests). Full article ">Figure 5
MuHV-4 priming educates AMs without help from monocyte-derived macrophages. (A) Schematic of experimental protocol. Wildtype (WT) and CCR2−/− C57BL/6 mice were inoculated intranasally (i.n.) with either MuHV-4 or PBS, and their lungs were analyzed 28 days later. (B) Flow cytometry plot showing expression of AMs’ surface markers 28 days post priming. (C) Magnitude of several markers expression at the AM’s surface, as determined by mean fluorescence intensity (MFI) 28 days post priming. All results are reported as mean ± SD, with n = 6 mice/mouse strain/priming condition, representative of three independent experiments. Significantly different means are highlighted, with *** p < 0.001. n.s., not significant (one-way ANOVA and Bonferroni post-tests). Full article ">Figure 6
MuHV-4 priming resets AMs’ immediate response to PVM and Streptococcus pneumoniae. (A) Schematic of experimental protocol. WT and CCR2−/− C57BL/6 mice were inoculated intranasally (i.n.) with either MuHV-4 or PBS; lung CD11c+ AMs were then isolated 28 days after and ex vivo stimulated by PVM or S. pneumoniae inoculation before cyto- and chemokines measurement over 72 h. (B) Heatmap of IL-6 production in CD11c+ AMs harvested from 28 days PBS or MuHV-4 primed mice, at 0, 2, 12, 24, 48, and 72 h post PVM inoculation. (C) Supernatant cyto- and chemokine concentrations normalized to sample total protein content. All results are reported as mean ± SD, with n = 6 mice/mouse strain/priming condition, representative of three independent experiments. Significantly different means are highlighted, with * p < 0.05, ** p < 0.01, or *** p < 0.001. n.s., not significant (one-way ANOVA and Bonferroni post-tests). Full article ">

14 pages, 7377 KiB

Open AccessArticle

A Population of CD4⁺CD8⁺ Double-Positive T Cells Associated with Risk of Plasma Leakage in Dengue Viral Infection

by Esther Dawen Yu, Hao Wang, Ricardo da Silva Antunes, Yuan Tian, Rashmi Tippalagama, Shakila U. Alahakoon, Gayani Premawansa, Ananda Wijewickrama, Sunil Premawansa, Aruna Dharshan De Silva, April Frazier, Alba Grifoni, Alessandro Sette and Daniela Weiskopf

Viruses 2022, 14(1), 90; https://doi.org/10.3390/v14010090 - 5 Jan 2022

Cited by 7 | Viewed by 3233

Abstract

According to the WHO 2009 classification, dengue with warning signs is at the risk of developing severe form of dengue disease. One of the most important warning signs is plasma leakage, which can be a serious complication associated with higher morbidity and mortality. [...] Read more.

According to the WHO 2009 classification, dengue with warning signs is at the risk of developing severe form of dengue disease. One of the most important warning signs is plasma leakage, which can be a serious complication associated with higher morbidity and mortality. We report that the frequency of CD4⁺CD8⁺ double-positive (DP) T cells is significantly increased in patients at risk of developing plasma leakage. Transcriptomic analysis demonstrated that CD4⁺CD8⁺ DP cells were distinct from CD4⁺ Single Positive (SP) T cells but co-clustered with CD8⁺ SP cells, indicating a largely similar transcriptional profile. Twenty significant differentially expressed (DE) genes were identified between CD4⁺CD8⁺ DP and CD8⁺ SP cells. These genes encode OX40 and CCR4 proteins as well as other molecules associated with cell signaling on the cell surface (NT5E, MXRA8, and PTPRK). While comparing the profile of gene expression in CD4⁺CD8⁺ DP cells from patients with and without warning signs of plasma leakage, similar expression profile was observed, implying a role of CD4⁺CD8⁺ DP cells in plasma leakage through a quantitative increase rather than functional alteration. This study provided novel insight into the host immune response during the acute febrile phase of DENV infection and the role of CD4⁺CD8⁺ DP T cells in the pathogenesis of plasma leakage. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 667 KiB

Open AccessArticle

Clinical and Laboratory Findings of Nosocomial Sepsis in Extremely Low Birth Weight Infants According to Causative Organisms

by Kyung-Hee Park, Su-Jung Park, Mi-Hye Bae, Seong-Hee Jeong, Mun-Hui Jeong, Narae Lee, Young-Mi Han and Shin-Yun Byun

J. Clin. Med. 2022, 11(1), 260; https://doi.org/10.3390/jcm11010260 - 4 Jan 2022

Cited by 2 | Viewed by 1939

Abstract

Background: nosocomial sepsis remains a significant source of morbidity and mortality in extremely low birth weight (ELBW) infants. Early and accurate diagnosis is very important, but it is difficult due to the similarities in clinical manifestation between the causative microorganisms. We tried to [...] Read more.

Background: nosocomial sepsis remains a significant source of morbidity and mortality in extremely low birth weight (ELBW) infants. Early and accurate diagnosis is very important, but it is difficult due to the similarities in clinical manifestation between the causative microorganisms. We tried to identify the differences between causative microorganisms in clinical and laboratory findings and to help choose antibiotics, when sepsis was suspected in ELBW infants. Methods: a retrospective study was conducted on preterm infants, born at less than 28 weeks of gestation, with a birth weight of less than 1000 g between January 2009 and December 2019. Clinical and laboratory findings of suspected sepsis, after the first 72 h of life, were assessed. We classified them into four groups according to blood culture results (gram positive, gram negative, fungal, and negative culture groups) and compared them. Results: a total of 158 patients were included after using the exclusion criteria, with 45 (29%) in the gram positive group, 35 (22%) in the gram negative group, 27 (17%) in the fungal group, and 51 (32%) in the negative culture group. There were no significant differences in mean gestational age, birth weight, and neonatal morbidities, except for the age of onset, which was earlier in the fungal group than other groups. White blood cell (WBC) counts were the highest in the gram negative group and the lowest in the fungal group. The mean platelet counts were the lowest in the fungal group. C-reactive protein (CRP) levels were the highest in the gram negative group, while glucose was the highest in the fungal group. Conclusions: in conclusion, we showed that there are some differences in laboratory findings, according to causative microorganisms in the nosocomial sepsis of ELBW infants. Increased WBC and CRP were associated with gram negative infection, while decreased platelet and glucose level were associated with fungal infection. These data may be helpful for choosing empirical antibiotics when sepsis is suspected. Full article

(This article belongs to the Topic Infectious Diseases)

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14 pages, 1079 KiB

Open AccessArticle

Genotyping and Molecular Diagnosis of Hepatitis A Virus in Human Clinical Samples Using Multiplex PCR-Based Next-Generation Sequencing

by Geum-Young Lee, Won-Keun Kim, Seungchan Cho, Kyungmin Park, Jongwoo Kim, Seung-Ho Lee, Jingyeong Lee, Young-Sun Lee, Ji Hoon Kim, Kwan Soo Byun and Jin-Won Song

Microorganisms 2022, 10(1), 100; https://doi.org/10.3390/microorganisms10010100 - 4 Jan 2022

Cited by 7 | Viewed by 3540

Abstract

Hepatitis A virus (HAV) is a serious threat to public health worldwide. We used multiplex polymerase chain reaction (PCR)-based next-generation sequencing (NGS) to derive information on viral genetic diversity and conduct precise phylogenetic analysis. Four HAV genome sequences were obtained using multiplex PCR-based [...] Read more.

Hepatitis A virus (HAV) is a serious threat to public health worldwide. We used multiplex polymerase chain reaction (PCR)-based next-generation sequencing (NGS) to derive information on viral genetic diversity and conduct precise phylogenetic analysis. Four HAV genome sequences were obtained using multiplex PCR-based NGS. HAV whole-genome sequence of one sample was obtained by conventional Sanger sequencing. The HAV strains demonstrated a geographic cluster with sub-genotype IA strains in the Republic of Korea. The phylogenetic pattern of HAV viral protein (VP) 3 region showed no phylogenetic conflict between the whole-genome and partial-genome sequences. The VP3 region in serum and stool samples showed sensitive detection of HAV with differences of quantification that did not exceed <10 copies/μL than the consensus VP4 region using quantitative PCR (qPCR). In conclusion, multiplex PCR-based NGS was implemented to define HAV genotypes using nearly whole-genome sequences obtained directly from hepatitis A patients. The VP3 region might be a potential candidate for tracking the genotypic origin of emerging HAV outbreaks. VP3-specific qPCR was developed for the molecular diagnosis of HAV infection. This study may be useful to predict for the disease management and subsequent development of hepatitis A infection at high risk of severe illness. Full article

(This article belongs to the Topic Infectious Diseases)

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Figure 1
Quantitation of hepatitis A virus (HAV) RNA genome in clinical samples from patients in the Republic of Korea. Real-time quantitative polymerase chain reaction assay was performed for molecular diagnosis and quantification of HAV genomes in serum and stool samples. The vertical axis shows the HAV RNA copy numbers of VP4 and VP3 regions. Each data point represents the mean threshold cycle (Ct) value obtained from triplicates. Full article ">Figure 2
Phylogenetic analysis of the nearly whole-genome hepatitis A virus (HAV) sequences in the Republic of Korea (ROK). Nearly whole-genome sequences of HAV from serum and stool samples were obtained by multiplex polymerase chain reaction-based next-generation sequencing. Branch lengths are proportional to the number of nucleotide substitutions. Vertical distances are included for clarity. Phylogenetic trees of HAV were generated by the maximum likelihood method, with 1000 bootstrap iterations. Colored circles indicate specific HAV strains from ROK; red, genotype IA; blue, genotype IB; orange, genotype IIA; green, genotype IIB; pink, genotype IIIA; sky blue, genotype IIIB; and violet, genotype V. Full article ">Figure 3
Tanglegram of hepatitis A virus (HAV) nucleotide sequences based on the whole- (left) and partial- (right) genome phylogenies. (A) VP3 region (1470–2207 nt), (B) VP1/P2A region (2984–3217 nt), (C) VP1/P2B region (2896–3289 nt), and (D) entire VP1 region (2172–3125 nt). Color indicates individual six sub-genotypes of human and one of sub-genotype of animal in HAV strains. Whole-genome and partial-genome phylogenies were generated using the maximum likelihood method. Full lines indicate significant phylogenetic conflicts. Grey lines indicate phylogenetic clade patterns falling between two different regions. Full article ">

22 pages, 5602 KiB

Open AccessArticle

Transcriptional Shift and Metabolic Adaptations during Leishmania Quiescence Using Stationary Phase and Drug Pressure as Models

by Marlene Jara, Michael Barrett, Ilse Maes, Clement Regnault, Hideo Imamura, Malgorzata Anna Domagalska and Jean-Claude Dujardin

Microorganisms 2022, 10(1), 97; https://doi.org/10.3390/microorganisms10010097 (registering DOI) - 3 Jan 2022

Cited by 6 | Viewed by 3174

Abstract

Microorganisms can adopt a quiescent physiological condition which acts as a survival strategy under unfavorable conditions. Quiescent cells are characterized by slow or non-proliferation and a deep downregulation of processes related to biosynthesis. Although quiescence has been described mostly in bacteria, this survival [...] Read more.

Microorganisms can adopt a quiescent physiological condition which acts as a survival strategy under unfavorable conditions. Quiescent cells are characterized by slow or non-proliferation and a deep downregulation of processes related to biosynthesis. Although quiescence has been described mostly in bacteria, this survival skill is widespread, including in eukaryotic microorganisms. In Leishmania, a digenetic parasitic protozoan that causes a major infectious disease, quiescence has been demonstrated, but the molecular and metabolic features enabling its maintenance are unknown. Here, we quantified the transcriptome and metabolome of Leishmania promastigotes and amastigotes where quiescence was induced in vitro either, through drug pressure or by stationary phase. Quiescent cells have a global and coordinated reduction in overall transcription, with levels dropping to as low as 0.4% of those in proliferating cells. However, a subset of transcripts did not follow this trend and were relatively upregulated in quiescent populations, including those encoding membrane components, such as amastins and GP63, or processes like autophagy. The metabolome followed a similar trend of overall downregulation albeit to a lesser magnitude than the transcriptome. It is noteworthy that among the commonly upregulated metabolites were those involved in carbon sources as an alternative to glucose. This first integrated two omics layers afford novel insight into cell regulation and show commonly modulated features across stimuli and stages. Full article

(This article belongs to the Topic Infectious Diseases)

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Graphical abstract

Graphical abstract
Full article ">Figure 1
Evaluation of stationary phase and drug pressure as models of quiescence. Four parameters with associated downregulation in quiescent cells in addition to cell viability were evaluated. (a) Assessment of proliferation as indicated by growth curve of promastigotes and amastigotes in absence (solid lines) and presence (dashed lines) of Potassium Antimonyl tartrate (PAT). (b) rEGFP expression in proliferative (Log) and non-proliferative (Sta, Log_PAT) conditions. (c) Quantification of the total RNA content per million cells. (d) Quantification of the mitochondrial membrane potential as indicated by the fluorescence of Mitotracker. In figures (b–d), the results represent the mean ± SEM of three biological replicates. The asterisks represent statistically significant differences after Tukey’s post-hoc test; * p < 0.05, ** p < 0.01, *** p < 0.001. The asterisks in black and red represent statistically significant differences compared with promastigotes and amastigotes in Log, respectively. (e) Confocal images of Leishmania cells under the evaluated conditions (after enrichment of viable cells for condition Sta and Log_PAT). The pictures show their morphology, size, and cell viability, as indicated by their membrane integrity and absence of cytoplasmatic staining with the non-permeable dye LIVE/DEAD™ Fixable Red Stain. The maintenance of their nuclear and kinetoplast DNA is shown with DAPI staining. The sale bar represents 5 µM. Full article ">Figure 2
mRNA transcriptome size and global down-shift during quiescence. (a) Principal component analysis showing that most of the variability in the abundance of the mRNAs can be explained by the proliferative condition of Leishmania with quiescent cells induced by PAT drug pressure being the most dissimilar compared to proliferative cells in both promastigotes and amastigotes. (b) Sum of normalized mRNAs in each condition and stage of Leishmania showing the diminished transcriptome size in quiescent cells compared to proliferative cells. The bars represent the mean ± SE of three biological replicates. The asterisks in black color represent statistically significant differences after Tukey’s post-hoc test; * indicates p < 0.05, indicates *** p < 0.01. Black and red colors represent statistically significant differences in quiescent cells compared with promastigotes and amastigotes in Log, respectively. (c) Volcano plots showing the magnitude of change in the relative abundance of each mRNA in quiescent cells compared with proliferative cells. The plots show the global down-shift of the transcriptome in quiescent cells induced by both PAT or the stationary phase in both Leishmania stages as most of the mRNAs have substantially decreased levels and are located in the plots. On each plot, the difference is represented by the Log2 fold change between two conditions, and its significance is represented by the negative logarithm of the p value. The two vertical lines in each plot represent the Log2 fold change cutoff of 1 and −1 for increased or decreased levels, respectively. The horizontal line represents a 0.05 cutoff for the p value. (d), Venn diagram representing the number of mRNAs with decreased or increased abundance in quiescent cells compared with proliferative cells. (e), Pearson correlation between the abundance of mRNAs in quiescent conditions compared with proliferating cells. The color indicates the number of mRNAs within a particular bin. Full article ">Figure 3
Transcriptome composition and its modulations during quiescence. (a), Principal component analysis shows quiescent cells induced by stationary phase and PAT pressure differ in their transcriptome composition compared to proliferating cells in both promastigotes and amastigotes. (b), Summary of mRNAs modulated in each Leishmania stage and condition. (c), Venn Diagrams showing the number of mRNAs with modulated TPMs in the conditions Sta and Log_PAT compared to Log in each Leishmania stage. Pro, promastigotes; Ama, Amastigotes. Full article ">Figure 4
ORA and GSEA analysis. (a), ORA and network analysis for the core set of mRNAs modulated and shared among all quiescent conditions. ORA indicated that many biosynthetic processes are downregulated, while few processes related to ‘cell host modulation’ and the recycling of nutrients are upregulated. The color of the bubble from yellow to orange indicates more significant adjusted p values (cutoff adj p < 0.05). (b), GSEA shows the major set of mRNAs upregulated and shared among all quiescent cells correspond to: leishmanolysin (GP63), amastin and amastin-like proteins, and autophagy-related genes. On the contrary, among other processes, the biosynthesis of several amino acids and biosynthesis of aminoacyl tRNA are downregulated in all quiescent cells, regardless of the stimuli. The absolute value in each cell of the heatmap measures the magnitude of gene-set changes in log2 scale, and its sign indicates the direction of the change. The modulation of a particular set was considered up in all (red) or down in all (blue) if the p values were statistically significant in all conditions. While it was considered unchanged (grey) if the p value in all conditions were non-significant. Additional details are in <a href="#app1-microorganisms-10-00097" class="html-app">Table S2e,f</a>. Full article ">Figure 5
Quiescent cells have a distinct metabolic profile when compared to proliferating cells. The figures represent 689 putatively annotated metabolites. (a), In all quiescent cells of each Leishmania stage, there is an overall downregulation in the levels of metabolites (either in condition Sta or Log_PAT) as indicated by the decrease in the sum of the peaks intensities of all annotated features constituting their metabolome. The asterisks in the top of each bar in black color represent significant differences after Tukey’s test; * p < 0.05, *** p < 0.001. The asterisks in black and red represent differences in comparison to promastigotes and amastigotes in Log, respectively. (b), Summary of the number of modulated metabolites in quiescent cells induced by condition Sta or Log_PAT in both promastigotes and amastigotes. The results after normalizing by an equivalent amount of cells or by IPT are shown (cutoff |log2 FC| > 1 and BH adjusted p < 0.05). (c), Quiescent cells in both stages have a distinct metabolic profile, as indicated by the clear separation of quiescent and non-quiescent cells by the PCA 2. (d,e), Venn Diagrams showing the relationship between the set of modulated metabolites (panel b) across the different conditions and stages of the Leishmania. Pro, promastigotes; Ama, amastigotes. Full article ">Figure 6
Main metabolic categories having metabolites with modulated abundance in quiescent cells induced by stationary or drug pressure, compared to proliferating cells. The numbers represent the log2 FC compared to condition Log (cell normalized dataset). Only metabolites for which at least one of the conditions has an |log2 FC| > 1 and a BH adjusted p < 0.05 are shown. Pro, promastigotes; Ama, amastigotes. Full article ">

15 pages, 3049 KiB

Open AccessArticle

Genetic Diversity and Spatiotemporal Dynamics of Chikungunya Infections in Mexico during the Outbreak of 2014–2016

by Eduardo D. Rodríguez-Aguilar, Jesús Martínez-Barnetche, Cesar R. González-Bonilla, Juan M. Tellez-Sosa, Rocío Argotte-Ramos and Mario H. Rodríguez

Viruses 2022, 14(1), 70; https://doi.org/10.3390/v14010070 - 31 Dec 2021

Cited by 4 | Viewed by 2094

Abstract

Chikungunya virus (CHIKV) is an alphavirus transmitted by Aedes mosquitoes, which causes Chikungunya fever. Three CHIKV genotypes have been identified: West African, East-Central-South African and Asian. In 2014, CHIKV was detected for the first time in Mexico, accumulating 13,569 confirmed cases in the [...] Read more.

Chikungunya virus (CHIKV) is an alphavirus transmitted by Aedes mosquitoes, which causes Chikungunya fever. Three CHIKV genotypes have been identified: West African, East-Central-South African and Asian. In 2014, CHIKV was detected for the first time in Mexico, accumulating 13,569 confirmed cases in the following three years. Studies on the molecular diversification of CHIKV in Mexico focused on limited geographic regions or investigated only one structural gene of the virus. To describe the dynamics of this outbreak, we analyzed 309 serum samples from CHIKV acute clinical cases from 15 Mexican states. Partial NSP3, E1, and E2 genes were sequenced, mutations were identified, and their genetic variability was estimated. The evolutionary relationship with CHIKV sequences sampled globally were analyzed. Our sequences grouped with the Asian genotype within the Caribbean lineage, suggesting that the Asian was the only circulating genotype during the outbreak. Three non-synonymous mutations (E2 S248F and NSP3 A437T and L451F) were present in our sequences, which were also identified in sequences of the Caribbean lineage and in one Philippine sequence. Based on the phylogeographic analysis, the viral spread was reconstructed, suggesting that after the introduction through the Mexican southern border (Chiapas), CHIKV dispersed to neighboring states before reaching the center and north of the country through the Pacific Ocean states and Quintana Roo. This is the first viral phylogeographic reconstruction in Mexico characterizing the CHIKV outbreak across the country. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 800 KiB

Open AccessCase Report

Investigation of Inherited Chromosomally Integrated Human Herpesvirus-6A+ and -6B+ in a Patient with Ulipristal Acetate-Induced Fulminant Hepatic Failure

by Laure Izquierdo, Clémence M. Canivet, Eleonora De Martin, Teresa M. Antonini, Anne-Marie Roque-Afonso, Audrey Coilly and Claire Deback

Viruses 2022, 14(1), 62; https://doi.org/10.3390/v14010062 - 30 Dec 2021

Cited by 2 | Viewed by 2135

Abstract

Inherited chromosomally integrated (ici) human herpes virus 6 (HHV-6) is estimated to occur in 0.6–2.7% of people worldwide. HHV-6 comprises two distinct species: HHV-6A and HHV-6B. Both HHV-6A and HHV-6B integration have been reported. Several drugs are capable of activating iciHHV-6 in tissues, [...] Read more.

Inherited chromosomally integrated (ici) human herpes virus 6 (HHV-6) is estimated to occur in 0.6–2.7% of people worldwide. HHV-6 comprises two distinct species: HHV-6A and HHV-6B. Both HHV-6A and HHV-6B integration have been reported. Several drugs are capable of activating iciHHV-6 in tissues, the consequences of which are poorly understood. We report herein a case of a woman with iciHHV-6A+ and iciHHV-6B+, who developed ulipristal acetate (a selective progesterone receptor modulator)-induced fulminant hepatic failure that required liver transplantation. We confirmed the presence of ~one copy per cell of both HHV-6A and HHV-6B DNA in her hair follicles using multiplex HHV-6A/B real-time PCR and demonstrated the Mendelian inheritance of both iciHHV-6A and iciHHV-6B in her family members over three generations. Because of the rarity of this presentation, we discuss herein the possible links between reactivated HHV-6 from iciHHV-6A and/or iciHHV-6B and adverse drug reactions, suggesting that iciHHV-6 could be screened before the introduction of any hepatotoxic drugs to exclude HHV-6 active disease or combined idiosyncratic drug-induced liver injury in these patients. Full article

(This article belongs to the Topic Infectious Diseases)

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9 pages, 603 KiB

Open AccessArticle

Changes in Inflammatory Markers after Administration of Tocilizumab in COVID-19: A Single-Center Retrospective Study

by Anna Olewicz-Gawlik, Barbara Ginter-Matuszewska, Mikołaj Kamiński, Agnieszka Adamek, Maciej Bura, Iwona Mozer-Lisewska and Arleta Kowala-Piaskowska

J. Clin. Med. 2022, 11(1), 107; https://doi.org/10.3390/jcm11010107 - 25 Dec 2021

Cited by 4 | Viewed by 2587

Abstract

The COVID-19 pandemic requires the development of effective methods for the treatment of severe cases. We aimed to describe clinical outcomes and changes in inflammatory markers in Polish patients treated with tocilizumab. The medical charts of SARS-CoV-2-positive patients treated in the Department of [...] Read more.

The COVID-19 pandemic requires the development of effective methods for the treatment of severe cases. We aimed to describe clinical outcomes and changes in inflammatory markers in Polish patients treated with tocilizumab. The medical charts of SARS-CoV-2-positive patients treated in the Department of Infectious Diseases between 4 March and 2 September 2020 were retrospectively analyzed. The patients who received tocilizumab according to the Polish Association of Epidemiologists and Infectiologists guidelines were selected for the study. We identified 29 individuals who received tocilizumab, out of whom 11 (37.9%) died. The individuals who died had significantly higher maximal interleukin-6 (IL-6) and lactate dehydrogenase (LDH) serum levels than survivors. After administration of tocilizumab, further increase in LDH and IL-6 was a prognostic factor for unfavorable outcomes. Among inflammatory markers, 7-day mean of IL-6 serum concentration was the best predictor of death (cut-off: ≥417 pg/mL; area under ROC curve = 0.81 [95% Confidence Interval: 0.63–0.98]). The serum concentrations of inflammatory markers before administration of tocilizumab did not predict the outcome, whereas IL-6 and LDH measurements after administration of tocilizumab seemed to be of predictive value. Full article

(This article belongs to the Topic Infectious Diseases)

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9 pages, 470 KiB

Open AccessArticle

Trends in Sexually Transmitted Infections in United States Ambulatory Care Clinics from 2005–2016

by Ikenna Unigwe, Seonkyeong Yang, Hyun Jin Song, Wei-Hsuan Lo-Ciganic, Juan Hincapie-Castillo, Robert L. Cook and Haesuk Park

J. Clin. Med. 2022, 11(1), 71; https://doi.org/10.3390/jcm11010071 - 24 Dec 2021

Cited by 4 | Viewed by 3519

Abstract

We examined the prevalence trends of non-human immunodeficiency virus (HIV) sexually transmitted infections (STI) and associated patient characteristics in U.S. ambulatory-care settings from 2005–2016. We conducted a retrospective repeated cross-sectional analysis using data from the National Ambulatory Medical Care Survey (NAMCS) for individuals [...] Read more.

We examined the prevalence trends of non-human immunodeficiency virus (HIV) sexually transmitted infections (STI) and associated patient characteristics in U.S. ambulatory-care settings from 2005–2016. We conducted a retrospective repeated cross-sectional analysis using data from the National Ambulatory Medical Care Survey (NAMCS) for individuals aged 15–64 with a non-HIV STI-related visit. Data were combined into three periods (2005–2008, 2009–2012, and 2013–2016) to obtain reliable estimates. Logistic regression was used for analysis. A total of 19.5 million weighted, non-HIV STI-related ambulatory visits from 2005–2016 were identified. STI-related visits per 100,000 ambulatory care visits increased significantly over the study period: 206 (95% CI = 153–259), 343 (95% CI = 279–407), and 361 (95% CI = 277–446) in 2005–2008, 2009–2012, and 2013–2016, respectively (P_trend = 0.003). These increases were mainly driven by increases in HPV-related visits (56 to 163 per 100,000 visits) from 2005–2008 to 2009–2012, followed by syphilis- or gonorrhea-related visits (30 to 67 per 100,000 visits) from 2009–2012 to 2013–2016. Higher odds of having STI-related visit were associated with younger age (aged 15–24: aOR = 4.45; 95% CI = 3.19–6.20 and aged 25–44: aOR = 3.59; 95% CI = 2.71–4.77) vs. 45–64-year-olds, Black race (aOR = 2.41; 95% CI = 1.78–3.25) vs. White, and HIV diagnosis (aOR = 10.60; 95% CI = 5.50–20.27) vs. no HIV diagnosis. STI-related office visits increased by over 75% from 2005–2016, and were largely driven by HPV-related STIs and syphilis- or gonorrhea-related STIs. Full article

(This article belongs to the Topic Infectious Diseases)

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8 pages, 1002 KiB

Open AccessArticle

Waning Humoral Response 3 to 6 Months after Vaccination with the SARS-COV-2 BNT162b2 mRNA Vaccine in Dialysis Patients

by Noa Berar-Yanay, Sarit Freiman, Maʹanit Shapira, Amer Saffoury, Ameer Elemy, Munir Hamze, Mohamad Elhaj, Maha Zaher, Loai Matanis and Zaher Anis Armaly

J. Clin. Med. 2022, 11(1), 64; https://doi.org/10.3390/jcm11010064 - 23 Dec 2021

Cited by 17 | Viewed by 2635

Abstract

Background and objectives: The short-term reported antibody response to SARS-COV-2 vaccination in dialysis patients is high, with a seroconversion response rate up to 97%. Data on the long-term durability of this response are scarce. Our objective was to characterize the long-term anti-spike antibody [...] Read more.

Background and objectives: The short-term reported antibody response to SARS-COV-2 vaccination in dialysis patients is high, with a seroconversion response rate up to 97%. Data on the long-term durability of this response are scarce. Our objective was to characterize the long-term anti-spike antibody level in dialysis patients. Design, setting, participants, and measurements: In an observational study, we measured SARS-COV-2 anti-spike antibody levels in dialysis patients who completed 2 doses of the BNT162b2 mRNA SAR S-COV-2 vaccine at 1, 3 and 6 months after the second vaccine dose. We compared the response to dialysis patients who were infected with COVD-19 and to a control group of healthcare-employees. Results: One hundred and forty-two dialysis patients who had been vaccinated (ages 64 ± 11.9 years, 61% male), 33 dialysis patients who had COVID-19 infection (ages 54 ± 14.3 years, 55% male) and 104 individuals in the control group (ages 50 ± 12.2 years, 44% male) were included. The response rate in the vaccinated dialysis patients was 94%, 78% and 73% at 1, 3 and 6 months after the second vaccine dose. In the COVID-19 infected dialysis group and in the control group, the response rate remained at 100% over 6 months. The percentage of change in antibody levels between one and 6 months was −66% in the vaccinated dialysis group, −28% in the control group (p < 0.001) and +48% in dialysis patients who had been infected with COVID-19 (p < 0.001). A non-responder status at 6 months was associated with a lower albumin level. No serious adverse events following vaccination were reported. In conclusion: the initially high response rate to the BNT162b2 vaccine in dialysis patients decreases rapidly. Our results indicate that an early booster (3rd) dose, at three months after the second dose, may be advised for this population to preserve the humoral immunity. Full article

(This article belongs to the Topic Infectious Diseases)

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11 pages, 1432 KiB

Open AccessArticle

Characterization of Erysipelothrix rhusiopathiae Isolates from Diseased Pigs in 15 Chinese Provinces from 2012 to 2018

by Chao Wu, Changjie Lv, Ya Zhao, Weifeng Zhu, Liang Liu, Ting Wang, Chao Kang, Ying Yang, Xiaomei Sun, Qiang Zhang and Meilin Jin

Microorganisms 2021, 9(12), 2615; https://doi.org/10.3390/microorganisms9122615 - 17 Dec 2021

Cited by 7 | Viewed by 2448

Abstract

Erysipelothrix rhusiopathiae can cause erysipelas in animals and erysipeloid in humans. Since its recurrence in 2012, swine erysipelas has caused serious losses within the pig industry in China. The aim of this study was to perform multilocus sequence typing and understand the virulence [...] Read more.

Erysipelothrix rhusiopathiae can cause erysipelas in animals and erysipeloid in humans. Since its recurrence in 2012, swine erysipelas has caused serious losses within the pig industry in China. The aim of this study was to perform multilocus sequence typing and understand the virulence and antimicrobial susceptibility of E. rhusiopathiae isolates in China. Multilocus sequence typing (MLST) of a total of 120 strains was performed, and as a result, three different sequence types were identified, of which ST48 was the main one. Five isolates of each MLST type were randomly selected to be used to challenge mice. ST48 was associated with a higher virulence. Antimicrobial susceptibility was tested using a microdilution technique and, to analyze the resistance mechanism, six strains were selected for genome sequencing. A comparison of the six genomes indicated the presence of a suspected macrolide resistance gene, namely, Erm(A)-like, in erythromycin-resistant strains, which increased the minimum inhibitory concentration (MIC) of erythromycin against E. coli C600 at least four-fold. In addition, three mutations (gyrA86T-I, gyrA90D-N, and parC81S-I) were observed in the quinolone resistance-determining regions (QRDRs) of gyrA and parC in quinolone-resistant strains. After the gyrA gene with the 86T-I mutation or the parC gene with the 81S-I mutation was transfected into E. coli C600, the MIC of enrofloxacin against this strain increased at least two-fold. Our findings provide a theoretical basis for developing antibacterial drugs and may contribute to the clinical prevention and control of E. rhusiopathiae. Full article

(This article belongs to the Topic Infectious Diseases)

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15 pages, 1005 KiB

Open AccessArticle

Circulating IgG Levels in SARS-CoV-2 Convalescent Individuals in Cyprus

by Ioannis Mamais, Apostolos Malatras, Gregory Papagregoriou, Natasa Giallourou, Andrea C. Kakouri, Peter Karayiannis, Maria Koliou, Eirini Christaki, Georgios K. Nikolopoulos and Constantinos Deltas

J. Clin. Med. 2021, 10(24), 5882; https://doi.org/10.3390/jcm10245882 - 15 Dec 2021

Cited by 4 | Viewed by 2922

Abstract

Long-term persistence and the heterogeneity of humoral response to SARS-CoV-2 have not yet been thoroughly investigated. The aim of this work is to study the production of circulating immunoglobulin class G (IgG) antibodies against SARS-CoV-2 in individuals with past infection in Cyprus. Individuals [...] Read more.

Long-term persistence and the heterogeneity of humoral response to SARS-CoV-2 have not yet been thoroughly investigated. The aim of this work is to study the production of circulating immunoglobulin class G (IgG) antibodies against SARS-CoV-2 in individuals with past infection in Cyprus. Individuals of the general population, with or without previous SARS-CoV-2 infection, were invited to visit the Biobank at the Center of Excellence in Biobanking and Biomedical Research of the University of Cyprus. Serum IgG antibodies were measured using the SARS-CoV-2 IgG and the SARS-CoV-2 IgG II Quant assays of Abbott Laboratories. Antibody responses to SARS-CoV-2 were also evaluated against participants’ demographic and clinical data. All statistical analyses were conducted in Stata 16. The median levels of receptor binding domain (RBD)-specific IgG in 969 unvaccinated individuals, who were reportedly infected between November 2020 and September 2021, were 432.1 arbitrary units (AI)/mL (interquartile range—IQR: 182.4–1147.3). Higher antibody levels were observed in older participants, males, and those who reportedly developed symptoms or were hospitalized. The RBD-specific IgG levels peaked at three months post symptom onset and subsequently decreased up to month six, with a slower decay thereafter. IgG response to the RBD of SARS-CoV-2 is bi-phasic with considerable titer variability. Levels of IgG are significantly associated with several parameters, including age, gender, and severity of symptoms. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 1680 KiB

Open AccessArticle

Multicenter Technical Validation of 30 Rapid Antigen Tests for the Detection of SARS-CoV-2 (VALIDATE)

by Gilbert Greub, Giorgia Caruana, Michael Schweitzer, Mauro Imperiali, Veronika Muigg, Martin Risch, Antony Croxatto, Onya Opota, Stefanie Heller, Diana Albertos Torres, Marie-Lise Tritten, Karoline Leuzinger, Hans H. Hirsch, Reto Lienhard and Adrian Egli

Microorganisms 2021, 9(12), 2589; https://doi.org/10.3390/microorganisms9122589 - 15 Dec 2021

Cited by 6 | Viewed by 4328

Abstract

During COVID19 pandemic, SARS-CoV-2 rapid antigen tests (RATs) were marketed with minimal or no performance data. We aimed at closing this gap by determining technical sensitivities and specificities of 30 RATs prior to market release. We developed a standardized technical validation protocol and [...] Read more.

During COVID19 pandemic, SARS-CoV-2 rapid antigen tests (RATs) were marketed with minimal or no performance data. We aimed at closing this gap by determining technical sensitivities and specificities of 30 RATs prior to market release. We developed a standardized technical validation protocol and assessed 30 RATs across four diagnostic laboratories. RATs were tested in parallel using the Standard Q^® (SD Biosensor/Roche) assay as internal reference. We used left-over universal transport/optimum media from nasopharyngeal swabs of 200 SARS-CoV-2 PCR-negative and 100 PCR-positive tested patients. Transport media was mixed with assay buffer and applied to RATs according to manufacturer instructions. Sensitivities were determined according to viral loads. Specificity of at least 99% and sensitivity of 95%, 90%, and 80% had to be reached for 10⁷, 10⁶, 10⁵ virus copies/mL, respectively. Sensitivities ranged from 43.5% to 98.6%, 62.3% to 100%, and 66.7% to 100% at 10⁵, 10⁶, 10⁷ copies/mL, respectively. Automated assay readers such as ExDia or LumiraDx showed higher performances. Specificities ranged from 88.8% to 100%. Only 15 of 30 (50%) RATs passed our technical validation. Due to the high failure rate of 50%, mainly caused by lack of sensitivity, we recommend a thorough validation of RATs prior to market release. Full article

(This article belongs to the Topic Infectious Diseases)

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Box-plots of Ct values distributions according to different batches of validation series. <a href="#microorganisms-09-02589-f001" class="html-fig">Figure 1</a> legend. RATs were grouped according to the validation series. For each series, there was one internal reference (Standard Q®, white box-plot). Black solid lines represent the Ct medians, box-plots and whiskers represent the Ct values distribution. RATs results are displayed on the x-axis: Negative or Positive. Cycle thresholds (Ct) are shown on the y-axis. Full article ">Figure 2
RATs sensitivity rates for viral loads above 105 copies/mL compared to the internal reference test. <a href="#microorganisms-09-02589-f002" class="html-fig">Figure 2</a> legend. Green and red dots represent the assays passing and not passing FOPH validation criteria, respectively; orange dots represent the assays validated using the non-inferiority criteria to the internal reference. The solid line represents the internal reference (Standard Q®, SD Biosensor/Roche). Dashed horizontal lines represent the limits of difference in percentage within which sensitivity rates’ variations were considered acceptable compared to the IR. The vertical dashed line coincides with 80% cut-off, which was considered the minimal sensitivity threshold for FOPH validation above 105 copies/mL of viral load. ^: this test did not pass the validation criteria for insufficient sensitivity at viral loads above 106–107 copies/mL. °: this test did not pass the validation because of lack of specificity. Full article ">Figure 3
Comparative cumulated sensitivity curves for all rapid antigen tests (RATs) evaluated in the study. <a href="#microorganisms-09-02589-f003" class="html-fig">Figure 3</a> legend. (A). All RATs passing the validation criteria. (B). All RATs failing the validation. (C). RATs with an automated reader (Exdia from Precision Biosensor and LumiraDx assay from LumiraDx, Alloa) showed higher sensitivity performances compared to the internal reference (Roche). (D). Sensitivity curves comparing all the internal reference tests (Roche) used along each series showing the inter-laboratory and inter-series variability. RAT: rapid antigen test. On the x-axis there is the number of Ct; horizontal lines represent the Ct cut-offs considered for the validation criteria. Horizontal dotted lines and the three arrows represent the threshold of sensitivity rates to be considered for validation at different Ct cut-offs. Full article ">

19 pages, 1034 KiB

Open AccessReview

Occult Infection with Hepatitis C Virus: Looking for Clear-Cut Boundaries and Methodological Consensus

by Anna Wróblewska, Krzysztof Piotr Bielawski and Katarzyna Sikorska

J. Clin. Med. 2021, 10(24), 5874; https://doi.org/10.3390/jcm10245874 - 14 Dec 2021

Cited by 6 | Viewed by 3438

Abstract

The sustained virologic response and elimination of HCV is widely viewed as a true cure of chronic hepatitis C as it associates with amelioration of histological liver damage and improved clinical outcomes. Therefore, the existence and clinical burden of occult HCV infection (OCI) [...] Read more.

The sustained virologic response and elimination of HCV is widely viewed as a true cure of chronic hepatitis C as it associates with amelioration of histological liver damage and improved clinical outcomes. Therefore, the existence and clinical burden of occult HCV infection (OCI) has been a controversial issue for many years. In this review, we summarize recently published data that adds new information on the molecular and clinical background of OCI and its epidemiological significance. We also identify and discuss the most important methodological pitfalls, which can be a source of inconsistency between studies. Data that have accumulated so far, strongly support the existence of extrahepatic HCV replication in individuals negative for serum HCV-RNA by conventional clinical tests. OCI emerges as a condition where the immune system is unable to fully resolve infection but it is continuously stimulated by low levels of HCV antigens, leading to progression of liver pathology and extrahepatic HCV-related complications. Moreover, the development of monitoring strategies or management guidelines for OCI is still hampered by the lack of clear definition and the confusion regarding its clinical significance. Careful study design and the introduction of uniform protocols for the detection of low-level HCV-RNA are crucial for obtaining reliable data on OCI. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 825 KiB

Open AccessArticle

Comparison between Dexamethasone and Methylprednisolone Therapy in Patients with COVID-19 Pneumonia Admitted to Non-Intensive Medical Units

by Roberta Buso, Francesco Cinetto, Alessandro Dell’Edera, Nicola Veneran, Cesarina Facchini, Valeria Biscaro, Stefania Schiavon, Elisa Vian, Ugo Grossi, Giacomo Zanus, Mario Giobbia, Riccardo Scarpa, Carlo Agostini, Marcello Rattazzi and Carla Felice

J. Clin. Med. 2021, 10(24), 5812; https://doi.org/10.3390/jcm10245812 - 12 Dec 2021

Cited by 4 | Viewed by 2412

Abstract

(1) Background: Data on different steroid compounds for the treatment of hospitalized COVID-19 (coronavirus disease 2019) patients are still limited. The aim of this study was to compare COVID-19 patients admitted to non-intensive units and treated with methylprednisolone or dexamethasone. (2) Methods: This [...] Read more.

(1) Background: Data on different steroid compounds for the treatment of hospitalized COVID-19 (coronavirus disease 2019) patients are still limited. The aim of this study was to compare COVID-19 patients admitted to non-intensive units and treated with methylprednisolone or dexamethasone. (2) Methods: This was a single-center retrospective study that included consecutive patients with COVID-19 hospitalized in medical wards during the second wave of the pandemic. Thirty-day mortality and the need for intensive or semi-intensive care were the main clinical outcomes analyzed in patients receiving methylprednisolone (60 mg/day) compared with dexamethasone (6 mg/day). Secondary outcomes included complication rates, length of hospital stay, and time to viral clearance. (3) Results: Two-hundred-forty-six patients were included in the analysis, 110 treated with dexamethasone and 136 with methylprednisolone. No statistically significant differences were found between the two groups of patients regarding 30-day mortality (OR 1.35, CI95% 0.71–2.56, p = 0.351) and the need for intensive or semi-intensive care (OR 1.94, CI95% 0.81–4.66, p = 0.136). The complication rates, length of hospital stay, and time to viral clearance did not significantly differ between the two groups. (4) Conclusions: In patients hospitalized for COVID-19 in non-intensive units, the choice of different steroid compounds, such as dexamethasone or methylprednisolone, did not affect the main clinical outcomes. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 751 KiB

Open AccessArticle

Sex Differences in Salmonellosis Incidence Rates—An Eight-Country National Data-Pooled Analysis

by Victoria Peer, Naama Schwartz and Manfred S. Green

J. Clin. Med. 2021, 10(24), 5767; https://doi.org/10.3390/jcm10245767 - 9 Dec 2021

Cited by 5 | Viewed by 2456

Abstract

Background: There are few studies on sex differences in the incidence rates (IR) for salmonellosis over several countries by age and time period. The purpose of this study was to explore the extent and consistency of the sex and age-specific differences. Methods: We [...] Read more.

Background: There are few studies on sex differences in the incidence rates (IR) for salmonellosis over several countries by age and time period. The purpose of this study was to explore the extent and consistency of the sex and age-specific differences. Methods: We analyzed national data from eight countries between 1994 and 2016. We computed country-specific male to female incidence rate ratios (IRRs) for each age group and pooled the data using meta-analytic methods. Variations of the IRRs by age, country and time period were evaluated using meta-regression. Results: The pooled male to female incidence RRs for ages 0–1, 1–4, 5–9 and 10–14, were 1.04 (1.02–1.06), 1.02 (1.01–1.03), 1.07 (1.05–1.08) and 1.28 (1.23–1.33), respectively. For the ages 15–44 and 45–64, the incidence rates were significantly higher in females. Meta-regression analyses indicate that age groups contributed most of the variation in the male to female IRRs. Conclusions: We suggest that genetic and hormonal factors and interactions between hormones and gut microbiota could contribute to the sex differences observed in young children. These findings should provide clues about the mechanisms of the infection, and should be useful in targeting treatments and development of vaccines. Highlights: (1) This manuscript provides consistent estimates of the excess salmonellosis incidence rates in male children up to age 15, which suggests an impact of sex hormones or genetic differences. (2) Our findings should promote the further investigations on sex-related determinants of infectious diseases. Full article

(This article belongs to the Topic Infectious Diseases)

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10 pages, 729 KiB

Open AccessArticle

Self-Collected Samples to Detect SARS-CoV-2: Direct Comparison of Saliva, Tongue Swab, Nasal Swab, Chewed Cotton Pads and Gargle Lavage

by Niko Kohmer, Lisa Eckermann, Boris Böddinghaus, Udo Götsch, Annemarie Berger, Eva Herrmann, Marhild Kortenbusch, Peter Tinnemann, Rene Gottschalk, Sebastian Hoehl and Sandra Ciesek

J. Clin. Med. 2021, 10(24), 5751; https://doi.org/10.3390/jcm10245751 - 8 Dec 2021

Cited by 16 | Viewed by 3445

Abstract

Testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by RT-PCR is a vital public health tool in the pandemic. Self-collected samples are increasingly used as an alternative to nasopharyngeal swabs. Several studies suggested that they are sufficiently sensitive to be a useful [...] Read more.

Testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by RT-PCR is a vital public health tool in the pandemic. Self-collected samples are increasingly used as an alternative to nasopharyngeal swabs. Several studies suggested that they are sufficiently sensitive to be a useful alternative. However, there are limited data directly comparing several different types of self-collected materials to determine which material is preferable. A total of 102 predominantly symptomatic adults with a confirmed SARS-CoV-2 infection self-collected native saliva, a tongue swab, a mid-turbinate nasal swab, saliva obtained by chewing a cotton pad and gargle lavage, within 48 h of initial diagnosis. Sample collection was unsupervised. Both native saliva and gargling with tap water had high diagnostic sensitivity of 92.8% and 89.1%, respectively. Nasal swabs had a sensitivity of 85.1%, which was not significantly inferior to saliva (p = 0.092), but 16.6% of participants reported they had difficult in self-collection of this sample. A tongue swab and saliva obtained by chewing a cotton pad had a significantly lower sensitivity of 74.2% and 70.2%, respectively. Diagnostic sensitivity was not related to the presence of clinical symptoms or to age. When comparing self-collected specimens from different material, saliva, gargle lavage or mid-turbinate nasal swabs may be considered for most symptomatic patients. However, complementary experiments are required to verify that differences in performance observed among the five sampling modes were not attributed to collection impairment. Full article

(This article belongs to the Topic Infectious Diseases)

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16 pages, 811 KiB

Open AccessArticle

Propagation of SARS-CoV-2 in Calu-3 Cells to Eliminate Mutations in the Furin Cleavage Site of Spike

by John James Baczenas, Hanne Andersen, Sujatha Rashid, David Yarmosh, Nikhita Puthuveetil, Michael Parker, Rebecca Bradford, Clint Florence, Kimberly J. Stemple, Mark G. Lewis and Shelby L. O’Connor

Viruses 2021, 13(12), 2434; https://doi.org/10.3390/v13122434 - 4 Dec 2021

Cited by 20 | Viewed by 4808

Abstract

SARS-CoV-2 pathogenesis, vaccine, and therapeutic studies rely on the use of animals challenged with highly pathogenic virus stocks produced in cell cultures. Ideally, these virus stocks should be genetically and functionally similar to the original clinical isolate, retaining wild-type properties to be reliably [...] Read more.

SARS-CoV-2 pathogenesis, vaccine, and therapeutic studies rely on the use of animals challenged with highly pathogenic virus stocks produced in cell cultures. Ideally, these virus stocks should be genetically and functionally similar to the original clinical isolate, retaining wild-type properties to be reliably used in animal model studies. It is well-established that SARS-CoV-2 isolates serially passaged on Vero cell lines accumulate mutations and deletions in the furin cleavage site; however, these can be eliminated when passaged on Calu-3 lung epithelial cell lines, as presented in this study. As numerous stocks of SARS-CoV-2 variants of concern are being grown in cell cultures with the intent for use in animal models, it is essential that propagation methods generate virus stocks that are pathogenic in vivo. Here, we found that the propagation of a B.1.351 SARS-CoV-2 stock on Calu-3 cells eliminated viruses that previously accumulated mutations in the furin cleavage site. Notably, there were alternative variants that accumulated at the same nucleotide positions in virus populations grown on Calu-3 cells at multiple independent facilities. When a Calu-3-derived B.1.351 virus stock was used to infect hamsters, the virus remained pathogenic and the Calu-3-specific variants persisted in the population. These results suggest that Calu-3-derived virus stocks are pathogenic but care should still be taken to evaluate virus stocks for newly arising mutations during propagation. Full article

(This article belongs to the Topic Infectious Diseases)

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12 pages, 2048 KiB

Open AccessArticle

Epstein-Barr Virus Infection Alone or Jointly with Human Papillomavirus Associates with Down-Regulation of miR-145 in Oral Squamous-Cell Carcinoma

by Chukkris Heawchaiyaphum, Tipaya Ekalaksananan, Natcha Patarapadungkit, Suchin Worawichawong and Chamsai Pientong

Microorganisms 2021, 9(12), 2496; https://doi.org/10.3390/microorganisms9122496 - 2 Dec 2021

Cited by 3 | Viewed by 1938

Abstract

Down-regulation of tumor-suppressive miR-145 has been reported in various malignancies, including oral squamous-cell carcinoma (OSCC) that is influenced by several factors, including Epstein-Barr virus (EBV) and human papillomavirus (HPV). Oncoviruses can modulate the expression of cellular microRNAs. Therefore, we sought to investigate the [...] Read more.

Down-regulation of tumor-suppressive miR-145 has been reported in various malignancies, including oral squamous-cell carcinoma (OSCC) that is influenced by several factors, including Epstein-Barr virus (EBV) and human papillomavirus (HPV). Oncoviruses can modulate the expression of cellular microRNAs. Therefore, we sought to investigate the association of miR-145 down-regulation in OSCC with EBV and/or HPV infection, which might be a possible mechanism of these viruses in oral carcinogenesis. Herein, prevalence of EBV, HPV, and their co-infection was significantly higher in tumors than normal tissues of OSCC. EBV infection alone or jointly with HPV was significantly associated with down-regulation of miR-145 in tumors compared with normal adjacent tissues. In cell lines infected with EBV or HPV, miR-145 was also down-regulated. Consistently, methylation of miR-145 was significantly greater in tumors, and well correlated with increased expression of DNMT3B, which was influenced by infection with EBV and HPV. In cell lines, only EBV infection was associated with increased expression of DNMT3B. Moreover, the level of EBV-LMP1 mRNA in tumors was negatively correlated with miR-145 and positively correlated with DNMT3B. Therefore, EBV alone or jointly with HPV is associated with down-regulation of miR-145 and may influence on miR-145 promoter methylation through the induction of DNMT3B in OSCC. Full article

(This article belongs to the Topic Infectious Diseases)

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EBV and HPV infection is more frequently detected in OSCC tumor tissues than in normal tissues. Prevalence of HPV, EBV, and their co-occurrence in tumor and normal adjacent tissues (A). The LMP1 expression in tumor and normal adjacent tissues was determined by qRT-PCR (B). Distribution of HPV genotypes in OSCC tissues as determined by RLBH (C) ***: p < 0.001. Full article ">Figure 2
Representative scatter plots of miR-145 expression in normal and HNSCC tissues in microarrays. Expression levels of miR-145 in normal and HNSCC tissues plotted from microarray data; GSE82064 (A), GSE45238 (B), GSE103931 (C), GSE137865 (D) and GSE11163 (E). *: p < 0.05; **: p < 0.01; ***: p < 0.001. Full article ">Figure 3
EBV infection alone or jointly with HPV associates with the down-regulation of miR-145 in OSCC. The expression of miR-145 in OSCC tissues (A) and OSCC tissues with or without EBV and/or HPV (B) and in cancer cell lines (C) was examined by qRT-PCR. *: p < 0.05; **: p < 0.01; ***: p < 0.001. Full article ">Figure 4
EBV silences miR-145 by DNA methylation via DNMT3B. The methylation status of miR-145 was determined by MSP using specific primers. The number of samples in which hypermethylation occurred in tumor and normal adjacent tissues (A). The expression of DNMT3B in OSCC tissues (B), OSCC tissues with or without the infection of EBV and/or HPV (C) and cancer cell lines (D) were examined by qRT-PCR. The expression levels of DNMT1 in OSCC tissues (E) and cell lines (F) were examined by qRT-PCR. *: p < 0.05; **: p < 0.01; ***: p < 0.001. Full article ">Figure 5
EBV infection is associated with the down-regulation of miR-145. The correlation of LMP1 mRNA level with miR-145 (A) and DNMT3B (B) mRNA levels was analyzed by Pearson correlation. Expression data of miR-145 in normal and HNSCC tissues, that were obtained from microarray data (GSE82064), were analyzed and plotted according to the infection of EBV and/or HPV (C). ***: p < 0.0001. Full article ">

23 pages, 1013 KiB

Open AccessReview

Antifungal Resistance in Dermatophytes: Genetic Considerations, Clinical Presentations and Alternative Therapies

by Rosalie Sacheli and Marie-Pierre Hayette

J. Fungi 2021, 7(11), 983; https://doi.org/10.3390/jof7110983 - 18 Nov 2021

Cited by 55 | Viewed by 4921

Abstract

Numerous reports describe the emergence of resistance in dermatophytes, especially in T. rubrum and T. mentagrophytes/indotineae strains. We here present a review of the current status of resistance in dermatophytes worldwide. Resistance to terbinafine is mainly discussed, with different mutations found in the [...] Read more.

Numerous reports describe the emergence of resistance in dermatophytes, especially in T. rubrum and T. mentagrophytes/indotineae strains. We here present a review of the current status of resistance in dermatophytes worldwide. Resistance to terbinafine is mainly discussed, with different mutations found in the squalene epoxidase gene also considered. Resistance to azoles is also approached. Clinical presentations caused by resistant dermatophytes are presented, together with alternative therapies that help to better manage these kind of infections. Full article

(This article belongs to the Topic Infectious Diseases)

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