To colonize and infect the host, arthroconidial yeasts must avoid being killed by the host’s defe... more To colonize and infect the host, arthroconidial yeasts must avoid being killed by the host’s defenses. The formation of biofilms on implanted devices allows fungi to avoid host responses and to disseminate into the host. To better study the mechanisms of infection by arthroconidial yeasts, adherence and biofilm formation were assayed using patient samples collected over 10 years. In clinical samples, adherence varies within species, but the relative adherence is constant for those samples isolated from the same infection site. Herein we document, for the first time, in-vitro biofilm formation by Trichosporon dohaense, T. ovoides, T. japonicum, T. coremiiforme, Cutaneotrichosporon mucoides, Cutaneotrichosporon cutaneum, Galactomyces candidus, and Magnusiomyces capitatus on clinically relevant catheter material. Analysis of biofilm biomass assays indicated that biofilm mass changes less than 2-fold, regardless of the species. Our results support the hypothesis that most pathogenic fun...
Background : Pseudomonas aeruginosa is one of the primary pathogens being isolated more frequentl... more Background : Pseudomonas aeruginosa is one of the primary pathogens being isolated more frequently in cystic fibrosis (CF) and exhibits innate resistant to a wide range of antibiotics. Purpose: To determine whether the highly prevalent genotypes of P. aeruginosa are specifically linked to CF patients, isolates from non-CF patients and environment sources were genotypically analyzed. Methods: Collections of P. aeruginosa from lower respiratory secretions (n= 57) were genotyped using pulse-field gel electrophoresis (PFGE). Phenotypic screening for antibiotic susceptibility was performed for the common antimicrobial agents by Etest and automated Phoenix. Results: P. aeruginosa isolates from CF (n=39), non-CF patients (n=13), and environment sources (n=5) were analyzed. The population structure of P. aeruginosa is highly diverse and population specific. All the strains fall among 3 major clusters. Cluster A contained 16 isolates from CF patients and 2 environmental; cluster B contained 12 isolates from CF and one environmental while cluster C contained all the isolates from non CF patients and one environmental. The majority of P. aeruginosa strains in CF were resistant to ciprofloxacin (25.7%) followed by amikacin and gentamicin (each 23.6%). Whereas, the majority of isolates from non-CF were resistant to meropenem (69%), which grouped in cluster C. Conclusion: The fingerprints obtained with P. aeruginosa isolates from CF patients have a high degree of similarity, suggesting specific adaptation of these two clones to CF lung. The third non-CF cluster has different clonal origin, indicating specific clustering in both location and patient group.
Candida glabratais the second leading cause of candidemia in many countries and is one of the mos... more Candida glabratais the second leading cause of candidemia in many countries and is one of the most concerning yeast species of nosocomial importance due to its increasing rate of antifungal drug resistance and emerging multidrug-resistant isolates. Application of multilocus sequence typing (MLST) to clinicalC. glabrataisolates revealed an association of certain sequence types (STs) with drug resistance and mortality. The currentC. glabrataMLST scheme is based on single nucleotide polymorphisms (SNPs) at six loci and is therefore relatively laborious and costly. Furthermore, only a few high-qualityC. glabratareference genomes are available, limiting rapid analysis of clinical isolates by whole genome sequencing. In this study we provide long-read based assemblies for seven additional clinical strains belonging to three different STs and use this information to simplify theC. glabrataMLST scheme. Specifically, a comparison of these genomes identified highly polymorphic loci (HPL) defined by frequent insertions and deletions (indels), two of which proved to be highly resolutive for ST. When challenged with 53 additional isolates, a combination ofTRP1(a component of the current MLST scheme) with either of the two HPL fully recapitulated ST identification. Therefore, our comparative genomic analysis identified a new typing approach combining SNPs and indels and based on only two loci, thus significantly simplifying ST identification inC. glabrata. Because typing tools are instrumental in addressing numerous clinical and biological questions, our new MLST scheme can be used for high throughput typing ofC. glabratain clinical and research settings.
Osteoarticular mycoses are chronic debilitating infections that require extended courses of antif... more Osteoarticular mycoses are chronic debilitating infections that require extended courses of antifungal therapy and may warrant expert surgical intervention. As there has been no comprehensive review of these diseases, the International Consortium for Osteoarticular Mycoses prepared a definitive treatise for this important class of infections.
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is wi... more Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is widely used in clinical laboratories for routine identification of bacteria and yeasts. However, methodological difficulties are still apparent when applied to filamentous fungi. The liquid cultivation method recommended by Bruker Daltonics GmbH for identification of filamentous fungi by MALDI-TOF MS is labour intensive and time-consuming. In this study, growth of Aspergillus species on different (porous) surfaces was investigated with the aim to develop a more reliable, quicker and less laborious identification method using MALDI-TOF MS. Mycelial growth without sporulation mimicking liquid cultivation and reliable MALDI-TOF MS spectra were obtained when A. fumigatus strains were grown on and in between a polycarbonate membrane filter on Sabouraud dextrose agar. A database of in-house reference spectra was created by growing Aspergillus reference strains (mainly focusing on sections Fumiga...
A total of 301 Candida bloodstream isolates collected from 289 patients over 5 years at a tertiar... more A total of 301 Candida bloodstream isolates collected from 289 patients over 5 years at a tertiary hospital in Qatar were evaluated. Out of all Candida infections, 53% were diagnosed in patients admitted to the intensive care units.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, Jan 13, 2017
A prospective international multicentre surveillance study was conducted to investigate the preva... more A prospective international multicentre surveillance study was conducted to investigate the prevalence and amphotericin B (AMB) susceptibility of Aspergillus terreus species complex infections. Three hundred seventy cases from 21 countries were evaluated. The overall prevalence of A. terreus species complex among patients investigated and with mold positive cultures was 5.2% (370/7116). AMB MICs were ranging from 0.125 to 32 mg/L, (median 8mg/L). A. terreus species complex infections cause a wide spectrum of aspergillosis and the majority of cryptic species display high AMB MICs.
Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptoc... more Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi.org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature "C. neoformans species complex" and "C. gattii species complex." Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant ...
Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM Objectives We describe a fatal case of... more Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM Objectives We describe a fatal case of trichosporonosis caused by Trichosporon asahii. The aim was to molecularly characterize the T. asahii strains from blood and foot tissue samples to investigate their genetic relatedness. Case An 85-year-old morbidly obese female with a prior cerebrovascular accident, hypertension, and diabetes mellitus was admitted to a peripheral hospital with type II respiratory failure, metabolic acidosis, and chronic anemia. Three weeks post-hospitalization the patient remained febrile, physical examination showed that the patient had paronychia, nail pigmentation, subungual onychomycosis, and a diabetic foot ulcer. Blood culture, as well as nail and ulcer samples, became positive for Trichosporon yeasts. Methods Trichosporon yeasts were subjected to molecular identification by sequencing the intergenic spacer (IGS1) region. Minimal inhibitory concentrations (MICs) were determined by the EUCAST micr...
Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM Objectives Due to an increasing number... more Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM Objectives Due to an increasing number of patients at risk, (ie, with a highly compromised immune system and/or receiving aggressive chemotherapy treatment), invasive fungal infections (IFI) are increasingly being reported. They are associated with significantly high mortality rates. Aspergillus spp., particularly A. fumigatus, is the major cause of mold-related IFI around the world followed by Fusarium spp., however, other molds are emerging as human pathogens. The aim of this study was to explore the epidemiology and prevalence of the non-Aspergillus and non-Fusarium molds in human clinical samples over 11 years period in Qatar based tertiary hospital using molecular techniques. Methods A total of 91 clinical specimens positive for molds belonging to 90 patients were recorded in about 11 years (September 2003 to November 2014). The isolates were identified based on morphological characteristics and by sequencing the intern...
To colonize and infect the host, arthroconidial yeasts must avoid being killed by the host’s defe... more To colonize and infect the host, arthroconidial yeasts must avoid being killed by the host’s defenses. The formation of biofilms on implanted devices allows fungi to avoid host responses and to disseminate into the host. To better study the mechanisms of infection by arthroconidial yeasts, adherence and biofilm formation were assayed using patient samples collected over 10 years. In clinical samples, adherence varies within species, but the relative adherence is constant for those samples isolated from the same infection site. Herein we document, for the first time, in-vitro biofilm formation by Trichosporon dohaense, T. ovoides, T. japonicum, T. coremiiforme, Cutaneotrichosporon mucoides, Cutaneotrichosporon cutaneum, Galactomyces candidus, and Magnusiomyces capitatus on clinically relevant catheter material. Analysis of biofilm biomass assays indicated that biofilm mass changes less than 2-fold, regardless of the species. Our results support the hypothesis that most pathogenic fun...
Background : Pseudomonas aeruginosa is one of the primary pathogens being isolated more frequentl... more Background : Pseudomonas aeruginosa is one of the primary pathogens being isolated more frequently in cystic fibrosis (CF) and exhibits innate resistant to a wide range of antibiotics. Purpose: To determine whether the highly prevalent genotypes of P. aeruginosa are specifically linked to CF patients, isolates from non-CF patients and environment sources were genotypically analyzed. Methods: Collections of P. aeruginosa from lower respiratory secretions (n= 57) were genotyped using pulse-field gel electrophoresis (PFGE). Phenotypic screening for antibiotic susceptibility was performed for the common antimicrobial agents by Etest and automated Phoenix. Results: P. aeruginosa isolates from CF (n=39), non-CF patients (n=13), and environment sources (n=5) were analyzed. The population structure of P. aeruginosa is highly diverse and population specific. All the strains fall among 3 major clusters. Cluster A contained 16 isolates from CF patients and 2 environmental; cluster B contained 12 isolates from CF and one environmental while cluster C contained all the isolates from non CF patients and one environmental. The majority of P. aeruginosa strains in CF were resistant to ciprofloxacin (25.7%) followed by amikacin and gentamicin (each 23.6%). Whereas, the majority of isolates from non-CF were resistant to meropenem (69%), which grouped in cluster C. Conclusion: The fingerprints obtained with P. aeruginosa isolates from CF patients have a high degree of similarity, suggesting specific adaptation of these two clones to CF lung. The third non-CF cluster has different clonal origin, indicating specific clustering in both location and patient group.
Candida glabratais the second leading cause of candidemia in many countries and is one of the mos... more Candida glabratais the second leading cause of candidemia in many countries and is one of the most concerning yeast species of nosocomial importance due to its increasing rate of antifungal drug resistance and emerging multidrug-resistant isolates. Application of multilocus sequence typing (MLST) to clinicalC. glabrataisolates revealed an association of certain sequence types (STs) with drug resistance and mortality. The currentC. glabrataMLST scheme is based on single nucleotide polymorphisms (SNPs) at six loci and is therefore relatively laborious and costly. Furthermore, only a few high-qualityC. glabratareference genomes are available, limiting rapid analysis of clinical isolates by whole genome sequencing. In this study we provide long-read based assemblies for seven additional clinical strains belonging to three different STs and use this information to simplify theC. glabrataMLST scheme. Specifically, a comparison of these genomes identified highly polymorphic loci (HPL) defined by frequent insertions and deletions (indels), two of which proved to be highly resolutive for ST. When challenged with 53 additional isolates, a combination ofTRP1(a component of the current MLST scheme) with either of the two HPL fully recapitulated ST identification. Therefore, our comparative genomic analysis identified a new typing approach combining SNPs and indels and based on only two loci, thus significantly simplifying ST identification inC. glabrata. Because typing tools are instrumental in addressing numerous clinical and biological questions, our new MLST scheme can be used for high throughput typing ofC. glabratain clinical and research settings.
Osteoarticular mycoses are chronic debilitating infections that require extended courses of antif... more Osteoarticular mycoses are chronic debilitating infections that require extended courses of antifungal therapy and may warrant expert surgical intervention. As there has been no comprehensive review of these diseases, the International Consortium for Osteoarticular Mycoses prepared a definitive treatise for this important class of infections.
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is wi... more Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) is widely used in clinical laboratories for routine identification of bacteria and yeasts. However, methodological difficulties are still apparent when applied to filamentous fungi. The liquid cultivation method recommended by Bruker Daltonics GmbH for identification of filamentous fungi by MALDI-TOF MS is labour intensive and time-consuming. In this study, growth of Aspergillus species on different (porous) surfaces was investigated with the aim to develop a more reliable, quicker and less laborious identification method using MALDI-TOF MS. Mycelial growth without sporulation mimicking liquid cultivation and reliable MALDI-TOF MS spectra were obtained when A. fumigatus strains were grown on and in between a polycarbonate membrane filter on Sabouraud dextrose agar. A database of in-house reference spectra was created by growing Aspergillus reference strains (mainly focusing on sections Fumiga...
A total of 301 Candida bloodstream isolates collected from 289 patients over 5 years at a tertiar... more A total of 301 Candida bloodstream isolates collected from 289 patients over 5 years at a tertiary hospital in Qatar were evaluated. Out of all Candida infections, 53% were diagnosed in patients admitted to the intensive care units.
Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases, Jan 13, 2017
A prospective international multicentre surveillance study was conducted to investigate the preva... more A prospective international multicentre surveillance study was conducted to investigate the prevalence and amphotericin B (AMB) susceptibility of Aspergillus terreus species complex infections. Three hundred seventy cases from 21 countries were evaluated. The overall prevalence of A. terreus species complex among patients investigated and with mold positive cultures was 5.2% (370/7116). AMB MICs were ranging from 0.125 to 32 mg/L, (median 8mg/L). A. terreus species complex infections cause a wide spectrum of aspergillosis and the majority of cryptic species display high AMB MICs.
Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptoc... more Cryptococcosis is a major fungal disease caused by members of the Cryptococcus gattii and Cryptococcus neoformans species complexes. After more than 15 years of molecular genetic and phenotypic studies and much debate, a proposal for a taxonomic revision was made. The two varieties within C. neoformans were raised to species level, and the same was done for five genotypes within C. gattii. In a recent perspective (K. J. Kwon-Chung et al., mSphere 2:e00357-16, 2017, https://doi.org/10.1128/mSphere.00357-16), it was argued that this taxonomic proposal was premature and without consensus in the community. Although the authors of the perspective recognized the existence of genetic diversity, they preferred the use of the informal nomenclature "C. neoformans species complex" and "C. gattii species complex." Here we highlight the advantage of recognizing these seven species, as ignoring these species will impede deciphering further biologically and clinically relevant ...
Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM Objectives We describe a fatal case of... more Poster session 1, September 21, 2022, 12:30 PM - 1:30 PM Objectives We describe a fatal case of trichosporonosis caused by Trichosporon asahii. The aim was to molecularly characterize the T. asahii strains from blood and foot tissue samples to investigate their genetic relatedness. Case An 85-year-old morbidly obese female with a prior cerebrovascular accident, hypertension, and diabetes mellitus was admitted to a peripheral hospital with type II respiratory failure, metabolic acidosis, and chronic anemia. Three weeks post-hospitalization the patient remained febrile, physical examination showed that the patient had paronychia, nail pigmentation, subungual onychomycosis, and a diabetic foot ulcer. Blood culture, as well as nail and ulcer samples, became positive for Trichosporon yeasts. Methods Trichosporon yeasts were subjected to molecular identification by sequencing the intergenic spacer (IGS1) region. Minimal inhibitory concentrations (MICs) were determined by the EUCAST micr...
Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM Objectives Due to an increasing number... more Poster session 2, September 22, 2022, 12:30 PM - 1:30 PM Objectives Due to an increasing number of patients at risk, (ie, with a highly compromised immune system and/or receiving aggressive chemotherapy treatment), invasive fungal infections (IFI) are increasingly being reported. They are associated with significantly high mortality rates. Aspergillus spp., particularly A. fumigatus, is the major cause of mold-related IFI around the world followed by Fusarium spp., however, other molds are emerging as human pathogens. The aim of this study was to explore the epidemiology and prevalence of the non-Aspergillus and non-Fusarium molds in human clinical samples over 11 years period in Qatar based tertiary hospital using molecular techniques. Methods A total of 91 clinical specimens positive for molds belonging to 90 patients were recorded in about 11 years (September 2003 to November 2014). The isolates were identified based on morphological characteristics and by sequencing the intern...
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