Whole-genome sequencing is increasingly being used to investigate the spatial and temporal distri... more Whole-genome sequencing is increasingly being used to investigate the spatial and temporal distribution of viral pathogens including the Severe Acute Respiratory Syndrome Coronavirus Variant 2 (SARS-CoV-2) which is responsible for the ongoing COVID-19 pandemic. In this study, we determined 55 complete genome sequences of SARS-CoV-2 strains isolated from patients from Noakhali, a South-Eastern district in Bangladesh. Variant analysis of our sequenced genomes identified sixteen rare variations in S, six in N, two in M, one in E protein and the S protein variation, Y204F, identified in two of our sequenced strains, has not been reported from any other countries in the GISAID database. Comparison of the prevalence pattern across the country showed GH clade lineages B.1.36 and B.1.36.16 to be abundant in Noakhali and the South-Eastern region of Chittagong when compared to the rest of the country. Phylodynamic analysis of our sequenced genomes revealed that the virus was estimated to be e...
Background: Acinetobacter calcoaceticus-A. baumannii (ACB) complex pathogens are known for their ... more Background: Acinetobacter calcoaceticus-A. baumannii (ACB) complex pathogens are known for their prevalence in nosocomial infections and extensive antimicrobial resistance (AMR) capabilities. While genomic studies worldwide have elucidated the genetic context of antibiotic resistance in major international clones (ICs) of clinical Acinetobacter spp., not much information is available from Bangladesh. In this study, we analysed the AMR profiles of 63 ACB complex strains collected from Dhaka, Bangladesh. Following this, we generated draft genomes of 15 of these strains to understand the prevalence and genomic environments of AMR, virulence and mobilization associated genes in different Acinetobacter clones. Results: Around 84% (n = 53) of the strains were extensively drug resistant (XDR) with two showing pan-drug resistance. Draft genomes generated for 15 strains confirmed 14 to be A. baumannii while one was A. nosocomialis. Most A. baumannii genomes fell under three clonal complexes ...
Abstract Multidrug-resistant (MDR) Escherichia coli has been previously detected in other locatio... more Abstract Multidrug-resistant (MDR) Escherichia coli has been previously detected in other locations, but not in Chhatak, a diarrhea endemic region of Bangladesh. In this study, 36 E. coli isolated from diarrhea stools of adults and children from Chhatak were investigated for the prevalence of drug resistance, virulence and resistance related genes, genotyping, and other molecular characteristics. Antibiotic resistance profiling was performed by disk diffusion method whereas the presence of virulence genes, mobile genetic elements, plasmids, and resistance-related genes were monitored by PCR assay. Multiple resistance to drugs was observed in 94.4% of the isolates and 24 (66.7%) of the strains were found as enterotoxigenic E. coli (ETEC) pathogroup. Genotyping by ERIC-PCR fingerprinting revealed genetic heterogeneity among the MDR E. coli strains. Overall, 88% of E. coli strains possessed plasmids ranging from 0.6 to 140Â MDa. Of the detected integrases (69%), intl1 was predominant (53%). Erythromycin esterase-B (ereB) was present in 8 out of 36 macrolide resistant strains (22%). Of 27 beta-lactam resistant isolates, 70%, 41%, and 33% carried blaCTX-M-1, blaTEM, and blaOXA, respectively. Of 23 tetracycline resistant strains, 13 tetB (57%) and 8 tetA (35%) were detected. All 24 ciprofloxacin resistant strains tested positive for gyrA, but none for qnrA. Sequence analysis of the quinolone resistance-determining regions (QRDR) of gyrA of two ciprofloxacin resistant strains showed two point mutations (S83L, D87N). Computational docking studies revealed a decreased interaction of the drug with the target due to this mutation. In conclusion, high incidence of plasmids and antimicrobial resistance in E. coli carrying virulence genes and resistance markers for antimicrobial drugs in diarrheagenic patients of Bangladesh is alarming as lateral transfer of these virulence and resistance genes in other infectious agents can make them irresistible, and infection control more challenging in the days to come.
2019 International Conference on Mechatronics, Robotics and Systems Engineering (MoRSE), 2019
Human pregnancies underlie many common pregnancy diseases for trophoblast-decidual interaction, s... more Human pregnancies underlie many common pregnancy diseases for trophoblast-decidual interaction, such as pre-eclampsia, still birth. As uterine mucosa transforms into the decidua and fetal placenta implants there, many morphological changes occur due to immunological, metabolical changes. In this work, we analyzed single-cell RNA-seq data of pregnant women. The data was downloaded from the study of the University of Cambridge's Sarah Teichman Lab. We analyzed disease symptoms and investigated responsible genes by checking RNA-editing sites and gene functionality. The aim of this study is to identify editing sites, their impact on pregnancy complications and to make a profile for detecting disease criteria. The result shows the chromosome-wise distribution of RNA-editing sites which have a reflection of intra-chromosomal distribution. We found that the highest edited sites are in the regulatory region and also classified genes according to their functions and identified their role in pregnancy complications. Our result indicates that there are common RNA editing sites for a particular cell-like T-cell and CD-cell with probability more than 0.5.
The fingerprint pattern in the gel was analyzed using a computer software package, Bionumeric (Ap... more The fingerprint pattern in the gel was analyzed using a computer software package, Bionumeric (Applied Maths, Belgium). After background subtraction and gel normalization, the fingerprint patterns were typed according to banding similarity and dissimilarity as recommended by the manufacturer. , using the Dice similarity coefficient and unweighted-pair group method employing average linkage (UPGMA) clustering, by using pulsed-field gel electrophoresis (PFGE) images of NotI- restriction digested genomic DNA of the tested Nepalese V. cholerae strains; PFGE images of contemporary V. cholerae O1 El Tor strains from Haiti and Bangladesh, including El Tor reference strain N16961 were also included. The scale bar at the top (left) indicates similarity coefficient. The banding patterns and the similarity coefficient revealed 100% similarity for all the tested Nepalese, Haitian, and Bangladeshi V. cholerae strains included in the dendrogram, suggesting high level of clonal relatedness
Aeromonads are aquatic bacteria associated with frequent outbreaks of diarrhea in coastal Banglad... more Aeromonads are aquatic bacteria associated with frequent outbreaks of diarrhea in coastal Bangladesh, but their potential risks from environmental sources have remained largely unexplored. This study, over 2 years, examined homestead pond waters in the region for monthly dynamics and diversity of Aeromonas spp. The bacterial counts showed bi-modal annual growth peak, pre- and post-monsoon, strongly correlating (p < 0.0005) with temperature. Of 200 isolates characterized, Aeromonas veronii bv. sobria (27%) was predominant among co-existent Aeromonas schubertii (20%), Aeromonas hydrophila (17%), Aeromonas caviae (13%), and three more. PCR screening of virulence-related genes identified 15 genotypes (I to XV), however, enterotoxigenicity in animal model was observed for five genotypes, ca. 18% (nine of 50) strains, prevalent in A. veronii bv. sobria, A. hydrophila, and A. caviae. Pathogenic strains were distinguishable by possessing at least three of the major virulence genes: ascV,...
Morganella morganii, a gram negative, facultative anaerobic bacterium belonging to the Proteeae t... more Morganella morganii, a gram negative, facultative anaerobic bacterium belonging to the Proteeae tribe of the Morganellaceae family, is an unusual opportunistic pathogen mainly responsible for nosocomial and urinary tract infections. While cattle have long been established as a source of a few zoonotic pathogens, no such data has been recorded for M. morganii despite its ubiquitous presence in nature and a number of animal hosts. In this study, draft genomes were produced of three M. morganii isolates from Bangladeshi cattle. The three isolates, named B2, B3 and B5, possessed an average genome size of 3.9 Mp, a GC% of ∼51% and pan and core genomes of 4637 and 3812 genes, respectively. All strains were bearers of the qnrD1 carrying plasmid Col3M and possessed roughly similar virulence profiles and prophage regions. The strains also carried genes that were unique when compared with other publicly available M. morganii genomes. Many of these genes belonged to metabolic pathways associat...
In this study we announce the draft genome sequence of a newly identified Acinetobacter species c... more In this study we announce the draft genome sequence of a newly identified Acinetobacter species cross-reacting with E. coli serotype 0157:H7. The advent of Next-Generation technology has paved to way to discover new species which could otherwise be misidentified using conventional cultural and serotyping methods. The whole genome sequence of this isolate will help to identify potential marker/s of intervention and further genomic analysis might also shed light onto the virulence properties of this newly identified Acinetobacter species which has been provided the new name of Acinetobacter maqsudiensis.
We report here the first draft genome sequence of the non-O1/non-O139strain VcN1, isolated from D... more We report here the first draft genome sequence of the non-O1/non-O139strain VcN1, isolated from Dhaka, Bangladesh. The data submitted to GenBank for this strain will contribute to advancing our understanding of this environmentally disseminated bacterium, including its virulence and its evolution as an important pathogen.
Vibrio parahaemolyticus is responsible for seafood-related gastroenteritis worldwide. In Banglade... more Vibrio parahaemolyticus is responsible for seafood-related gastroenteritis worldwide. In Bangladesh, diarrhea is endemic and diarrheagenic V. parahaemolyticus serotypes occur naturally in the coastal and estuarine aquatic environment. V. parahaemolyticus strains, isolated from estuarine surface water of the Bay of Bengal villages of Bangladesh during 2006-2008, were tested for the presence of virulence and pandemic-marker genes, serodiversity, and phylogenetic relatedness. PCR analysis of V. parahaemolyticus (n=175) showed 53 (30.3%) strains to possess tdh, the major virulence gene encoding thermostable direct hemolysin. Serotyping results revealed the tdh(+)V. parahaemolyticus strains to belong to 10 different serotypes, of which the O8:K21 (30.2%) and O3:K6 (24.5%) were predominantly non-pandemic and pandemic serotypes, respectively; while O5:K30 and O9:KUT were new. The pandemic markers, orf8 and toxRS(variant), were present only in the pandemic serotype O3:K6 (n=13) and its serovariant O4:K68 (n=2). Temporal distribution of the tdh(+) serotypes revealed the O8:K21 to be predominant in 2006 and 2007, while O3:K6 was the predominant tdh(+) serotype in 2008. Pulsed-field gel electrophoresis (PFGE) of SfiI-digested genomic DNA revealed high genetic diversity among the V. parahaemolyticus strains, while dendrogram constructed with the PFGE patterns formed two major clusters separating the tdh(+) O3:K6 and its pandemic serovariants from the tdh(+) non-pandemic (O8:K21) strains, suggesting different lineages for them. The potential health risk related to the prevalent tdh(+) strains, including the observed temporal change of the predominant tdh(+) serotype, from O8:K21 to the pandemic serotype O3:K6 in estuarine surface waters serving as the major source of drinking water suggests the need for routine environmental monitoring to prevent V. parahaemolyticus infection in Bangladesh.
Whole-genome sequencing is increasingly being used to investigate the spatial and temporal distri... more Whole-genome sequencing is increasingly being used to investigate the spatial and temporal distribution of viral pathogens including the Severe Acute Respiratory Syndrome Coronavirus Variant 2 (SARS-CoV-2) which is responsible for the ongoing COVID-19 pandemic. In this study, we determined 55 complete genome sequences of SARS-CoV-2 strains isolated from patients from Noakhali, a South-Eastern district in Bangladesh. Variant analysis of our sequenced genomes identified sixteen rare variations in S, six in N, two in M, one in E protein and the S protein variation, Y204F, identified in two of our sequenced strains, has not been reported from any other countries in the GISAID database. Comparison of the prevalence pattern across the country showed GH clade lineages B.1.36 and B.1.36.16 to be abundant in Noakhali and the South-Eastern region of Chittagong when compared to the rest of the country. Phylodynamic analysis of our sequenced genomes revealed that the virus was estimated to be e...
Background: Acinetobacter calcoaceticus-A. baumannii (ACB) complex pathogens are known for their ... more Background: Acinetobacter calcoaceticus-A. baumannii (ACB) complex pathogens are known for their prevalence in nosocomial infections and extensive antimicrobial resistance (AMR) capabilities. While genomic studies worldwide have elucidated the genetic context of antibiotic resistance in major international clones (ICs) of clinical Acinetobacter spp., not much information is available from Bangladesh. In this study, we analysed the AMR profiles of 63 ACB complex strains collected from Dhaka, Bangladesh. Following this, we generated draft genomes of 15 of these strains to understand the prevalence and genomic environments of AMR, virulence and mobilization associated genes in different Acinetobacter clones. Results: Around 84% (n = 53) of the strains were extensively drug resistant (XDR) with two showing pan-drug resistance. Draft genomes generated for 15 strains confirmed 14 to be A. baumannii while one was A. nosocomialis. Most A. baumannii genomes fell under three clonal complexes ...
Abstract Multidrug-resistant (MDR) Escherichia coli has been previously detected in other locatio... more Abstract Multidrug-resistant (MDR) Escherichia coli has been previously detected in other locations, but not in Chhatak, a diarrhea endemic region of Bangladesh. In this study, 36 E. coli isolated from diarrhea stools of adults and children from Chhatak were investigated for the prevalence of drug resistance, virulence and resistance related genes, genotyping, and other molecular characteristics. Antibiotic resistance profiling was performed by disk diffusion method whereas the presence of virulence genes, mobile genetic elements, plasmids, and resistance-related genes were monitored by PCR assay. Multiple resistance to drugs was observed in 94.4% of the isolates and 24 (66.7%) of the strains were found as enterotoxigenic E. coli (ETEC) pathogroup. Genotyping by ERIC-PCR fingerprinting revealed genetic heterogeneity among the MDR E. coli strains. Overall, 88% of E. coli strains possessed plasmids ranging from 0.6 to 140Â MDa. Of the detected integrases (69%), intl1 was predominant (53%). Erythromycin esterase-B (ereB) was present in 8 out of 36 macrolide resistant strains (22%). Of 27 beta-lactam resistant isolates, 70%, 41%, and 33% carried blaCTX-M-1, blaTEM, and blaOXA, respectively. Of 23 tetracycline resistant strains, 13 tetB (57%) and 8 tetA (35%) were detected. All 24 ciprofloxacin resistant strains tested positive for gyrA, but none for qnrA. Sequence analysis of the quinolone resistance-determining regions (QRDR) of gyrA of two ciprofloxacin resistant strains showed two point mutations (S83L, D87N). Computational docking studies revealed a decreased interaction of the drug with the target due to this mutation. In conclusion, high incidence of plasmids and antimicrobial resistance in E. coli carrying virulence genes and resistance markers for antimicrobial drugs in diarrheagenic patients of Bangladesh is alarming as lateral transfer of these virulence and resistance genes in other infectious agents can make them irresistible, and infection control more challenging in the days to come.
2019 International Conference on Mechatronics, Robotics and Systems Engineering (MoRSE), 2019
Human pregnancies underlie many common pregnancy diseases for trophoblast-decidual interaction, s... more Human pregnancies underlie many common pregnancy diseases for trophoblast-decidual interaction, such as pre-eclampsia, still birth. As uterine mucosa transforms into the decidua and fetal placenta implants there, many morphological changes occur due to immunological, metabolical changes. In this work, we analyzed single-cell RNA-seq data of pregnant women. The data was downloaded from the study of the University of Cambridge's Sarah Teichman Lab. We analyzed disease symptoms and investigated responsible genes by checking RNA-editing sites and gene functionality. The aim of this study is to identify editing sites, their impact on pregnancy complications and to make a profile for detecting disease criteria. The result shows the chromosome-wise distribution of RNA-editing sites which have a reflection of intra-chromosomal distribution. We found that the highest edited sites are in the regulatory region and also classified genes according to their functions and identified their role in pregnancy complications. Our result indicates that there are common RNA editing sites for a particular cell-like T-cell and CD-cell with probability more than 0.5.
The fingerprint pattern in the gel was analyzed using a computer software package, Bionumeric (Ap... more The fingerprint pattern in the gel was analyzed using a computer software package, Bionumeric (Applied Maths, Belgium). After background subtraction and gel normalization, the fingerprint patterns were typed according to banding similarity and dissimilarity as recommended by the manufacturer. , using the Dice similarity coefficient and unweighted-pair group method employing average linkage (UPGMA) clustering, by using pulsed-field gel electrophoresis (PFGE) images of NotI- restriction digested genomic DNA of the tested Nepalese V. cholerae strains; PFGE images of contemporary V. cholerae O1 El Tor strains from Haiti and Bangladesh, including El Tor reference strain N16961 were also included. The scale bar at the top (left) indicates similarity coefficient. The banding patterns and the similarity coefficient revealed 100% similarity for all the tested Nepalese, Haitian, and Bangladeshi V. cholerae strains included in the dendrogram, suggesting high level of clonal relatedness
Aeromonads are aquatic bacteria associated with frequent outbreaks of diarrhea in coastal Banglad... more Aeromonads are aquatic bacteria associated with frequent outbreaks of diarrhea in coastal Bangladesh, but their potential risks from environmental sources have remained largely unexplored. This study, over 2 years, examined homestead pond waters in the region for monthly dynamics and diversity of Aeromonas spp. The bacterial counts showed bi-modal annual growth peak, pre- and post-monsoon, strongly correlating (p < 0.0005) with temperature. Of 200 isolates characterized, Aeromonas veronii bv. sobria (27%) was predominant among co-existent Aeromonas schubertii (20%), Aeromonas hydrophila (17%), Aeromonas caviae (13%), and three more. PCR screening of virulence-related genes identified 15 genotypes (I to XV), however, enterotoxigenicity in animal model was observed for five genotypes, ca. 18% (nine of 50) strains, prevalent in A. veronii bv. sobria, A. hydrophila, and A. caviae. Pathogenic strains were distinguishable by possessing at least three of the major virulence genes: ascV,...
Morganella morganii, a gram negative, facultative anaerobic bacterium belonging to the Proteeae t... more Morganella morganii, a gram negative, facultative anaerobic bacterium belonging to the Proteeae tribe of the Morganellaceae family, is an unusual opportunistic pathogen mainly responsible for nosocomial and urinary tract infections. While cattle have long been established as a source of a few zoonotic pathogens, no such data has been recorded for M. morganii despite its ubiquitous presence in nature and a number of animal hosts. In this study, draft genomes were produced of three M. morganii isolates from Bangladeshi cattle. The three isolates, named B2, B3 and B5, possessed an average genome size of 3.9 Mp, a GC% of ∼51% and pan and core genomes of 4637 and 3812 genes, respectively. All strains were bearers of the qnrD1 carrying plasmid Col3M and possessed roughly similar virulence profiles and prophage regions. The strains also carried genes that were unique when compared with other publicly available M. morganii genomes. Many of these genes belonged to metabolic pathways associat...
In this study we announce the draft genome sequence of a newly identified Acinetobacter species c... more In this study we announce the draft genome sequence of a newly identified Acinetobacter species cross-reacting with E. coli serotype 0157:H7. The advent of Next-Generation technology has paved to way to discover new species which could otherwise be misidentified using conventional cultural and serotyping methods. The whole genome sequence of this isolate will help to identify potential marker/s of intervention and further genomic analysis might also shed light onto the virulence properties of this newly identified Acinetobacter species which has been provided the new name of Acinetobacter maqsudiensis.
We report here the first draft genome sequence of the non-O1/non-O139strain VcN1, isolated from D... more We report here the first draft genome sequence of the non-O1/non-O139strain VcN1, isolated from Dhaka, Bangladesh. The data submitted to GenBank for this strain will contribute to advancing our understanding of this environmentally disseminated bacterium, including its virulence and its evolution as an important pathogen.
Vibrio parahaemolyticus is responsible for seafood-related gastroenteritis worldwide. In Banglade... more Vibrio parahaemolyticus is responsible for seafood-related gastroenteritis worldwide. In Bangladesh, diarrhea is endemic and diarrheagenic V. parahaemolyticus serotypes occur naturally in the coastal and estuarine aquatic environment. V. parahaemolyticus strains, isolated from estuarine surface water of the Bay of Bengal villages of Bangladesh during 2006-2008, were tested for the presence of virulence and pandemic-marker genes, serodiversity, and phylogenetic relatedness. PCR analysis of V. parahaemolyticus (n=175) showed 53 (30.3%) strains to possess tdh, the major virulence gene encoding thermostable direct hemolysin. Serotyping results revealed the tdh(+)V. parahaemolyticus strains to belong to 10 different serotypes, of which the O8:K21 (30.2%) and O3:K6 (24.5%) were predominantly non-pandemic and pandemic serotypes, respectively; while O5:K30 and O9:KUT were new. The pandemic markers, orf8 and toxRS(variant), were present only in the pandemic serotype O3:K6 (n=13) and its serovariant O4:K68 (n=2). Temporal distribution of the tdh(+) serotypes revealed the O8:K21 to be predominant in 2006 and 2007, while O3:K6 was the predominant tdh(+) serotype in 2008. Pulsed-field gel electrophoresis (PFGE) of SfiI-digested genomic DNA revealed high genetic diversity among the V. parahaemolyticus strains, while dendrogram constructed with the PFGE patterns formed two major clusters separating the tdh(+) O3:K6 and its pandemic serovariants from the tdh(+) non-pandemic (O8:K21) strains, suggesting different lineages for them. The potential health risk related to the prevalent tdh(+) strains, including the observed temporal change of the predominant tdh(+) serotype, from O8:K21 to the pandemic serotype O3:K6 in estuarine surface waters serving as the major source of drinking water suggests the need for routine environmental monitoring to prevent V. parahaemolyticus infection in Bangladesh.
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