Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has been linked to both life-t... more Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has been linked to both life-threatening hospital-and community-acquired infections across the globe. Here, we conducted a systematic review and meta-analysis to evaluate the prevalence of ESBL in E. coli isolated from humans, animals, and environments in Bangladesh. Following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines, the current systematic review and meta-analysis was taken into account for studies published between 2010 and 2021 in peer-reviewed journals. The meta-analysis was performed on "R" version 4.2.2. A total of 36 studies were included in this systematic review and meta-analysis; among them, 22 were human, seven were animal, four were environmental, and three were multidisciplinary studies. The meta-analysis revealed that the pooled prevalence of ESBL-producing E. coli in Bangladesh was 21% (95% CI: 15%-27%). On the sample basis, the pooled prevalence of ESBL-producing E. coli in humans, animals, and environments was 17% (95% CI: 11%-23%), 22% (95% CI: 9%-34%), and 39% (95% CI: 16%-62%), respectively. All the pooled prevalence of ESBL-producing E. coli showed substantial heterogeneity (I 2 > 75%; p < 0.05) among the selected studies. This systematic review reported 13 different types of resistance genes encoding ESBL, such as bla TEM-1 (37.5%), bla CMY (34.6%), bla CTX-M-1 (20.7%), bla CTX-M-15 (16.1%), bla TEM (12.3%), bla CTX-M and bla OXA (9.6%), bla OXA-1 (5.8%), bla ampC (3.9%), bla SHV (3.8%), bla CMY-2 (2.3%), bla CTX-M-14 (1.3%), and bla CTX-M-9 (0.3%). Moreover, 39 types of epidemiologically important clones (including ST10 and ST131) were detected in ESBL-producing E. coli isolated from humans, animals, and environments in Bangladesh. To the best of our knowledge, this is the first systematic review and meta-analysis of integrated studies on ESBL-producing E. coli using the One Health approach in Bangladesh. The high prevalence of ESBL-producing E. coli, their resistance genes, and epidemiologically important clones in humans, animals, and environments highlights the importance of implementing comprehensive antimicrobial resistance (AMR) surveillance under a One Health perspective to mitigate the AMR consequences in Bangladesh.
Journal of Advanced Veterinary and Animal Research, 2022
Objectives: This study aimed to develop a computerized deep learning (DL) technique to identify b... more Objectives: This study aimed to develop a computerized deep learning (DL) technique to identify bacterial genera more precisely in minimum time than the usual, traditional, and commonly used techniques like cultural, staining, and morphological characteristics. Materials and Methods: A convolutional neural network as a part of machine learning (ML) for bacterial genera identification methods was developed using python programming language and the Keras API with TensorFlow ML or DL framework to discriminate bacterial genera, e.g., Streptococcus, Staphylococcus, Escherichia, Salmonella, and Corynebacterium. A total of 200 dig¬ital microscopic cell images comprising 40 of each of the genera mentioned above were used in this study. Results: The developed technique could identify and distinguish microscopic images of Streptococcus, Staphylococcus, Escherichia, Salmonella, and Corynebacterium with the highest accuracy of 92.20% for Staphylococcus and the lowest of 77.40% for Salmonella. Among the five epochs, the accuracy rate of bacterial genera identification of Staphylococcus was graded 1, and Streptococcus, Escherichia, Corynebacterium, and Salmonella as 2, 3, 4, and 5, respectively. Conclusion: The experimental results suggest using the DL method to predict bacterial genera included in this study. However, further improvement with more bacterial genera, especially of similar morphology, is necessary to make the technique widely used for bacterial genera identification.
Pathogenic, antibiotic-resistant, and biofilm-forming bacteria can be transferred to humans throu... more Pathogenic, antibiotic-resistant, and biofilm-forming bacteria can be transferred to humans through the consumption of contaminated seafood. The present study was carried out to determine antibiotic resistance profiles and virulence determinants in biofilm-forming Enterococcus faecium isolated from seafood in Bangladesh. A total of 150 seafood samples, including shrimp (n = 50), crabs (n = 25), and marine fish (n = 75), were screened using cultural, staining, biochemical, polymerase chain reaction (PCR), Congo red (CR), and disk diffusion (DD) assays. In PCR, E. faecium was detected in 27.3% (41/150; CI95% 20.8; 34.9) of samples, where marine fish (34.7%, CI95% 24.9; 45.9) had the highest prevalence (p < 0.05) compared to crabs (32%, CI95% 17.2; 51.6) and shrimp (14%, CI95% 7.0; 26.1). Thirty-two (78.1%, CI95% 63.3; 88.0) of the E. faecium isolates were determined to be biofilm formers in the CR test, where 43.9% (18/41, CI95% 29.9; 59.0) and 34.2% (14/41, CI95% 21.6; 49.5) of th...
Here, we sequence and analyze a biofilm-forming strain of Enterococcus faecalis BAU_Ef01 isolated... more Here, we sequence and analyze a biofilm-forming strain of Enterococcus faecalis BAU_Ef01 isolated from a shrimp in Bangladesh. The whole genome of the strain had a length of 2,862,301 bp, 38 contigs, an average G+C content of 37.36%, 80.0× genome coverage, and 35 predicted antibiotic resistance and virulence genes each.
Enterococci are commensal bacteria that inhabit the digestive tracts of animals and humans. The t... more Enterococci are commensal bacteria that inhabit the digestive tracts of animals and humans. The transmission of antibiotic-resistant genes through human–animal contact poses a potential public health risk worldwide, as zoonoses from wildlife reservoirs can occur on every continent. The purpose of this study was to detect Enterococcus spp. in rhesus macaques (Macaca mulatta) and to investigate their resistance patterns, virulence profiles, and biofilm-forming ability. Conventional screening of rectal swabs (n = 67) from macaques was followed by polymerase chain reaction (PCR). The biofilm-forming enterococci were determined using the Congo red agar plate assay. Using the disk diffusion test (DDT), antibiogram profiles were determined, followed by resistance and virulence genes identification by PCR. PCR for bacterial species confirmation revealed that 65.7% (44/67) and 22.4% (15/67) of the samples tested positive for E. faecalis and E. faecium, respectively. All the isolated enteroco...
Infectious bursal disease (IBD) is a highly contagious disease that causes significant economic l... more Infectious bursal disease (IBD) is a highly contagious disease that causes significant economic loss in chickens. A cross-sectional study was conducted in the Mymensingh district of Bangladesh to determine the seroprevalence of IBD virus (IBDV) antibodies in backyard chickens and their association with different epidemiological risk factors. A total of 460 serum samples were randomly collected from backyard chickens that had not been previously vaccinated against IBDV. The collected sera were examined using an enzyme-linked immunosorbent assay (ELISA). Data on epidemiological risk factors were collected through face-to-face interviews with owners and subjected to both uni- and multivariable risk analyses to determine their association with IBDV infection. Using ELISA, the overall seroprevalence of IBDV antibodies in backyard chickens was 83.4% (95% confidence interval: 79.8%–86.6%), among which, a significantly higher seroprevalence was recorded in females (83.4%, 345/350), 4–6 week...
Journal of Advanced Veterinary and Animal Research
Anthrax is a rapidly fatal infectious disease affecting herbivores and people. In the farm ani¬ma... more Anthrax is a rapidly fatal infectious disease affecting herbivores and people. In the farm ani¬mals, cattle and sheep are more susceptible, followed by goats and horses, while dwarf pigs and Algerian sheep are relatively resistant. Bacillus anthracis, the causative agent of anthrax, produces spores and persists for decades in the soil, initiating an outbreak through a favorable climate shift. Anthrax is enzootic in many Asian and African countries, and is reported in Australia, some parts of Europe, and America. The clinical courses of this disease in animals are peracute, acute, sub¬acute, and chronic forms. In severely infected cases, the animals are dead without premonitory clinical signs. The blood may fail to clot and can be found in the mouth, nostrils, and anus in the animals that die from anthrax. This bacterium is susceptible to many antibiotics, yet only penicillin and oxytetracycline have the most effective under field conditions. When an outbreak occurs in a defined area...
BackgroundColibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most ... more BackgroundColibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting poultry worldwide. APEC is one of the leading causes of mortality and morbidity associated with significant economic losses in the poultry industry.ObjectiveThis study was aimed to determine the genomic diversity, virulence factor genes (VFGs) and antimicrobial resistance (AMR) genes in the APEC isolated from layer chickens using whole-genome sequencing (WGS).MethodAPEC MTR_BAU02 strain was isolated from the sick and dead birds. Genomic DNA from APEC MTR_BAU02 strain was extracted using commercial DNA extraction kit, WGS libraries were prepared using the Nextera™ DNA Flex Library Prep Kit, and finally, paired-end (2 × 250) WGS performed using Illumina MiSeq sequencer.ResultsThe genome size of strain APEC MTR_BAU02 is 4,924,680 bp with a GC content of 51.1% and 4,681 protein-coding sequences. Among the annotated WGS reads, 99.71% reads mapped to E...
Bovine rotavirus (BRV) is considered the leading cause of calf diarrhea worldwide, including Bang... more Bovine rotavirus (BRV) is considered the leading cause of calf diarrhea worldwide, including Bangladesh. In this study we aimed to identify risk factors for BRV infection and determine the G and P genotypes of BRV strains in diarrheic calves. Fecal samples were collected from 200 diarrheic calves in three districts between January 2014 and October 2015. These samples were screened to detect the presence of BRV using rapid test-strips BIO K 152 (RTSBK). The RTSBK positive samples were further tested by polyacrylamide gel electrophoresis and the silver staining technique to detect rotavirus dsRNA. Risk factors were identified by multivariable logistic regression analysis. The G and P genotypes of BRV were determined by RT-PCR and sequencing. A phylogenetic tree was constructed based on the neighbor-joining method using CLC sequence viewer 8.0. About 23% of the diarrheic calves were BRV positive. The odds of BRV infection were 3.8- (95% confidence interval [95% CI]: 1.0–14.7) and 3.9-t...
BackgroundThe study was aimed to estimate the true prevalence of human tuberculosis (TB); identif... more BackgroundThe study was aimed to estimate the true prevalence of human tuberculosis (TB); identify risk factors and clinical symptoms of TB; and detect rifampicin (RIF) sensitivity in Bangladesh.MethodsThe cross-sectional study was conducted in three Bangladesh districts during 2018. Potential risk factors, clinical symptoms, and comorbidities were collected from 684 TB suspects. Sputum specimens were examined by LED microscopy. TB hierarchical true prevalence, risk factors and clinical symptoms were estimated and identified using a Bayesian analysis framework. Rifampicin sensitivity of M. tuberculosis (MTB) was detected by GeneXpert MTB/RIF assay.ResultsThe median TB true prevalence was 14.2% (3.8; 34.5). Although overall clustering of prevalence was not found, several DOTS centers were identified with high prevalence (22.3% to 43.7%). Risk factors for TB identified (odds ratio) were age (> 25 to 45 years 2.67 (1.09; 6.99), > 45 to 60 years 3.43 (1.38; 9.19) and individuals i...
Antimicrobial resistance (AMR) in Salmonella in poultry poses a serious human health threat as it... more Antimicrobial resistance (AMR) in Salmonella in poultry poses a serious human health threat as it has zoonotic importance. Poultry is often linked with outbreaks of Salmonella-associated foodborne illness. Since antimicrobials are heavily used in poultry in Bangladesh, multidrug-resistant (MDR) Salmonella is quite frequently found there. MDR Salmonella is challenging to treat with antimicrobials and often causes a severe economic loss in the poultry sector. By horizontal gene transfer and/or evolutionary mutations, antimicrobials primarily exert selection pressure that contributes to antimicrobials resistance. In addition, resistance patterns can vary with variations in time and space. Without having prior knowledge of resistance patterns, no effective drugs could be prescribed. Therefore, it is crucial to have updated knowledge on the status of AMR in Salmonella in Bangladesh for effective treatment and management of the flocks against salmonellosis. There are several review articl...
Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has been linked to both life-t... more Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has been linked to both life-threatening hospital-and community-acquired infections across the globe. Here, we conducted a systematic review and meta-analysis to evaluate the prevalence of ESBL in E. coli isolated from humans, animals, and environments in Bangladesh. Following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines, the current systematic review and meta-analysis was taken into account for studies published between 2010 and 2021 in peer-reviewed journals. The meta-analysis was performed on &quot;R&quot; version 4.2.2. A total of 36 studies were included in this systematic review and meta-analysis; among them, 22 were human, seven were animal, four were environmental, and three were multidisciplinary studies. The meta-analysis revealed that the pooled prevalence of ESBL-producing E. coli in Bangladesh was 21% (95% CI: 15%-27%). On the sample basis, the pooled prevalence of ESBL-producing E. coli in humans, animals, and environments was 17% (95% CI: 11%-23%), 22% (95% CI: 9%-34%), and 39% (95% CI: 16%-62%), respectively. All the pooled prevalence of ESBL-producing E. coli showed substantial heterogeneity (I 2 &gt; 75%; p &lt; 0.05) among the selected studies. This systematic review reported 13 different types of resistance genes encoding ESBL, such as bla TEM-1 (37.5%), bla CMY (34.6%), bla CTX-M-1 (20.7%), bla CTX-M-15 (16.1%), bla TEM (12.3%), bla CTX-M and bla OXA (9.6%), bla OXA-1 (5.8%), bla ampC (3.9%), bla SHV (3.8%), bla CMY-2 (2.3%), bla CTX-M-14 (1.3%), and bla CTX-M-9 (0.3%). Moreover, 39 types of epidemiologically important clones (including ST10 and ST131) were detected in ESBL-producing E. coli isolated from humans, animals, and environments in Bangladesh. To the best of our knowledge, this is the first systematic review and meta-analysis of integrated studies on ESBL-producing E. coli using the One Health approach in Bangladesh. The high prevalence of ESBL-producing E. coli, their resistance genes, and epidemiologically important clones in humans, animals, and environments highlights the importance of implementing comprehensive antimicrobial resistance (AMR) surveillance under a One Health perspective to mitigate the AMR consequences in Bangladesh.
Journal of Advanced Veterinary and Animal Research, 2022
Objectives: This study aimed to develop a computerized deep learning (DL) technique to identify b... more Objectives: This study aimed to develop a computerized deep learning (DL) technique to identify bacterial genera more precisely in minimum time than the usual, traditional, and commonly used techniques like cultural, staining, and morphological characteristics. Materials and Methods: A convolutional neural network as a part of machine learning (ML) for bacterial genera identification methods was developed using python programming language and the Keras API with TensorFlow ML or DL framework to discriminate bacterial genera, e.g., Streptococcus, Staphylococcus, Escherichia, Salmonella, and Corynebacterium. A total of 200 dig¬ital microscopic cell images comprising 40 of each of the genera mentioned above were used in this study. Results: The developed technique could identify and distinguish microscopic images of Streptococcus, Staphylococcus, Escherichia, Salmonella, and Corynebacterium with the highest accuracy of 92.20% for Staphylococcus and the lowest of 77.40% for Salmonella. Among the five epochs, the accuracy rate of bacterial genera identification of Staphylococcus was graded 1, and Streptococcus, Escherichia, Corynebacterium, and Salmonella as 2, 3, 4, and 5, respectively. Conclusion: The experimental results suggest using the DL method to predict bacterial genera included in this study. However, further improvement with more bacterial genera, especially of similar morphology, is necessary to make the technique widely used for bacterial genera identification.
Pathogenic, antibiotic-resistant, and biofilm-forming bacteria can be transferred to humans throu... more Pathogenic, antibiotic-resistant, and biofilm-forming bacteria can be transferred to humans through the consumption of contaminated seafood. The present study was carried out to determine antibiotic resistance profiles and virulence determinants in biofilm-forming Enterococcus faecium isolated from seafood in Bangladesh. A total of 150 seafood samples, including shrimp (n = 50), crabs (n = 25), and marine fish (n = 75), were screened using cultural, staining, biochemical, polymerase chain reaction (PCR), Congo red (CR), and disk diffusion (DD) assays. In PCR, E. faecium was detected in 27.3% (41/150; CI95% 20.8; 34.9) of samples, where marine fish (34.7%, CI95% 24.9; 45.9) had the highest prevalence (p < 0.05) compared to crabs (32%, CI95% 17.2; 51.6) and shrimp (14%, CI95% 7.0; 26.1). Thirty-two (78.1%, CI95% 63.3; 88.0) of the E. faecium isolates were determined to be biofilm formers in the CR test, where 43.9% (18/41, CI95% 29.9; 59.0) and 34.2% (14/41, CI95% 21.6; 49.5) of th...
Here, we sequence and analyze a biofilm-forming strain of Enterococcus faecalis BAU_Ef01 isolated... more Here, we sequence and analyze a biofilm-forming strain of Enterococcus faecalis BAU_Ef01 isolated from a shrimp in Bangladesh. The whole genome of the strain had a length of 2,862,301 bp, 38 contigs, an average G+C content of 37.36%, 80.0× genome coverage, and 35 predicted antibiotic resistance and virulence genes each.
Enterococci are commensal bacteria that inhabit the digestive tracts of animals and humans. The t... more Enterococci are commensal bacteria that inhabit the digestive tracts of animals and humans. The transmission of antibiotic-resistant genes through human–animal contact poses a potential public health risk worldwide, as zoonoses from wildlife reservoirs can occur on every continent. The purpose of this study was to detect Enterococcus spp. in rhesus macaques (Macaca mulatta) and to investigate their resistance patterns, virulence profiles, and biofilm-forming ability. Conventional screening of rectal swabs (n = 67) from macaques was followed by polymerase chain reaction (PCR). The biofilm-forming enterococci were determined using the Congo red agar plate assay. Using the disk diffusion test (DDT), antibiogram profiles were determined, followed by resistance and virulence genes identification by PCR. PCR for bacterial species confirmation revealed that 65.7% (44/67) and 22.4% (15/67) of the samples tested positive for E. faecalis and E. faecium, respectively. All the isolated enteroco...
Infectious bursal disease (IBD) is a highly contagious disease that causes significant economic l... more Infectious bursal disease (IBD) is a highly contagious disease that causes significant economic loss in chickens. A cross-sectional study was conducted in the Mymensingh district of Bangladesh to determine the seroprevalence of IBD virus (IBDV) antibodies in backyard chickens and their association with different epidemiological risk factors. A total of 460 serum samples were randomly collected from backyard chickens that had not been previously vaccinated against IBDV. The collected sera were examined using an enzyme-linked immunosorbent assay (ELISA). Data on epidemiological risk factors were collected through face-to-face interviews with owners and subjected to both uni- and multivariable risk analyses to determine their association with IBDV infection. Using ELISA, the overall seroprevalence of IBDV antibodies in backyard chickens was 83.4% (95% confidence interval: 79.8%–86.6%), among which, a significantly higher seroprevalence was recorded in females (83.4%, 345/350), 4–6 week...
Journal of Advanced Veterinary and Animal Research
Anthrax is a rapidly fatal infectious disease affecting herbivores and people. In the farm ani¬ma... more Anthrax is a rapidly fatal infectious disease affecting herbivores and people. In the farm ani¬mals, cattle and sheep are more susceptible, followed by goats and horses, while dwarf pigs and Algerian sheep are relatively resistant. Bacillus anthracis, the causative agent of anthrax, produces spores and persists for decades in the soil, initiating an outbreak through a favorable climate shift. Anthrax is enzootic in many Asian and African countries, and is reported in Australia, some parts of Europe, and America. The clinical courses of this disease in animals are peracute, acute, sub¬acute, and chronic forms. In severely infected cases, the animals are dead without premonitory clinical signs. The blood may fail to clot and can be found in the mouth, nostrils, and anus in the animals that die from anthrax. This bacterium is susceptible to many antibiotics, yet only penicillin and oxytetracycline have the most effective under field conditions. When an outbreak occurs in a defined area...
BackgroundColibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most ... more BackgroundColibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting poultry worldwide. APEC is one of the leading causes of mortality and morbidity associated with significant economic losses in the poultry industry.ObjectiveThis study was aimed to determine the genomic diversity, virulence factor genes (VFGs) and antimicrobial resistance (AMR) genes in the APEC isolated from layer chickens using whole-genome sequencing (WGS).MethodAPEC MTR_BAU02 strain was isolated from the sick and dead birds. Genomic DNA from APEC MTR_BAU02 strain was extracted using commercial DNA extraction kit, WGS libraries were prepared using the Nextera™ DNA Flex Library Prep Kit, and finally, paired-end (2 × 250) WGS performed using Illumina MiSeq sequencer.ResultsThe genome size of strain APEC MTR_BAU02 is 4,924,680 bp with a GC content of 51.1% and 4,681 protein-coding sequences. Among the annotated WGS reads, 99.71% reads mapped to E...
Bovine rotavirus (BRV) is considered the leading cause of calf diarrhea worldwide, including Bang... more Bovine rotavirus (BRV) is considered the leading cause of calf diarrhea worldwide, including Bangladesh. In this study we aimed to identify risk factors for BRV infection and determine the G and P genotypes of BRV strains in diarrheic calves. Fecal samples were collected from 200 diarrheic calves in three districts between January 2014 and October 2015. These samples were screened to detect the presence of BRV using rapid test-strips BIO K 152 (RTSBK). The RTSBK positive samples were further tested by polyacrylamide gel electrophoresis and the silver staining technique to detect rotavirus dsRNA. Risk factors were identified by multivariable logistic regression analysis. The G and P genotypes of BRV were determined by RT-PCR and sequencing. A phylogenetic tree was constructed based on the neighbor-joining method using CLC sequence viewer 8.0. About 23% of the diarrheic calves were BRV positive. The odds of BRV infection were 3.8- (95% confidence interval [95% CI]: 1.0–14.7) and 3.9-t...
BackgroundThe study was aimed to estimate the true prevalence of human tuberculosis (TB); identif... more BackgroundThe study was aimed to estimate the true prevalence of human tuberculosis (TB); identify risk factors and clinical symptoms of TB; and detect rifampicin (RIF) sensitivity in Bangladesh.MethodsThe cross-sectional study was conducted in three Bangladesh districts during 2018. Potential risk factors, clinical symptoms, and comorbidities were collected from 684 TB suspects. Sputum specimens were examined by LED microscopy. TB hierarchical true prevalence, risk factors and clinical symptoms were estimated and identified using a Bayesian analysis framework. Rifampicin sensitivity of M. tuberculosis (MTB) was detected by GeneXpert MTB/RIF assay.ResultsThe median TB true prevalence was 14.2% (3.8; 34.5). Although overall clustering of prevalence was not found, several DOTS centers were identified with high prevalence (22.3% to 43.7%). Risk factors for TB identified (odds ratio) were age (> 25 to 45 years 2.67 (1.09; 6.99), > 45 to 60 years 3.43 (1.38; 9.19) and individuals i...
Antimicrobial resistance (AMR) in Salmonella in poultry poses a serious human health threat as it... more Antimicrobial resistance (AMR) in Salmonella in poultry poses a serious human health threat as it has zoonotic importance. Poultry is often linked with outbreaks of Salmonella-associated foodborne illness. Since antimicrobials are heavily used in poultry in Bangladesh, multidrug-resistant (MDR) Salmonella is quite frequently found there. MDR Salmonella is challenging to treat with antimicrobials and often causes a severe economic loss in the poultry sector. By horizontal gene transfer and/or evolutionary mutations, antimicrobials primarily exert selection pressure that contributes to antimicrobials resistance. In addition, resistance patterns can vary with variations in time and space. Without having prior knowledge of resistance patterns, no effective drugs could be prescribed. Therefore, it is crucial to have updated knowledge on the status of AMR in Salmonella in Bangladesh for effective treatment and management of the flocks against salmonellosis. There are several review articl...
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Papers by Jayedul Hassan