Predictive Modeling of Phenotypic Antimicrobial Susceptibility of Selected Beta-Lactam Antimicrobials from Beta-Lactamase Resistance Genes.

The outcome of bacterial infection management relies on prompt diagnosis and effective treatment, but conventional antimicrobial susceptibility testing can be slow and labor-intensive. Therefore, this study aims to predict phenotypic antimicrobial susceptibility of selected beta-lactam antimicrobials in the bacteria of the family Enterobacteriaceae from different beta-lactamase resistance genotypes. Using human datasets extracted from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program conducted by Pfizer and retail meat datasets from the National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS), we used a robust or weighted least square multivariable linear regression modeling framework to explore the relationship between antimicrobial susceptibility data of beta-lactam antimicrobials and different types of beta-lactamase resistance genes. In humans, in the presence of the blaCTX-M-1, blaCTX-M-2, blaCTX-M-8/25, and blaCTX-M-9 groups, MICs of cephalosporins significantly increased by values between 0.34-3.07 µg/mL, however, the MICs of carbapenem significantly decreased by values between 0.81-0.87 µg/mL. In the presence of carbapenemase genes (blaKPC, blaNDM, blaIMP, and blaVIM), the MICs of cephalosporin antimicrobials significantly increased by values between 1.06-5.77 µg/mL, while the MICs of carbapenem antimicrobials significantly increased by values between 5.39-67.38 µg/mL. In retail meat, MIC of ceftriaxone increased significantly in the presence of blaCMY-2, blaCTX-M-1, blaCTX-M-55, blaCTX-M-65, and blaSHV-2 by 55.16 µg/mL, 222.70 µg/mL, 250.81 µg/mL, 204.89 µg/mL, and 31.51 µg/mL respectively. MIC of cefoxitin increased significantly in the presence of blaCTX-M-65 and blaTEM-1 by 1.57 µg/mL and 1.04 µg/mL respectively. In the presence of blaCMY-2, MIC of cefoxitin increased by an average of 8.66 µg/mL over 17 years. Compared to E. coli isolates, MIC of cefoxitin in Salmonella enterica isolates decreased significantly by 0.67 µg/mL. On the other hand, MIC of ceftiofur increased in the presence of blaCTX-M-1, blaCTX-M-65, blaSHV-2, and blaTEM-1 by 8.82 µg/mL, 9.11 µg/mL, 8.18 µg/mL, and 1.04 µg/mL respectively. In the presence of blaCMY-2, MIC of ceftiofur increased by an average of 10.20 µg/mL over 14 years. The ability to predict antimicrobial susceptibility of beta-lactam antimicrobials directly from beta-lactamase resistance genes may help reduce the reliance on routine phenotypic testing with higher turnaround times in diagnostic, therapeutic, and surveillance of antimicrobial-resistant bacteria of the family Enterobacteriaceae.

Beta-lactamase genes in bacteria from food animals, retail meat, and human surveillance programs in the United States from 2002 to 2021.

The spread of beta-lactamase-producing bacteria is a global public-health concern. This study aimed to explore the distribution of beta-lactamases reported in three sampling sources (cecal, retail meat, and human) collected as part of integrated surveillance in the United States. We retrieved and analyzed data from the United States National Antimicrobial Resistance Monitoring Systems (NARMS) from 2002 to 2021. A total of 115 beta-lactamase genes were detected in E. coli, Salmonella enterica, Campylobacter, Shigella and Vibrio: including 35 genes from cecal isolates, 32 genes from the retail meat isolates, and 104 genes from the human isolates. Three genes in E. coli (blaCMY-2,blaTEM-1A, and blaTEM-1B), 6 genes in Salmonella enterica (blaCARB-2, blaCMY-2, blaCTXM-65, blaTEM-1A, blaTEM-1B, and blaHERA-3), and 2 genes in Campylobacter spp. (blaOXA-61 and blaOXA-449) have been detected across food animals (cattle, chicken, swine, and turkey) and humans over the study period. blaCTXM-55 has been detected in E. coli isolates from the four food animal sources while blaCTXM-15 and blaCTXM-27 were found only in cattle and swine. In Salmonella enterica, blaCTXM-2, blaCTXM-9, blaCTXM-14, blaCTXM-15, blaCTXM-27, blaCTXM-55, and blaNDM-1 were only detected among human isolates. blaOXAs and blaCARB were bacteria-specific and the only beta-lactamase genes detected in Campylobacter spp. and Vibrio spp respectively. The proportions of beta-lactamase genes detected varies from bacteria to bacteria. This study provided insights on the beta-lactamase genes detected in bacteria in food animals and humans in the United States. This is necessary for better understanding the molecular epidemiology of clinically important beta-lactamases in one health interface.

Effect of Tryptic Digestion on Sensitivity and Specificity in MALDI-TOF-Based Molecular Diagnostics through Machine Learning.

The digestion of protein into peptide fragments reduces the size and complexity of protein molecules. Peptide fragments can be analyzed with higher sensitivity (often > 102 fold) and resolution using MALDI-TOF mass spectrometers, leading to improved pattern recognition by common machine learning algorithms. In turn, enhanced sensitivity and specificity for bacterial sorting and/or disease diagnosis may be obtained. To test this hypothesis, four exemplar case studies have been pursued in which samples are sorted into dichotomous groups by machine learning (ML) software based on MALDI-TOF spectra. Samples were analyzed in 'intact' mode in which the proteins present in the sample were not digested with protease prior to MALDI-TOF analysis and separately after the standard overnight tryptic digestion of the same samples. For each case, sensitivity (sens), specificity (spc), and the Youdin index (J) were used to assess the ML model performance. The proteolytic digestion of samples prior to MALDI-TOF analysis substantially enhanced the sensitivity and specificity of dichotomous sorting. Two exceptions were when substantial differences in chemical composition between the samples were present and, in such cases, both 'intact' and 'digested' protocols performed similarly. The results suggest proteolytic digestion prior to analysis can improve sorting in MALDI/ML-based workflows and may enable improved biomarker discovery. However, when samples are easily distinguishable protein digestion is not necessary to obtain useful diagnostic results.

Comparing individual antimicrobial resistant and multi-drug resistant Salmonella enterica across serotypes, sampling sources, sampling periods, and food animal types in the United States (2014-2018).

This study aimed to compare the antimicrobial-resistant Salmonella enterica profiles from three sampling sources cecal contents, HACCP (during processing), and retail meat using phenotypic antibiotic susceptibility and serotype data gathered from 2014 and 2018. Antimicrobial resistance data for 29 major Salmonella serotypes from three sampling sources and associated food animal types (cattle, swine, chicken, and turkey) were obtained from the database of the United States National Antimicrobial Resistance Monitoring System. Using multivariable logistic regression models, we compared individual and multi-drug resistance (MDR) in Salmonella enterica between the three sampling sources, food animal types, sampling period, and Salmonella serotypes. Across the three sources and throughout the sampling period, the recovery of antimicrobial-resistant Salmonella enterica - including MDR, MDR-AmpC, and ACSSuT - among food animal types were dependent on the sampling period and, in some cases, sampling sources and period for the selected antimicrobials. The predicted probability of antimicrobial resistance was greater in Salmonella serotypes from turkey compared to other food animal types, conditional on sampling sources. Ceftriaxone-resistant (OR=0.83, 95% CI: 0.69-0.99), and Sulfisoxazole-resistant (OR=0.84, 95% CI: 0.72-0.98) Salmonella serotypes were less likely to be recovered from the Hazard Analysis and Critical Control Point (HACCP) sources than with the cecal sources. Except for Salmonella serotypes Dublin and Newport, most of the Salmonella serotypes were less likely to be resistant to the selected antimicrobials, or found as MDR, compared to serotype Typhimurium. This study offers an integrated view on the predicted probability of MDR Salmonella serotypes, as well as insights into which serotypes are persistent, emerging or declining across sampling sources and food animal types in the United States.

Genomic Characterization of Fecal Escherichia coli Isolates with Reduced Susceptibility to Beta-Lactam Antimicrobials from Wild Hogs and Coyotes.

This study was carried out to determine the antimicrobial resistance (AMR) genes and mobile genetic elements of 16 Escherichia coli isolates-with reduced susceptibility to ceftazidime and imipenem-that were recovered from the fecal samples of coyotes and wild hogs from West Texas, USA. Whole-genome sequencing data analyses revealed distinct isolates with a unique sequence type and serotype designation. Among 16 isolates, 4 isolates were multidrug resistant, and 5 isolates harbored at least 1 beta-lactamase gene (blaCMY-2, blaCTX-M-55, or blaCTX-M-27) that confers resistance to beta-lactam antimicrobials. Several isolates carried genes conferring resistance to tetracyclines (tet(A), tet(B), and tet(C)), aminoglycosides (aac(3)-IId, ant(3″)-Ia, aph(3')-Ia, aph(3″)-lb, aadA5, and aph(6)-ld), sulfonamides (sul1, sul2, and sul3), amphenicol (floR), trimethoprim (dfrA1 and dfrA17), and macrolide, lincosamide, and streptogramin B (MLSB) agents (Inu(F), erm(B), and mph(A)). Nine isolates showed chromosomal mutations in the promoter region G of ampC beta-lactamase gene, while three isolates showed mutations in gyrA, parC, and parE quinolone resistance-determining regions, which confer resistance to quinolones. We also detected seven incompatibility plasmid groups, with incF being the most common. Different types of virulence genes were detected, including those that enhance bacterial fitness and pathogenicity. One blaCMY-2 positive isolate (O8:H28) from a wild hog was also a Shiga toxin-producing E. coli and was a carrier of the stx2A virulence toxin subtype. We report the detection of blaCMY-2, blaCTX-M-55, and blaCTX-M-27 beta-lactamase genes in E. coli from coyotes for the first time. This study demonstrates the importance of wildlife as reservoirs of important multi-drug-resistant bacteria and provides information for future comparative genomic analysis with the limited literature on antimicrobial resistance dynamics in wildlife such as coyotes.

Fecal Microbial Diversity of Coyotes and Wild Hogs in Texas Panhandle, USA.

The ecology of infectious diseases involves wildlife, yet the wildlife interface is often neglected and understudied. Pathogens related to infectious diseases are often maintained within wildlife populations and can spread to livestock and humans. In this study, we explored the fecal microbiome of coyotes and wild hogs in the Texas panhandle using polymerase chain reactions and 16S sequencing methods. The fecal microbiota of coyotes was dominated by members of the phyla Bacteroidetes, Firmicutes, and Proteobacteria. At the genus taxonomic level, Odoribacter, Allobaculum, Coprobacillus, and Alloprevotella were the dominant genera of the core fecal microbiota of coyotes. While for wild hogs, the fecal microbiota was dominated by bacterial members of the phyla Bacteroidetes, Spirochaetes, Firmicutes, and Proteobacteria. Five genera, Treponema, Prevotella, Alloprevotella, Vampirovibrio, and Sphaerochaeta, constitute the most abundant genera of the core microbiota of wild hogs in this study. Functional profile of the microbiota of coyotes and wild hogs identified 13 and 17 human-related diseases that were statistically associated with the fecal microbiota, respectively (p < 0.05). Our study is a unique investigation of the microbiota using free-living wildlife in the Texas Panhandle and contributes to awareness of the role played by gastrointestinal microbiota of wild canids and hogs in infectious disease reservoir and transmission risk. This report will contribute to the lacking information on coyote and wild hog microbial communities by providing insights into their composition and ecology which may likely be different from those of captive species or domesticated animals. This study will contribute to baseline knowledge for future studies on wildlife gut microbiomes.

Prevalence and risk factors for avian influenza virus (H5 and H9) contamination in peri-urban and rural live bird markets in Bangladesh.

Avian influenza viruses (AIV) have been frequently detected in live bird markets (LBMs) around the world, primarily in urban areas, and have the ability to spillover to other species, including humans. Despite frequent detection of AIV in urban LBMs, the contamination of AIV on environmental surfaces in rural and peri-urban LBMs in Bangladesh is poorly documented. Therefore, we conducted this study to determine the prevalence of AIV subtypes within a subset of peri-urban and rural LBMs in Bangladesh and to further identify associated risk factors. Between 2017 and 2018, we collected faecal and offal samples from 200 stalls in 63 LBMs across four sub-districts. We tested the samples for the AIV matrix gene (M-gene) followed by H5, H7, and H9 subtypes using real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). We performed a descriptive analysis of market cleanliness and sanitation practices in order to further elucidate the relationship between LBM biosecurity and AIV subtypes by species, sample types, and landscape. Subsequently, we conducted a univariate analysis and a generalized linear mixed model (GLMM) to determine the risk factors associated with AIV contamination at individual stalls within LBMs. Our findings indicate that practices related to hygiene and the circulation of AIV significantly differed between rural and peri-urban live bird markets. 42.5% (95% CI: 35.56-49.67) of stalls were positive for AIV. A/H5, A/H9, and A HA/Untyped were detected in 10.5% (95% CI: 6.62-15.60), 9% (95% CI: 5.42-13.85), and 24.0% (95% CI: 18.26-30.53) of stalls respectively, with no detection of A/H7. Significantly higher levels of AIV were found in the Sonali chicken strain compared to the exotic broiler, and in offal samples compared to fecal samples. In the GLMM analysis, we identified several significant risk factors associated with AIV contamination in LBMs at the stall level. These include: landscape (AOR: 3.02; 95% CI: 1.18-7.72), the number of chicken breeds present (AOR: 2.4; 95% CI: 1.01-5.67), source of birds (AOR: 2.35; 95% CI: 1.0-5.53), separation of sick birds (AOR: 3.04; 95% CI: 1.34-6.92), disposal of waste/dead birds (AOR: 3.16; 95% CI: 1.41-7.05), cleaning agent (AOR: 5.99; 95% CI: 2.26-15.82), access of dogs (AOR: 2.52; 95% CI: 1.12-5.7), wild birds observed on site (AOR: 2.31; 95% CI: 1.01-5.3). The study further revealed a substantial prevalence of AIV with H5 and H9 subtypes in peri-urban and rural LBMs. The inadequate biosecurity measures at poultry stalls in Bangladesh increase the risk of AIV transmission from poultry to humans. To prevent the spread of AIV to humans and wild birds, we suggest implementing regular surveillance at live bird markets and enhancing biosecurity practices in peri-urban and rural areas in Bangladesh.

Characterization and epidemiology of antimicrobial resistance patterns of Salmonella spp. and Staphylococcus spp. in free-ranging rhesus macaque (Macaca mulatta) at high-risk interfaces with people and livestock in Bangladesh.

Introduction: Antimicrobial resistance (AMR) is a growing global health threat for humans and animals. Environmental contamination of antimicrobials from human and domestic animal feces has been linked to AMR in wildlife populations, including rhesus macaques. This study aimed to describe the eco-epidemiology of AMR within Salmonella and Staphylococcus species isolated from rhesus macaques. Methods: We followed macaque groups for 4 h per day (2 days) to observe the direct and indirect contact rate and type between macaques and people and livestock. We collected 399 freshly defecated, non-invasive fecal samples from macaques at seven sites in Bangladesh in January-June 2017. Bacterial isolation and identification were conducted using culture, biochemical characteristics, and polymerase chain reaction (PCR). An antimicrobial susceptibility test (AST) for 12 antimicrobials for each organism was conducted using the Kirby-Bauer disc diffusion method. Results: The overall prevalence of Salmonella spp. and Staphylococcus spp. in rhesus macaques was 5% (n = 18; 95% CI: 3-7%) and 16% (n = 64; 95% CI: 13-20%), respectively. All the isolated Salmonella spp. and most of the Staphylococcus spp. (95%; 61/64; 95% CI: 86.9-99%) were resistant to at least one antimicrobial. The odds of a fecal sample having antimicrobial-resistant Salmonella spp (OR = 6.6; CI: 0.9-45.8, P = 0.05) and Staphylococcus spp. (OR = 5.6; CI: 1.2-26, P = 0.02) were significantly higher in samples collected at peri-urban sites than those collected at rural and urban sites. Salmonella spp. were most frequently resistant to tetracycline (89%), azithromycin (83%), sulfamethoxazole-trimethoprim (50%), and nalidixic acid (44%). Staphylococcus spp. were found to be highly resistant to ampicillin (93%), methicillin (31%), clindamycin (26%), and rifampicin (18%). Both bacterial species produced colonies with multidrug resistance to up to seven antimicrobials. Direct and indirect contact rates (within 20 m for at least 15 min) and resource sharing between macaques and people were higher in urban sites, while macaque-livestock contact rates were higher in rural sites. Discussion: The study shows that resistant microorganisms are circulating in rhesus macaque, and direct and indirect contact with humans and livestock might expand the resistant organisms.

Epidemiology of Group A rotavirus in rodents and shrews in Bangladesh.

Rodents and shrews live in close proximity to humans and have been identified as important hosts of zoonotic pathogens. This study aimed to detect Group A rotavirus (RVA) and its potential risk factors in rodents and shrews in Bangladesh. We captured 417 small mammals from 10 districts with a high degree of contact between people and domestic animals and collected rectal swab samples between June 2011 and October 2013. We tested the swab samples for RVA RNA, targeting the NSP3 gene segment using real-time reverse transcription-polymerase chain reaction (rRT-PCR). Overall, RVA prevalence was the same (6.7%) in both rodents and shrews. We detected RVA RNA in 5.3% of Bandicota bengalensis (4/76; 95% CI: 1.4-12.9), 5.1% of B. indica (4/79; 95% CI: 1.4-12.4), 18.2% of Mus musculus (4/22; 95% CI: 5.2-40.3), 6.7% of Rattus rattus (6/90; 95% CI: 2.5-13.9), and 6.7% of Suncus murinus (10/150; 95% CI: 3.2-11.9). We found significantly more RVA in males (10.4%; OR: 3.4; P = 0.007), animals with a poor body condition score (13.9%; OR: 2.7; P = 0.05), during wet season (8.3%; OR: 4.1; P = 0.032), and in urban land gradients (10.04%; OR: 2.9; P = 0.056). These findings form a basis for understanding the prevalence of rotaviruses circulating among rodents and shrews in this region. We recommend additional molecular studies to ascertain the genotype and zoonotic potential of RVA circulating in rodents and shrews in Bangladesh.

Serological evidence of bluetongue virus and associated factors in small ruminants of Bangladesh.

Bluetongue (BT) is an infectious, vector-borne viral disease of animals having a substantial economic impact and it is endemic in the bordering states of the Indian subcontinent. Livestock enters frequently from India into Bangladesh without any screening. Hence, this study aimed to estimate the seroprevalence of Bluetongue virus (BTV) and associated risk factors in small ruminants of Bangladesh. We conducted a cross-sectional study in the Dhaka, Chattogram, and Faridpur districts of Bangladesh between 2017 and 2018. The team collected 333 serum samples from 123 goats and 210 sheep and tested them for the presence of antibodies against BTV using a competitive enzyme linked immunosorbent assay (c-ELISA). A mixed multivariable logistic regression model was built to identify risk factors. Sample collection location was included as a random effect and husbandry and demographic variables as fixed effects to identify the potential risk factors. The BTV seroprevalence was found to be 55.3% (n = 184; 95% CI: 49.74-60.68). In the mixed-effect logistic regression analysis, animal species (AOR: 4.69; 95% CI: 2.49-8.82; p = 0.001) and vector control measurement (AOR: 9.01; 95% CI: 4.01-20.00; p = 0.0001) were significantly associated with BTV seropositivity. However, no significant association was found in multivariable mixed-effect logistic regression for the variables age, body condition score (BCS), vaccination against PPR (p > 0.05). The study found evidence of high seroprevalence of BTV in both sheep and goats in different districts of Bangladesh, indicating natural exposure of the virus and the animals can serve as a potential threat for other animals. Further research is needed to isolate and identify the circulating virus serotype(s) of BTV in Bangladesh as well as longitudinal studies for epidemiological investigations to formulate sound control programs and to enhance the awareness about the possible impacts of this disease on the livelihood of the people.

Epidemiological Profile of a Human Hepatitis E Virus Outbreak in 2018, Chattogram, Bangladesh.

Hepatitis E virus (HEV) is a waterborne zoonotic disease that can result in a high fatality rate in pregnant women and infants. In 2018, a large HEV outbreak emerged in Chattogram, Bangladesh, resulting in 2800 cases and a significant public health response to mitigate the transmission. While the source of the outbreak remained poorly understood, authorities suggested that possible risk factors for HEV infection included contamination of water supply, exacerbated by concurrent severe flooding events in the community. A cross-sectional study was conducted to investigate the distribution and risk factors for HEV seroprevalence between January and December 2018 in the Chattogram city area. A total of 505 blood samples were collected from symptomatic patients of 10 hospitals who met the case definition for an HEV infection. Standard ELISA tests were performed in all patients to identify anti-HEV antibodies. The size and location of HEV seroprevalence clusters within Chattogram were investigated using SaTScan. We investigated the association between risk of HEV infection and individual and environmentally lagged risk factors using Bernoulli generalised linear regression models. Our results indicate an overall HEV seroprevalence of 35% with significant variation according to sex, source of drinking water, and boiling of drinking water. A positive cross-correlation was found between HEV exposure and precipitation, modified normalised difference water index (MNDWI), and normalised difference vegetation index (NDVI). Our model indicated that risk of infection was associated with sex, age, source of drinking water, boiling of water, increased precipitation, and increased MNDWI. The results from this study indicate that source and boiling of drinking water and increased precipitation were critical drivers of the 2018 HEV outbreak. The communities at highest risk identified in our analyses should be targeted for investments in safe water infrastructure to reduce the likelihood of future HEV outbreaks in Chattogram.

Resistance to extended-spectrum cephalosporins in Escherichia coli and Salmonella enterica isolated from food-producing animals: Ecological study from selected national surveillance programs.

Extended-spectrum cephalosporins (ESC) are categorized by World Health Organization as critically important antimicrobials with limited therapeutic alternatives for the treatment of severe bacterial infections in humans. Preserving the effectiveness of ESC requires continuous monitoring of resistance and comparison of associated data across national surveillance programs in the face of globalization. In this ecological study, we compared ESC resistance in Escherichia coli and Salmonella enterica isolated from food-producing animals from 2003 to 2019 between nine countries (Canada, Denmark, Finland, Japan, Netherlands, Norway, Sweden, United Kingdom, and the United States). Using the beta-regression model, compared to Canada, non-selective ESC-R Salmonella enterica was less likely isolated from food producing animals in other eight countries (Odds ratio range: 0.07-0.76). We observed an interaction between the country and the year with a significantly decreased proportion (P < 0.05) of non-selective ESC-R Escherichia coli from the Netherlands, the United Kingdom, and the United States compared to Canada over the years. There was a linear correlation between non-selective ESC-R Escherichia coli and ESC use from Netherlands (Spearman's ρ = 0.91, P < 0.0001). For the six European countries, the interaction between the country and year showed a significant decrease in the proportion of selective ESC-R Escherichia coli over the years for the Netherlands compared to Denmark (P = 0.002). While there were variations in the proportion of beta-lactamase genes reported over the years, blaCTX-M and blaCMY-2 genes were commonly detected among the selective ESC-R Escherichia coli. This study reveals variability in the recovery of ESC-resistant bacteria among the countries that seems likely influenced by the individual country policy on the use of critically important antimicrobials and resistance surveillance programs. However, there is a need for harmonization and consistency in food animal sources of bacterial isolates used in surveillance programs within and between the countries for easy comparability.

Transmission dynamics and susceptibility patterns of SARS-CoV-2 in domestic, farmed and wild animals: Sustainable One Health surveillance for conservation and public health to prevent future epidemics and pandemics.

The exact origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and source of introduction into humans has not been established yet, though it might be originated from animals. Therefore, we conducted a study to understand the putative reservoirs, transmission dynamics, and susceptibility patterns of SARS-CoV-2 in animals. Rhinolophus bats are presumed to be natural progenitors of SARS-CoV-2-related viruses. Initially, pangolin was thought to be the source of spillover to humans, but they might be infected by human or other animal species. So, the virus spillover pathways to humans remain unknown. Human-to-animal transmission has been testified in pet, farmed, zoo and free-ranging wild animals. Infected animals can transmit the virus to other animals in natural settings like mink-to-mink and mink-to-cat transmission. Animal-to-human transmission is not a persistent pathway, while mink-to-human transmission continues to be illuminated. Multiple companions and captive wild animals were infected by an emerging alpha variant of concern (B.1.1.7 lineage) whereas Asiatic lions were infected by delta variant, (B.1.617.2). To date, multiple animal species - cat, ferrets, non-human primates, hamsters and bats - showed high susceptibility to SARS-CoV-2 in the experimental condition, while swine, poultry, cattle showed no susceptibility. The founding of SARS-CoV-2 in wild animal reservoirs can confront the control of the virus in humans and might carry a risk to the welfare and conservation of wildlife as well. We suggest vaccinating pets and captive animals to stop spillovers and spillback events. We recommend sustainable One Health surveillance at the animal-human-environmental interface to detect and prevent future epidemics and pandemics by Disease X.

Prevalence and diversity of gastrointestinal parasites in free-ranging rhesus macaques (Macaca mulatta) in different land gradients of Bangladesh.

Rhesus macaques are considered an important reservoir of different gastrointestinal (GI) zoonotic parasites affecting livestock and humans. Loads of GI parasites in the free-ranging rhesus macaques living in close proximity to communities in Bangladesh are still unknown. To estimate the prevalence and diversity of zoonotic GI parasites in rhesus macaques of Bangladesh, a total of 182 freshly voided fecal samples were collected from macaques living in rural (N = 67), peri-urban (N = 57), urban (N = 28), and Safari park (N = 30) between October 2015 and December 2016. All samples were tested by direct smear, sedimentation, flotation, and the McMaster techniques. A total of fourteen different taxa of GI parasites were detected, revealing an overall prevalence of 54.4% (n = 99; 95% confidence interval [CI]: 46.9-61.8). The prevalence of GI parasites was found to be significantly correlated with the mean parasitic taxa per individual in a group (r = 0.90; p = 0.002). The multivariable logistic regression analysis showed that the overall prevalence of GI parasites in macaques was significantly higher in those inhabiting rural areas (62.69%; odds ratio [OR]: 7.22; p = 0.001) and in macaques with interactions with other animals (60.98%; OR: 5.49; p = 0.005). Our results also indicated that the prevalence of Strongyloides spp. and Balantidium coli infections varied significantly between land gradients. Our results also indicate that macaques frequently visit human settlements for food and are found interacting with domestic animals. In conclusion, the high prevalence of zoonotic GI parasite infection in rhesus macaques found in our study may pose a significant public health risk to communities, particularly in rural areas of Bangladesh. Health promotion to at-risk communities focusing on limiting contact with rhesus macaques is necessary to mitigate potential zoonotic transmission.

Escalating SARS-CoV-2 circulation in environment and tracking waste management in South Asia.

The novel coronavirus disease of 2019 (COVID-19) pandemic has caused an exceptional drift of production, utilization, and disposal of personal protective equipment (PPE) and different microplastic objects for safety against the virus. Hence, we reviewed related literature on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA detected from household, biomedical waste, and sewage to identify possible health risks and status of existing laws, regulations, and policies regarding waste disposal in South Asian (SA) countries. The SARS-CoV-2 RNA was detected in sewage and wastewater samples of Nepal, India, Pakistan, and Bangladesh. Besides, this review reiterates the enormous amounts of PPE and other single-use plastic wastes generated from healthcare facilities and households in the SA region with inappropriate disposal, landfilling, and/or incineration techniques wind-up polluting the environment. Consequently, the Delta variant (B.1.617.2) of SARS-CoV-2 has been detected in sewer treatment plant in India. Moreover, the overuse of non-biodegradable plastics during the pandemic is deteriorating plastic pollution condition and causes a substantial health risk to the terrestrial and aquatic ecosystems. We recommend making necessary adjustments, adopting measures and strategies, and enforcement of the existing biomedical waste management and sanitation-related policy in SA countries. We propose to adopt the knowledge gaps to improve COVID-19-associated waste management and legislation to prevent further environmental pollution. Besides, the citizens should follow proper disposal procedures of COVID-19 waste to control the environmental pollution.

Molecular Epidemiology of SARS-CoV-2 in Diverse Environmental Samples Globally.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swamped the global environment greatly in the current pandemic. Wastewater-based epidemiology (WBE) effectively forecasts the surge of COVID-19 cases in humans in a particular region. To understand the genomic characteristics/footprints and diversity of SARS-CoV-2 in the environment, we analyzed 807 SARS-CoV-2 sequences from 20 countries deposited in GISAID till 22 May 2021. The highest number of sequences (n = 638) were reported in Austria, followed by the Netherlands, China, and Bangladesh. Wastewater samples were highest (40.0%) to successfully yield the virus genome followed by a 24 h composite wastewater sample (32.6%) and sewage (18.5%). Phylogenetic analysis revealed that SARS-CoV-2 environmental strains are a close congener with the strains mostly circulating in the human population from the same region. Clade GRY (32.7%), G (29.2%), GR (25.3%), O (7.2%), GH (3.4%), GV (1.4%), S (0.5%), and L (0.4%) were found in environmental samples. Various lineages were identified in environmental samples; nevertheless, the highest percentages (49.4%) of the alpha variant (B.1.1.7) were detected in Austria, Liechtenstein, Slovenia, Czech Republic, Switzerland, Germany, and Italy. Other prevalent lineages were B.1 (18.2%), B.1.1 (9.2%), and B.1.160 (3.9%). Furthermore, a significant number of amino acid substitutions were found in environmental strains where the D614G was found in 83.8% of the sequences. However, the key mutations-N501Y (44.6%), S982A (44.4%), A570D (43.3%), T716I (40.4%), and P681H (40.1%) were also recorded in spike protein. The identification of the environmental belvedere of SARS-CoV-2 and its genetic signature is crucial to detect outbreaks, forecast pandemic harshness, and prepare with the appropriate tools to control any impending pandemic. We recommend genomic environmental surveillance to trace the emerging variants and diversity of SARS-CoV-2 viruses circulating in the community. Additionally, proper disposal and treatment of wastewater, sewage, and medical wastes are important to prevent environmental contamination.

Study on bacterial pathogens through multiplex polymerase chain reaction system and their antimicrobial resistance pattern in goats presumed with fever and/or diarrhea.

BACKGROUND AND AIM: Goat is one of the major livestock species, plays an important role in the economy of Bangladesh. However, the outbreak of different infectious diseases in goats causes high mortality and economic losses due to lack of proper diagnosis and treatment. Conventional culture-based methods for detecting specific pathogens as confirmatory diagnosis are laborious as well as time-consuming in comparison to multiplex polymerase chain reaction (mPCR), by which multiple pathogens can be detected at a time. The present study was aimed to perform faster molecular identification of bacterial pathogens from goats presumed with fever and/or diarrhea and their antimicrobial resistance (AMR) pattern. MATERIALS AND METHODS: A total of 200 blood samples were collected from goats at S. A. Quaderi Teaching Veterinary Hospital (SAQTVH) in Chattogram Veterinary and Animal Sciences University for the period of July 2017-April 2018. DNA was extracted and subsequently, mPCR assay was performed for the screening of several bacterial pathogens (Salmonella spp., Listeria monocytogenes, Bacillus cereus, Yersinia enterocolitica, Campylobacter jejuni, Campylobacter coli, Clostridium perfringens, Vibrio cholerae, and Staphylococcus aureus). An antimicrobial susceptibility test against ten antimicrobials for positive samples of each organism was conducted using the Kirby-Bauer Disk-Diffusion Method on selective media. RESULTS: S. aureus, C. perfringens, L. monocytogenes, and Salmonella spp. were detected from collected samples and their overall prevalence was 11.5%, 3.5%, 1%, and 20.5%, respectively. The most common clinical signs were mild fever, nasal discharge, dyspnea, and coughing (39.1%) for S. aureus, diarrhea, convulsion, abdominal pain, and incoordination (57.1%) for C. perfringens, fever, protrusion of tongue, and incoordination (100%) for L. monocytogenes, and fever, anorexia, dehydration with mucous feces (36.6%) for Salmonella spp. infection in goats. AntimGentamicinicrobial diagram of S. aureus showed resistance against Cefotaxime (74%), Cefixime (65%), and Tetracycline (65%); highly sensitive against Amoxicillin (48%), Ciprofloxacin (44%), and Gentamicin (44%). On the other hand, C. perfringens showed highly resistant against Ampicillin (71%), Gentamicin (71%), sensitive against Penicillin (57%), and Cefotaxime (57%). L. monocytogenes were found to be sensitive to Penicillin (100%) and Cefixime (100%) and Salmonella spp. showed resistance to Ampicillin (78%) and Amoxicillin (59%) but sensitive to Ciprofloxacin (54%). CONCLUSION: This study identified pathogens with their specific clinical signs in goats presumed fever and/or diarrhea through mPCR with their AMR pattern in SAQTVH, Chattogram. Potential risk factors, measuring the strength of association of disease caused by these particular pathogens, were also determined. mPCR may use as an effective tool for rapid detection of pathogens in animal.

Knowledge, Attitudes and Practices Regarding Antibiotic Use and Resistance among Veterinary Students in Bangladesh.

The use of antibiotics in animals for both therapeutic and non-therapeutic purposes is a major driver of the emergence and spread of antimicrobial resistance (AMR). While several studies have investigated prescription and consumption patterns in humans, little attention has been paid to the veterinary sector. A cross-sectional study was conducted in 3002 veterinary students (VS) and non-medical students (NMS) from 12 universities in Bangladesh to explore their knowledge, attitudes and practices (KAP) about antibiotics and AMR using a self-administered questionnaire, and assess the influence of the veterinary curriculum. KAP regarding antibiotic use and AMR was significantly higher in veterinary than non-medical students, and in first-year than final-year students. However, gaps in knowledge and practices were highlighted, suggesting deficiencies in training. Moreover, final-year veterinary students were found to be more likely than first-year students to use antibiotics without instructions, which could indicate deficiencies in their curriculum. Although the study suggested a positive impact of the veterinary curriculum on KAP about antibiotics and AMR in Bangladesh, critical gaps remain that are likely to contribute to inadequate use in their future practice. Therefore, there is scope for improving educational programs on AMR in professional curricula.

Assessment of basic reproduction number (R0), spatial and temporal epidemiological determinants, and genetic characterization of SARS-CoV-2 in Bangladesh.

Epidemiological and molecular characterization of SARS-CoV-2 is essential for identifying the source of the virus and for effective control of the spread of local strains. We estimated case fatality rate, cumulative recovery number, basic reproduction number (R0) and future incidence of COVID-19 in Bangladesh. We illustrated the spatial distribution of cases throughout the country. We performed phylogenetic and mutation analysis of SARS-CoV-2 sequences from Bangladesh. As of July 31, 2020, Bangladesh had a case fatality rate of 1.32%. The cases were initially clustered in Dhaka and its surrounding districts in March but spreads throughout the country over time. The R0 calculated as 1.173 in Exponential Growth method. For the projection, a 20% change in R0 with subsequent infection trend has been calculated. The genomic analysis of 292 Bangladeshi SARS-CoV-2 strains suggests diverse genomic clades L, O, S, G, GH, where predominant circulating clade was GR (83.9%; 245/292). The GR clades' phylogenetic analysis revealed distinct clusters (I to XIII) with intra-clade variations. The mutation analysis revealed 1634 mutations where 94.6% and 5.4% were non-synonymous and unique mutation, respectively. The Spike, Nucleocapsid, NSP2, and RdRP showed substantially high mutation but no mutation was recorded in NSP9 and NSP11 protein. In spike (S) protein, 355 predominant mutations were recorded, highest in D614G. Alternatively, I120F in NSP2 protein, R203K and G204R in nucleocapsid protein, and P323L in RdRp were more recurrent. The Bangladeshi genomes belonged to phylogenetic lineages A, B, B.1, B.1.1, B.1.1.23, B.1.1.25, B.1.113, and B.1.36, among which 50.0% sequences owned by the pangolin lineage B.1.1.25. The study illustrates the spatial distribution of SARS-CoV-2, and molecular epidemiology of Bangladeshi isolates. We recommend continuous monitoring of R0 and genomic surveillance to understand the transmission dynamics and detect new variants of SARS-CoV-2 for proper control of the current pandemic and evaluate the effectiveness of vaccination globally.

Geospatial dynamics of COVID-19 clusters and hotspots in Bangladesh.

The coronavirus disease 2019 (COVID-19) is an emerging and rapidly evolving profound pandemic, which causes severe acute respiratory syndrome and results in significant case fatality around the world including Bangladesh. We conducted this study to assess how COVID-19 cases clustered across districts in Bangladesh and whether the pattern and duration of clusters changed following the country's containment strategy using Geographic information system (GIS) software. We calculated the epidemiological measures including incidence, case fatality rate (CFR) and spatiotemporal pattern of COVID-19. We used inverse distance weighting (IDW), Geographically weighted regression (GWR), Moran's I and Getis-Ord Gi* statistics for prediction, spatial autocorrelation and hotspot identification. We used retrospective space-time scan statistic to analyse clusters of COVID-19 cases. COVID-19 has a CFR of 1.4%. Over 50% of cases were reported among young adults (21-40 years age). The incidence varies from 0.03 - 0.95 at the end of March to 15.59-308.62 per 100,000, at the end of July. Global Moran's Index indicates a robust spatial autocorrelation of COVID-19 cases. Local Moran's I analysis stated a distinct High-High (HH) clustering of COVID-19 cases among Dhaka, Gazipur and Narayanganj districts. Twelve statistically significant high rated clusters were identified by space-time scan statistics using a discrete Poisson model. IDW predicted the cases at the undetermined area, and GWR showed a strong relationship between population density and case frequency, which was further established with Moran's I (0.734; p ≤ 0.01). Dhaka and its surrounding six districts were identified as the significant hotspot whereas Chattogram was an extended infected area, indicating the gradual spread of the virus to peripheral districts. This study provides novel insights into the geostatistical analysis of COVID-19 clusters and hotspots that might assist the policy planner to predict the spatiotemporal transmission dynamics and formulate imperative control strategies of SARS-CoV-2 in Bangladesh. The geospatial modeling tools can be used to prevent and control future epidemics and pandemics.