Multilocus sequence typing of multidrug-resistant Salmonella strains circulating in poultry farms of Bangladesh

Prevalence and antibiotic resistance of Escherichia coli in urban and peri-urban garden ecosystems in Bangladesh

In the past decade, there has been a notable rise in foodborne outbreaks, prominently featuring Escherichia coli as a primary pathogen. This bacterium, known for its prevalence in foodborne illnesses and as a reservoir of antimicrobial resistance, was isolated from raw vegetables, soil, and water samples collected from rooftop and surface gardens in urban (Dhaka North City Corporation; DNCC and Dhaka South City Corporation; DSCC) and peri-urban (Gazipur City Corporation; GCC) areas of Bangladesh. In this study, 145 samples including vegetables (n = 88), water (n = 27) and soils (n = 30) from DNCC (n = 85), DSCC (n = 30), and GCC (n = 30) were analyzed to assess the prevalence of E. coli using culture, biochemical tests, and PCR targeting the malB gene. E. coli was detected in 85 samples, indicating an overall prevalence of 58.62% (95% CI: 50.48-66.31). In urban areas (DNCC and DSCC), the prevalence rates were 44.70% and 80.0%, respectively, with surface gardens showing higher contamination rates (70.83%) than rooftop gardens (46.57%). In the peri-urban GCC, overall prevalence of E. coli was 76.7%, with rooftop gardens more contaminated (93.33%) than surface gardens (60.0%). Antibiogram profiling of 54 randomly selected isolates revealed 100% resistance to ampicillin, with varying resistance to ciprofloxacin (25.92%), tetracycline (14.81%), cotrimoxazole (14.81%), imipenem (9.25%), and fosfomycin (1.0%). Notably, all isolates were susceptible to ceftazidime, gentamicin, chloramphenicol, nitrofurantoin, and cefotaxime. Multidrug resistance (MDR) was found in 14.81% of isolates. The blaTEM gene was present in 81.48% of the isolates, while the tetA gene was detected in 3.70%. These findings underscore the urgent global health concern posed by the significant presence of E. coli in fresh vegetables, highlighting the need for improved safety measures and monitoring to prevent the spread of antimicrobial resistance through the food chain.

An Epidemiological Study on Salmonella in Tibetan Yaks from the Qinghai-Tibet Plateau Area in China

Salmonella is an important foodborne pathogen that can cause a range of illnesses in humans; it has also been a key focus for monitoring in the field of public health, including gastroenteritis, sepsis, and arthritis, and can also cause a decline in egg production in poultry and diarrhea and abortion in livestock, leading to death in severe cases, resulting in huge economic losses. This study aimed to investigate the isolation rate, antimicrobial resistance, serotypes, and genetic diversity of Salmonella isolated from yak feces in various regions on the Qinghai-Tibet Plateau. A total of 1222 samples of yak dung were collected from major cities in the Qinghai-Tibet Plateau area, and the sensitivity of the isolated bacteria to 10 major classes of antibiotics was determined using the K-B paper disk diffusion method for drug susceptibility. Meanwhile, the serotypes of the isolated bacteria were analyzed using the plate agglutination test for serum antigens, and their carriage of drug resistance and virulence genes was determined using PCR and gel electrophoresis experiments. The isolated bacteria were also classified using MLST (Multi-Locus Sequence Typing). The overall isolation rate for Salmonella was 18.25% (223/1222), and the results of the antibiotic susceptibility tests showed that 98.65% (220/223) of the isolated bacteria were resistant to multiple antibiotics. In the 223 isolates of Salmonella, eight classes of 20 different resistance genes, 30 serotypes, and 15 different types of virulence genes were detected. The MLST analysis identified 45 distinct sequence types (STs), including five clonal complexes, of which ST34, ST11, and ST19 were the most common. These findings contribute valuable information about strain resources, genetic profiles, and typing data for Salmonella in the Qinghai-Tibet Plateau area, facilitating improved bacterial surveillance, identification, and control in yak populations. They also provide certain data supplements for animal Salmonella infections globally, filling research gaps.

Characterization of β-lactamase and virulence genes in Pseudomonas aeruginosa isolated from clinical, environmental and poultry sources in Bangladesh

The emergence and spread of multidrug-resistant pathogens like Pseudomonas aeruginosa are major concerns for public health worldwide. This study aimed to assess the prevalence of P. aeruginosa in clinical, environmental, and poultry sources in Bangladesh, along with their antibiotic susceptibility and the profiling of β-lactamase and virulence genes using standard molecular and microbiology techniques. We collected 110 samples from five different locations, viz., BAU residential area (BAURA; n = 15), BAU Healthcare Center (BAUHCC; n = 20), BAU Veterinary Teaching Hospital (BAUVTH; n = 22), Poultry Market (PM; n = 30) and Mymensingh Medical College Hospital (MCCH; n = 23). After overnight enrichment in nutrient broth, 89 probable Pseudomonas isolates (80.90%) were screened through selective culture, gram-staining and biochemical tests. Using genus- and species-specific PCR, we confirmed 22 isolates (20.0%) as P. aeruginosa from these samples. Antibiogram profiling revealed that 100.0% P. aeruginosa isolates (n = 22) were multidrug-resistant isolates, showing resistance against Doripenem, Penicillin, Ceftazidime, Cefepime, and Imipenem. Furthermore, resistance to aztreonam was observed in 95.45% isolates. However, P. aeruginosa isolates showed a varying degree of sensitivity against Amikacin, Gentamicin, and Ciprofloxacin. The blaTEM gene was detected in 86.0% isolates, while blaCMY, blaSHV and blaOXA, were detected in 27.0%, 18.0% and 5.0% of the P. aeruginosa isolates, respectively. The algD gene was detected in 32.0% isolates, whereas lasB and exoA genes were identified in 9.0% and 5.0% P. aeruginosa isolates. However, none of the P. aeruginosa isolates harbored exoS gene. Hence, this study provides valuable and novel insights on the resistance and virulence of circulating P. aeruginosa within the clinical, environmental, and poultry environments of Bangladesh. These findings are crucial for understanding the emergence of β-lactamase resistance in P. aeruginosa, highlighting its usefulness in the treatment and control of P. aeruginosa infections in both human and animal populations.

Genome-Wide Investigation Reveals Potential Therapeutic Targets in Shigella spp

Shigella stands as a major contributor to bacterial dysentery worldwide scale, particularly in developing countries with inadequate sanitation and hygiene. The emergence of multidrug-resistant strains exacerbates the challenge of treating Shigella infections, particularly in regions where access to healthcare and alternative antibiotics is limited. Therefore, investigations on how bacteria evade antibiotics and eventually develop resistance could open new avenues for research to develop novel therapeutics. The aim of this study was to analyze whole genome sequence (WGS) of human pathogenic Shigella spp. to elucidate the antibiotic resistance genes (ARGs) and their mechanism of resistance, gene-drug interactions, protein-protein interactions, and functional pathways to screen potential therapeutic candidate(s). We comprehensively analyzed 45 WGS of Shigella, including S. flexneri (n = 17), S. dysenteriae (n = 14), S. boydii (n = 11), and S. sonnei (n = 13), through different bioinformatics tools. Evolutionary phylogenetic analysis showed three distinct clades among the circulating strains of Shigella worldwide, with less genomic diversity. In this study, 2,146 ARGs were predicted in 45 genomes (average 47.69 ARGs/genome), of which only 91 ARGs were found to be shared across the genomes. Majority of these ARGs conferred their resistance through antibiotic efflux pump (51.0%) followed by antibiotic target alteration (23%) and antibiotic target replacement (18%). We identified 13 hub proteins, of which four proteins (e.g., tolC, acrR, mdtA, and gyrA) were detected as potential hub proteins to be associated with antibiotic efflux pump and target alteration mechanisms. These hub proteins were significantly (p < 0.05) enriched in biological process, molecular function, and cellular components. Therefore, the finding of this study suggests that human pathogenic Shigella strains harbored a wide range of ARGs that confer resistance through antibiotic efflux pumps and antibiotic target modification mechanisms, which must be taken into account to devise and formulate treatment strategy against this pathogen. Moreover, the identified hub proteins could be exploited to design and develop novel therapeutics against MDR pathogens like Shigella.

Draft genome sequencing of a multidrug-resistant Salmonella enterica subspecies enterica serovar Typhimurium strain isolated from chicken in Bangladesh

Herein this study, we sequenced the genome of a multidrug-resistant Salmonella enterica serovar Typhimurium strain MBR-MFRK-23 isolated from the liver tissue of a diseased layer chicken. The 4,964,854-bp draft genome comprises 50 contigs with 50.5× coverage and 52.1% GC content and is typed as S. enterica sequence type 19.

Methodology for laboratory-based antimicrobial resistance surveillance in animals

Antimicrobial resistance (AMR) is a crucial and emerging multifactorial “One Health” problem involving human and animal health, agriculture, aquaculture, and environment; and posing a potential public health hazard globally. The containment of AMR justifies effective surveillance programs to explicate the magnitude of the problem across the contributing sectors. Laboratory-based AMR testing and characterization is the key component of an AMR surveillance program. An AMR surveillance program should have a “top management” for fund mobilization, planning, formulating, and multilateral coordinating of the surveillance activities. The top management should identify competent participating laboratories to form a network comprising a reference laboratory and an adequate number of sentinel laboratories. The responsibilities of the reference laboratory include the development of standardized test methods for ensuring quality and homogeneity of surveillance activities, providing training to the laboratory personnel, and in-depth AMR characterization. The sentinel laboratories will take the responsibilities of receiving samples, isolation and identification of microbes, and initial AMR characterization. The sentinel laboratories will use simple antimicrobial susceptibility test (AST) methods such as disk diffusion tests, whereas the reference laboratories should use automated quantitative AST methods as well as advanced molecular methods to explicit AMR emergence mechanisms. Standard guidelines set by Clinical Laboratory Standards Institute or the European Committee on Antimicrobial Susceptibility Testing, should be followed to bring about conformity and harmonization in the AST procedures. AMR surveillance program in animals is eventually similar to that in human health with the exception is that veterinary antibiotics and veterinary pathogens should be given preference here. Hence, the review study was envisaged to look deep into the structure of the AMR surveillance program with significance on laboratory-based AMR testing and characterization methods.