Association between phenotypes and genotypes of antimicrobial resistance in <i>E. coli</i> and <i>Salmonella</i> isolates from retail chicken meat and live bird market sewage in Bangladesh

ABSTRACT Retail chicken meat contaminated with Escherichia coli and Salmonella represents a significant global public health concern, particularly in developing countries like Bangladesh. The presence of antimicrobial-resistant (AMR) strains in retail chicken meat poses a serious health threat to consumers. Therefore, a cross-sectional live bird market (LBM) survey was conducted to determine the spectrum of AMR and association among AMR phenotypes, as well as between phenotypes and resistance genes in E. coli and Salmonella isolated from retail chicken meat ( n = 320) and LBM sewage ( n = 64) samples collected from 64 LBMs of 32 upazilas in 16 districts spanning 8 administrative divisions of Bangladesh. E. coli and Salmonella were identified using culture-based and molecular methods and were subsequently subjected to antimicrobial susceptibility testing. Genes encoding β-lactamases and plasmid-mediated quinolone resistance were detected by multiplex PCR and confirmed by sequencing. Multidrug resistance (MDR) was observed in 99.1% and 92.2% of E. coli and in 99.4% and 100% of Salmonella from retail chicken meat and LBM sewage samples, respectively. The most frequently detected resistance genes were bla_TEM , bla_CTX-M-1 , qnrA , qnrB , and qnrS . Strong associations between phenotypic resistance and corresponding resistance genes were observed for cefepime /bla_CTX-M-1 , ceftazidime/ bla_CTX-M-1 , aztreonam / bla_CTX-M-1 , cefuroxime /qnrA, ceftriaxone /qnrA, cefoxitin /qnrB , cefixime/ qnrB , cefaclor/ qnrB , trimethoprim-sulfamethoxazole/ qnrS , ampicillin/ qnrS , and amoxicillin-clavulanic acid /qnrS ( P &lt; 0.05). Overall, these findings indicate that retail chicken meat serves as a potential source of MDR E. coli and Salmonella harboring clinically relevant AMR genes. Urgent attention is needed, including strengthening antimicrobial stewardship and surveillance programs in poultry production systems in Bangladesh. IMPORTANCE Retail chicken meat is a potential reservoir of antimicrobial-resistant (AMR) Escherichia coli and Salmonella , which pose a major public health concern due to their ability to harbor a wide range of AMR genes. Given the high consumption of chicken meat and the increasing prevalence and invasiveness of multidrug-resistant E. coli and Salmonella , continuous monitoring of their prevalence and AMR patterns in retail chicken meat and sewage samples is essential. Understanding the associations among resistance genes may provide critical insights for developing effective antimicrobial stewardship and prudent-use guidelines. Moreover, these findings could serve as a foundation for future research addressing public health and food safety challenges associated with AMR foodborne bacteria.