Phenotypic and Genotypic Characterization of Colistin, ESBL, and Multidrug Resistance in Escherichia coli Across the Broiler Production Chain in Karnataka, India

The emergence of antimicrobial resistance (AMR) across the broiler production chain holds significant economic, animal, and public health implications. This study investigated phenotypic resistance to 13 antimicrobials and the presence of 35 antimicrobial resistance genes (ARGs) in Escherichia coli (n = 291) isolated across three broiler production chains (broiler breeder farms, hatcheries, commercial broiler farms, and retail meat shops). An extremely high phenotypic resistance (>70%) to doxycycline, ciprofloxacin, and cefpodoxime, and very high resistance (50–70%) to ampicillin, cefotaxime, gentamicin, and ceftazidime was observed. In addition, 97% of isolates were multidrug-resistant (resistant to ≥1 drug in ≥3 antimicrobial classes), 42% were extended-spectrum beta-lactamase (ESBL) producers, 65% were resistant to third-generation cephalosporins (3GCR), and 21% were resistant to colistin. The Poisson regression model revealed no significant difference in AMR among broiler production stages, except for colistin. Among 35 ARGs tested, 24 (67%) were detected at least once. The most prevalent were tetA, blaTEM, qnrB, qnrS, and aac(6′)-Ib-cr, while qnrD, sul2, blaOXA, and blaCTX-M were detected at lower levels (1–7%). All five tested mcr genes (mcr-1 to mcr-5) were identified in commercial farms and retail shops. No blaNDM, tetB, tetC, tetD, tetM, qnrC, aac(3)-IIa (aacC2), aph(3)-IIa (aphA2), or aac(6′)-Ib genes were found. A strong correlation was observed between AMR phenotypes and ARGs. High AMR among E. coli in broiler production poses significant One Health risks, with widespread MDR, ESBL production, and resistance to critically important antimicrobials. Prudent antimicrobial use, enhanced surveillance and education, farm biosecurity, and One Health strategies are crucial in mitigating these threats.