Comparable Multidrug Resistance Profile and ESBL Gene Flux Among <i>Escherichia coli</i> Strains Isolated from Slaughterhouses and Associated Poultry Farms

Multidrug resistant (MDR) Escherichia coli strains are ideal species to monitor the antimicrobial resistance (AMR) gene flux from a One Health perspective. Slaughterhouses serve as a potential hotspot for environmental AMR dissemination, and the current study thus aimed to identify MDR E. coli contamination in slaughterhouses in comparison with their associated poultry farms. Comparative resistome analysis has identified both shared a similar resistance pattern with highest resistance to tetracycline (85%), followed by ciprofloxacin, ampicillin (&gt;80% each), and cephalosporin (&gt;70%). Here, 58.8% of the MDR strains were also found to be extended-spectrum beta-lactamase (ESBL) positive, and ESBL gene screening shows high genotype-to-phenotype correlation. A strong ESBL-producing F2.4 strain was further selected for whole-genome sequencing (WGS) and the result revealed it to have close similarity to the pathogenic E. coli O101:H9 serotype, which is least reported from India. The pathogen finder has further predicted the strain to have 85% potential possibility to be a human pathogen. The WGS-based analysis of F2.4 has also revealed it to have the presence of hlyE , which encodes for the avian E. coli alpha-hemolysin, along with other virulence factors such as fdeC , iss2 , ibeC , csg , fim , and esp genes, which are of zoonotic potential. The genome also contained around seven beta-lactamase-encoding genes imparting resistance to penicillin and cephalosporin, whereas 74% of the antibiotic resistance genes predicted from F2.4 encoded for the efflux pump-related genes. Among them, genes such as emrK , emrY , acrD , evgS , evgA , and YojI were underreported, highlighting the importance and the need for geographical-based AMR risk analysis.