Whole-genome sequencing reveals diverse antimicrobial resistance genes in Escherichia coli from pig slaughterhouses in Banten Province, Indonesia

Objective: To characterize the distribution and genetic location of antimicrobial resistance genes (ARGs) in Escherichia coli isolated from pig slaughterhouses in Banten Province, Indonesia. Methods: 20 E coli isolates were collected from effluent and floor swabs in 10 slaughterhouses. Whole-genome sequencing was performed using Oxford Nanopore technology. Antimicrobial resistance genes were identified using AMRFinderPlus, and plasmid replicons were detected with PlasmidFinder. Results: ARGs representing 12 antibiotic classes were detected, including aminoglycosides, β-lactamases, colistin, fosfomycin, macrolides, phenicols, quinolones, sulfonamides, tetracyclines, and trimethoprim. Floor isolates carried 28 ARGs, whereas effluent isolates carried 23. β-Lactamase genes showed the greatest diversity (11 types), dominated by blaEC. Many ARGs were plasmid-borne, and 65% of isolates exhibited multidrug resistance potential. Conclusions: Pig slaughterhouse E coli harbor diverse, plasmid-associated ARGs, indicating active dissemination potential and emphasizing the importance of genomic surveillance. Clinical Relevance: Although this study did not involve clinical patients, the findings are highly relevant to veterinary and public health practice. The detection of diverse, plasmid-associated ARGs in slaughterhouse E coli highlights the need for antimicrobial stewardship and biosecurity measures in pig production systems to mitigate transmission risks to animals, workers, and consumers.