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.