Virulence genes and phylogenetic analysis of antibiotic-resistant Escherichia coli isolated from pig slaughterhouses in Banten Province, Indonesia

TL;DR

This study analyzed antibiotic-resistant E. coli from pig slaughterhouses in Indonesia, finding diverse virulence genes and highlighting zoonotic risks.

Contribution

The study provides the first comprehensive genomic analysis of E. coli from pig slaughterhouses in Indonesia.

Findings

Fifty-seven virulence genes were identified, including those linked to enteric and extraintestinal pathotypes.

Phylogenetic analysis revealed five phylogroups, with A and B1 being the most common.

Multidrug-resistant E. coli with diverse virulence genes pose zoonotic and environmental health risks.

Abstract

Escherichia coli is a prominent zoonotic pathogen with diverse virulence factors and significant antibiotic resistance, particularly in pig farming environments. Pig slaughterhouses are critical points of potential bacterial transmission to humans and the environment. Comprehensive genomic surveillance of E. coli in these settings remains limited in Indonesia. This study aimed to investigate the phylogenetic distribution, virulence gene profiles, pathotypes, and antibiotic resistance characteristics of E. coli isolated from pig slaughterhouses in Banten Province, Indonesia, using whole-genome sequencing.

Environmental samples, including effluent and floor swabs (n = 200), were collected from 10 pig slaughterhouses. E. coli isolates were identified and previously characterized for antibiotic resistance. Genomic DNA was extracted and sequenced using the Oxford Nanopore MinION platform. Bioinformatic analyses, including virulence gene detection (VirulenceFinder), phylogenetic reconstruction (RAxML), and phylogroup determination (Clermont method), were conducted to classify isolates based on pathotype and genetic lineage.

Fifty-seven virulence genes were identified, including 46 associated with enteric pathotypes (Enterohemorrhagic E. coli: 35%, enterotoxigenic E. coli: 15%, and enteropathogenic E. coli: 5%) and 15 linked to extraintestinal pathotypes (uropathogenic E. coli: 95%, and neonatal meningitis E. coli: 5%). Phylogenetic analysis revealed five phylogroups - A, B1, D, G, and clade I - with A and B1 predominating. Most isolates (60%) exhibited a single pathotype, while a minority (5%) carried genes from multiple pathotypes. Serotypes O73, O78, and O157 were identified, with O73 being the most prevalent. No strong correlation was observed between phylogenetic clustering and virulence gene pathotype.

The high prevalence of multidrug-resistant E. coli with diverse virulence genes in pig slaughterhouses highlights significant zoonotic and environmental health risks. These findings underscore the need for enhanced hygiene practices, antimicrobial stewardship, and longitudinal genomic surveillance in Indonesian pig production systems.

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