Herd-level heterogeneity of antimicrobial resistance in commensal Escherichia coli: A nationwide high-throughput survey of Australian pig herds.

Sam Abraham; David Jordan; Marin Milotic; Shewli Mukerji; Yvette Pollock; Samantha Sterndale; David J Hampson; Kittitat Lugsomya; Rebecca Abraham

doi:10.1016/j.vetmic.2026.111177

PubMed · 42561833

Herd-level heterogeneity of antimicrobial resistance in commensal Escherichia coli: A nationwide high-throughput survey of Australian pig herds.

Sam Abraham·David Jordan·Marin Milotic·Shewli Mukerji·Yvette Pollock·Samantha Sterndale·David J Hampson·Kittitat Lugsomya·Rebecca Abraham

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Abstract

Antimicrobial resistance in commensal Escherichia coli provides a useful indicator for overall antimicrobial resistance burden. We applied this approach to assess antimicrobial resistance within and between commercial pig herds across Australia. A high-throughput robotic workflow was used to isolate 2730 E. coli colonies from rectal contents collected in 2022 from healthy slaughter pigs (n = 300) representing 30 herds (∼70% of national production). Up to 94 isolates per herd underwent antimicrobial susceptibility testing using the Robotic Antimicrobial Susceptibility Platform. Isolate- and herd-level antimicrobial resistance indices were calculated, weighting antimicrobials by their human health importance. Resistance to first-line agents was widespread: ampicillin 77% and tetracycline 79%. By contrast, resistance to critically important antimicrobials was rare (ciprofloxacin 0.11%; extended-spectrum cephalosporins 0.04%), and no clinical resistance to carbapenems or colistin was detected. Overall, 56.9% of isolates were multi-class resistant. Herd-level antimicrobial resistance within indices ranged from 1.51 to 5.76, revealing substantial between-herd heterogeneity. Three herds carried critically important antimicrobials-resistant isolates that would likely have been missed using conventional, lower-density sampling approaches. Whole-genome sequencing identified fluoroquinolone-resistant isolates belonging to ST10 and ST69 (both qnrS1), and ST744 (Quinolone Resistance Determining Region mutations plus blaCTX-M-27). By testing approximately tenfold more isolates than conventional surveys, we uncovered considerable antimicrobial resistance with heterogeneity within and between animals and herds, including farm-specific variability. This expanded sampling also enabled detection of critically important antimicrobial resistance at very low prevalence. In conclusion, high-throughput, high-density testing offers a practical early-warning system and herd-level benchmark to inform surveillance and targeted interventions.

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Animals Escherichia coli Australia Swine Anti-Bacterial Agents Escherichia coli Infections Microbial Sensitivity Tests Drug Resistance, Bacterial Drug Resistance, Multiple, Bacterial Swine Diseases AMR Commensal Escherichia coli Pigs Public health Robotics Surveillance Journal Article

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Sam Abraham, David Jordan, Marin Milotic, Shewli Mukerji, Yvette Pollock, Samantha Sterndale, David J Hampson, Kittitat Lugsomya, Rebecca Abraham. 2026-08-03. Herd-level heterogeneity of antimicrobial resistance in commensal Escherichia coli: A nationwide high-throughput survey of Australian pig herds.. https://doi.org/10.1016/j.vetmic.2026.111177

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Journal Article resource Animals subject Anti-Bacterial Agents subject Drug Resistance, Bacterial subject Drug Resistance, Multiple, Bacterial subject Escherichia coli subject Escherichia coli Infections subject Journal Article subject Microbial Sensitivity Tests subject Pigs subject

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