High-resolution characterization of the temporal and spatial distribution of antimicrobial resistance in Escherichia coli from pigs

Sam Abraham; Zheng Zhou Lee; David Jordan; Marc Stegger; André Becker S Saidenberg; Kittitat Lugsomya; Terence Lee; Shewli Mukerji; Lance Price; Kim Nairn; Rebecca J Abraham

doi:10.1093/jac/dkag196

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High-resolution characterization of the temporal and spatial distribution of antimicrobial resistance in Escherichia coli from pigs

Journal article

Open access

High-resolution characterization of the temporal and spatial distribution of antimicrobial resistance in Escherichia coli from pigs

Sam Abraham, Zheng Zhou Lee, David Jordan, Marc Stegger, André Becker S Saidenberg, Kittitat Lugsomya, Terence Lee, Shewli Mukerji, Lance Price, Kim Nairn, …

Journal of antimicrobial chemotherapy, Vol.81(7), dkag196

2026

DOI: https://doi.org/10.1093/jac/dkag196

PMID: 42318923

Appears in Open Access via Read & Publish Agreements

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Abstract

Animals

Anti-Bacterial Agents - pharmacology

Drug Resistance, Bacterial

Escherichia coli - drug effects

Escherichia coli - genetics

Escherichia coli - isolation & purification

Escherichia coli Infections - microbiology

Escherichia coli Infections - veterinary

Feces - microbiology

Microbial Sensitivity Tests

Spatio-Temporal Analysis

Swine - microbiology

Whole Genome Sequencing

Livestock are recognized reservoirs of antimicrobial resistance (AMR). However, current surveillance often overlooks key ecological aspects such as spatial-temporal patterns and quantification of shedding levels of resistant bacteria. In particular, early detection of low-level shedding of resistance to critically important antimicrobials (CIAs), including extended-spectrum cephalosporins (ESCs) and fluoroquinolones (FQs), remains limited. Using commensal Escherichia coli as an indicator, we applied a high-throughput Robotic Antimicrobial Susceptibility Platform (RASP) to assess phenotypic resistance in isolates from 900 samples collected across 10 pig herds over 3 years. Quantitative assessments of antimicrobial resistance (cfu/g) were performed using selective agars containing antimicrobials, with plating and data capture (colony counting) automated on the RASP. Broth microdilution and whole-genome sequencing were performed on CIA-R E. coli using RASP. Persistent resistance to ampicillin and tetracycline (∼5.8 log10 cfu/g) showed minimal variation between herds and years. Gentamicin resistance declined significantly (-0.23 log10 cfu/g/year, P < 0.0001), while ESC resistance rose significantly (0.16 log10 cfu/g/year, P = 0.015), although some herds showed no ESC shedding. Ciprofloxacin resistance was detected in 58% of samples but generally at lower levels (∼2.1 log10 cfu/g) with herd-level variability. Genomic analysis identified FQ-resistant sequence types ST744 and ST167 with global phylogenetic links, and ESC resistance was associated with blaCTX-M-1 on IncI1 plasmids. These findings reveal the ecological complexity of AMR in livestock and highlight limitations of standard surveillance in detecting rare resistances. Our study demonstrates how high-throughput robotics integrated with robust field design can enhance AMR monitoring and inform One Health strategies for mitigation.

Details

Title: High-resolution characterization of the temporal and spatial distribution of antimicrobial resistance in Escherichia coli from pigs
Authors/Creators: Sam Abraham - Murdoch University, School of Medical, Molecular and Forensic Sciences
Zheng Zhou Lee - Murdoch University
David Jordan - Murdoch University
Marc Stegger - Murdoch University
André Becker S Saidenberg - Statens Serum Institut
Kittitat Lugsomya - Murdoch University
Terence Lee - Murdoch University
Shewli Mukerji - Murdoch University, School of Medical, Molecular and Forensic Sciences
Lance Price - Statens Serum Institut
Kim Nairn - Services Australia
Rebecca J Abraham - Murdoch University, School of Medical, Molecular and Forensic Sciences
Publication Details: Journal of antimicrobial chemotherapy, Vol.81(7), dkag196
Publisher: Oxford University Press on behalf of British Society for Antimicrobial Chemotherapy.
Number of pages: 12
Grant note: RnD4Profit-16-03-012 / Australian Government's Rural R&D for Profit program APL: 2019/0005 / Australian Pork Limited WANMA/EL2022/10 / WA Near Miss Fellowship through the Future Health Research and Innovation Fund (FHRI) APL: 2017/2240.01 / Australian Pork Limited
Identifiers: 991005891649407891
Murdoch Affiliation: Centre for Biosecurity and One Health; School of Medical, Molecular and Forensic Sciences
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.23 Infection Management & Resistance; 1.23.146 Antimicrobial Resistance
Web Of Science research areas: Infectious Diseases; Microbiology; Pharmacology & Pharmacy
ESI research areas: Pharmacology & Toxicology