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Journal article
High-resolution characterization of the temporal and spatial distribution of antimicrobial resistance in Escherichia coli from pigs
Journal of antimicrobial chemotherapy, Vol.81(7), dkag196
2026
PMID: 42318923
Abstract
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 SciencesZheng Zhou Lee - Murdoch UniversityDavid Jordan - Murdoch UniversityMarc Stegger - Murdoch UniversityAndré Becker S Saidenberg - Statens Serum InstitutKittitat Lugsomya - Murdoch UniversityTerence Lee - Murdoch UniversityShewli Mukerji - Murdoch University, School of Medical, Molecular and Forensic SciencesLance Price - Statens Serum InstitutKim Nairn - Services AustraliaRebecca 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
- Copyright
- © The Author(s) 2026.
- 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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