ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Antimicrobials, Resistance and Chemotherapy
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1683995
This article is part of the Research TopicBioinformatics approaches to investigate antimicrobial resistance (AMR) in human, animal and environmentView all 21 articles
Genomic dissection of the antimicrobial resistance epidemiology of Salmonella Typhimurium
Provisionally accepted
- 1University of New South Wales, Kensington, Australia
- 2Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research and Westmead Hospital, Westmead, Australia
- 3Faulty of Medicine and Health, The University of Sydney, NSW, Australia
- 4Sydney Infectious Diseases Institute, The University of Sydney, NSW, Australia
- 5University of New South Wales, Sydney, Australia
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Salmonella Typhimurium (STm) is a global foodborne pathogen with increasing resistance to several antibiotics, including fluoroquinolones and third-generation cephalosporins. Multiple countries have implemented ongoing genomic surveillance of STm, releasing their data in the public domain. In this study, we compiled a dataset of ~65,000 publicly available STm isolates (until August, 2023) and analysed the predicted resistance to 14 key antibiotics. All isolates were characterized using Multilevel Genome Typing (MGT) a standardized genome typing method, to assess predicted resistance profiles by MGT sequence type (ST). Approximately half of the isolates were predicted to be resistant to at least one antibiotic, but resistance levels varied according to geographic location, time of collection and MGT ST. We identified 407 MGT STs where ≥80% of the isolates were predicted to have resistance to at least one antibiotic, or intermediate resistance in the case of ciprofloxacin. We detected eight MGT STs defined as cefotaxime resistant and three MGT STs defined as ciprofloxacin-intermediate in the latest two years of data (2021–2022), these being two key antibiotics prescribed for severe salmonellosis. MGT STs defined as cefotaxime resistant were primarily linked to cattle or poultry in the USA, while MGT STs defined as having intermediate resistance to ciprofloxacin were predominantly associated with swine in the UK. Integration of MGT strain typing with AMR prediction provides scalable, sharable, standardised and precise tracking of resistant isolates, offering a powerful framework for global AMR surveillance. This approach is broadly applicable to other bacterial pathogens, enhancing data-driven monitoring and intervention strategies.
Keywords: antimicrobial resistance, Multilevel Genome Typing, Genomic surveillance, Typhimurium, Ciprofloxacin, Cefotaxime
Received: 11 Aug 2025; Accepted: 10 Oct 2025.
Copyright: © 2025 Kaur, Partridge, Payne, Sintchenko and Lan. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Ruiting Lan, r.lan@unsw.edu.au
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