The Broad Ecological Range of Salmonella enterica Serotype Typhimurium Is Associated With Genomic Diversification.
10 affiliations
- 1Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, USA.
- 2Department of Computer Science, Virginia Tech, Blacksburg, Virginia, USA.
- 3Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia, USA.
- 4Center for Emerging, Zoonotic, and Arthropod-Borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA.
- 5Global Change Center, Virginia Tech, Blacksburg, Virginia, USA.
- 6Department of Business Information Technology, Virginia Tech, Blacksburg, Virginia, USA.
- 7Center for Food Safety, University of Georgia, Griffin, Georgia, USA.
- 8Institute for Critical Technology and Applied Science, Virginia Tech, Blacksburg, Virginia, USA.
- 9Department of Food Science and Technology, Virginia Tech, Blacksburg, Virginia, USA.
- 10School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, Virginia, USA.
Abstract
Salmonella Typhimurium is a versatile foodborne pathogen with a broad ecological range, making it an ideal model to better understand pathogen adaptations that allow them to infect multiple hosts and persist across environments. Here, we analysed 595 genomes of S. Typhimurium representing three food animal sources (bovine, swine, and poultry) and one non-food animal source (wild birds). We found that S. Typhimurium from food animal sources generally had a more open pangenome and harboured more antimicrobial resistance genes (ARGs). Notably, swine isolates exhibited the most open pangenome and the highest prevalence of ARGs, patterns that were associated with a greater presence of mobile genetic elements, particularly plasmids. Despite similar core genome sizes, S. Typhimurium from different sources displayed distinct patterns of positive selection in the core genome that varied in frequency and targeted functional categories. In contrast, although accessory genome sizes varied substantially across sources, the frequency of positive selection remained similar. Using machine learning, we identified source-predictive genetic variants, many of which are associated with stress-response functions. These findings suggest that gain and loss of accessory genes and positive selection acting on core genes support differential adaptation in S. Typhimurium, potentially contributing to its broad ecological range.
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BibTeX
@article{ohri2026broad,
title = {{The Broad Ecological Range of Salmonella enterica Serotype Typhimurium Is Associated With Genomic Diversification.}},
author = {Leela Ohri and Sandeep Chinnareddy and Ying-Xian Goh and Hailong Zhang and Xiangyu Deng and Amy Pruden and Rachel Cheng and Song Li and Jingqiu Liao},
journal = {Environmental microbiology},
year = {2026},
month = nov,
doi = {10.1111/1462-2920.70466},
url = {https://europepmc.org/article/MED/42971789},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - The Broad Ecological Range of Salmonella enterica Serotype Typhimurium Is Associated With Genomic Diversification.
AU - Leela Ohri
AU - Sandeep Chinnareddy
AU - Ying-Xian Goh
AU - Hailong Zhang
AU - Xiangyu Deng
AU - Amy Pruden
AU - Rachel Cheng
AU - Song Li
AU - Jingqiu Liao
PY - 2026
DA - 2026/11/01
JO - Environmental microbiology
DO - 10.1111/1462-2920.70466
UR - https://europepmc.org/article/MED/42971789
AB - Salmonella Typhimurium is a versatile foodborne pathogen with a broad ecological range, making it an ideal model to better understand pathogen adaptations that allow them to infect multiple hosts and persist across environments. Here, we analysed 595 genomes of S. Typhimurium representing three food animal sources (bovine, swine, and poultry) and one non-food animal source (wild birds). We found that S. Typhimurium from food animal sources generally had a more open pangenome and harboured more antimicrobial resistance genes (ARGs). Notably, swine isolates exhibited the most open pangenome and the highest prevalence of ARGs, patterns that were associated with a greater presence of mobile genetic elements, particularly plasmids. Despite similar core genome sizes, S. Typhimurium from different sources displayed distinct patterns of positive selection in the core genome that varied in frequency and targeted functional categories. In contrast, although accessory genome sizes varied substantially across sources, the frequency of positive selection remained similar. Using machine learning, we identified source-predictive genetic variants, many of which are associated with stress-response functions. These findings suggest that gain and loss of accessory genes and positive selection acting on core genes support differential adaptation in S. Typhimurium, potentially contributing to its broad ecological range.
SN - 1462-2912
SN - 1462-2920
ER -