# Genomic epidemiology of Salmonella Typhimurium and its monophasic variants in Southern China: A spatiotemporal and source attribution analysis

## TL;DR

This study uses genomic data to trace the spread of Salmonella in southern China, showing how poultry and pork contribute to human infections and antibiotic resistance.

## Contribution

The study provides new genomic evidence of zoonotic transmission and cross-regional spread of Salmonella in southern China.

## Key findings

- Salmonella ST34, ST19, ST155, and ST469 were most common in human and food isolates, showing close genetic links.
- High antimicrobial resistance rates were found, especially in ST34 isolates, driven by SGI1 and specific resistance genes.
- Spatial clustering linked contamination to live poultry markets, slaughterhouses, and retail meat, suggesting foodborne transmission.

## Abstract

Salmonella Typhimurium and its monophasic variants are major contributors to foodborne illnesses globally, with zoonotic transmission posing significant public health risks. In southern China, persistent salmonellosis cases linked to poultry and pork highlight the need for advanced genomic tools to trace contamination sources and understand transmission dynamics. This study integrates whole-genome sequencing (WGS) and spatiotemporal data to investigate the molecular epidemiology of Salmonella in Jiangxi Province, a region with high incidence of foodborne salmonellosis. Analysis of 206 Salmonella isolates (2015–2021) revealed dominant sequence types (ST34, ST19, ST155, and ST469) associated with human clinical cases and food sources. High-resolution single nucleotide polymorphism (SNP) phylogenetic analysis revealed well-supported, monophasic clades corresponding to the major sequence types. This analysis provided strong genomic evidence for zoonotic transmission, with human clinical isolates being genetically almost identical (≤5 SNPs) to isolates from poultry (ST34/ST19) and pork (ST155/ST469) sources. Clonal clusters of monophasic Typhimurium variants (77.9 % of ST34 isolates) exhibited widespread geographic distribution across 11 prefectures, and the high genetic similarity among isolates suggests potential cross-regional transmission through contaminated food supply chains. High antimicrobial resistance (AMR) rates were detected against ampicillin (68.0 %), tetracycline (61.0 %), and sulfamethoxazole-trimethoprim (54.0 %), with multidrug-resistant (MDR) strains (60.2 %) prevalent in clinical and food-derived isolates. ST34 exhibited the highest MDR prevalence (75.4 %), driven by the presence of Salmonella Genomic Island 1 (SGI1) in many isolates. The β-lactamase gene blaTEM-1 was most prevalent (60.7 %), followed by tet(A) (54.4 %), and sul2 (47.6 %). Point mutations in the quinolone resistance-determining region (QRDR), specifically in gyrA, were identified as the primary mechanism for ciprofloxacin resistance. Spatial clustering identified significant clusters in live poultry markets, slaughterhouses, and retail meat, emphasizing the role of foodborne zoonotic reservoirs. Findings advocate for strengthened One Health interventions, including enhanced AMR monitoring, targeted food safety regulations, and real-time WGS-based surveillance to mitigate zoonotic transmission risks in southern China.