[Whole-genome sequencing-based molecular characterization of Salmonella associated with foodborne disease outbreaks in Wuxi City from 2014 to 2024].

This study analyzed the molecular characteristics of Salmonella isolates associated with foodborne outbreaks in Wuxi City using whole-genome sequencing (WGS). Epidemiological data from 16 outbreaks (2014-2024) and 68 Salmonella isolates were collected. Antimicrobial susceptibility testing and WGS were performed. ResFinder, PlasmidFinder, and PointFinder were used to annotate resistance genes, plasmids, and mutations. A core-genome SNP phylogenetic tree was constructed. Among the 68 Salmonella isolates, ST11 Salmonella Enteritidis was the predominant clone. The overall antimicrobial resistance rate was 95.59%, with a multidrug resistance (MDR) rate of 55.88%. High resistance rates were observed for nalidixic acid (75.00%), streptomycin (69.12%), and ampicillin (57.35%). Compared with the non-S. Enteritidis isolates, S. Enteritidis exhibited significantly higher MDR rates and resistance rates to penicillins, β-lactam inhibitor combinations, and quinolones (all P<0.05). A total of 24 antimicrobial resistance genes were identified, with aac(6')-Iaa and blaTEM-1B being the most prevalent, and a high concordance was observed between genotypic and phenotypic resistance. IncF and IncX were the predominant plasmid replicon types. Phylogenetic analysis showed that isolates clustered primarily according to serotype and sequence type (ST). Isolates from the same outbreak were highly homologous, with pairwise SNP differences ranging from 0 to 7, whereas isolates from one outbreak exhibited substantial genetic divergence (342 SNPs). In conclusion, Salmonella outbreaks in Wuxi from 2014 to 2024 are predominantly caused by ST11 S. Enteritidis, which exhibits a high level of resistance to commonly used antimicrobial agents. Whole-genome sequencing could effectively distinguish co-isolates with low genetic relatedness, providing high-resolution evidence for outbreak source tracing and epidemiological investigations.