Genomic characterization of Salmonella isolates from food and diarrheal patients in Ruian, China

Introduction Salmonella is a major foodborne pathogen threatening public health, and the cross-transmission between food and human sources remains a critical concern. To elucidate the epidemiological characteristics and potential transmission of Salmonella in Ruian City, China, we conducted a comprehensive phenotypic and genomic analysis of 173 archived Salmonella isolates collected from patients ( n = 101) and food samples ( n = 72) during 2020–2021. Methods We serotyped the strains and determined their antimicrobial resistance phenotypes, and used whole-genome sequencing(WGS) to analyze virulence genes, resistance genes, and the genetic relatedness among the isolates. Results A total of 28 distinct serovars were identified, with S . Typhimurium being the most prevalent in clinical isolates (26.73%) and S. London the dominant serovar in food isolates (29.85%); S . Typhimurium, S. I 4,5,12:i:-, S. London, S. Rissen and S. Goldcoast were detected in both sources. Clinical and food isolates exhibited high resistance rates to amoxicillin (72.28%/47.22%), piperacillin (67.33%/43.06%), minocycline (42.57%/41.67%), and trimethoprim-sulfamethoxazole (34.65%/40.28%), with multidrug-resistant (MDR) rates of 43.56 and 31.94%, respectively. Statistically significant differences in resistance to amoxicillin, piperacillin, gentamicin and minocycline were observed between S . Typhimurium and S. London. WGS identified 31 STs, with high concordance between serovar and ST. A total of 91 antimicrobial resistant genes (ARGs) were detected, with aac(6′)-Iaa (67.05%) being the most prevalent aminoglycoside resistance gene and bla TEM-1 being the dominant β-lactamase gene; a discrepancy between ARGs and phenotype was observed for several antibiotics. S. Rissen harbored fewer virulence genes (e.g., lacking lpfD , ratB , sodC1 , sseI and sspH2 ) and exhibited a gene-content pattern consistent with lower virulence potential. Phylogenomic analysis based on cgSNP showed that isolates of the same serovar clustered together, and cgSNP-based minimum spanning tree revealed close genetic relatedness (SNP ≤ 20) between pork and clinical isolates of S . Typhimurium, S. London, S. Goldcoast and S. Rissen, indicating potential cross-transmission between food and human sources. Discussion Our findings highlight the dis-tinct serotype distribution, ARGs and virulence characteristics of Salmonella from different sources in Ruian. These data provide a scientific basis for the prevention, control and clinical treatment of salmonellosis, and emphasize the necessity of continuous surveillance and the implementation of the One Health approach to mitigate Salmonella transmission along the food chain.