Whole-Genome Sequencing and Intestinal Metagenome Sequencing Revealed the Carriage and Transmission of Salmonella enterica in Xinjiang, China.

Background:Salmonella enterica, a major foodborne pathogen, poses a severe global public health threat. However, data regarding its carriage characteristics, transmission patterns, and association with intestinal microbiota in healthy populations of Xinjiang, China, remain insufficient, limiting the formulation of targeted salmonellosis prevention and control strategies. Methods: In this study, 31 Salmonella enterica strains isolated from more than 2000 healthy individuals in Urumqi were subjected to whole-genome sequencing to analyze serovars, antimicrobial resistance (AMR) genes, and virulence genes. Meanwhile, metagenomic sequencing was performed on 50 fecal samples (culture negative) from 2000 healthy individuals to investigate intestinal microbiota structure, Salmonella enterica prevalence, and related microbial taxa. Results: The results showed that 60% of samples (30/50) were positive by the read-based criterion (≥1000 Salmonella-specific reads), while the assembly-verified criterion (≥1000 reads and contigs > 1 kb) confirmed Salmonella-specific sequences in 12% (6/50). Among the 31 culture-confirmed isolates, Salmonella Typhimurium and Salmonella Paratyphi B were the dominant serovars, together accounting for 60%. All isolates harbored core virulence genes for Type III secretion system and adhesion factors, with low AMR gene carriage and no multidrug-resistant strains. Phylogenetic analysis showed that Urumqi-derived isolates were distributed across multiple genomic clusters, suggesting active inter-regional circulation of S. enterica within the available dataset. Salmonella enterica carriage did not affect gut microbial α-diversity but altered community composition, with Escherichia coli, Shigella flexneri, and Klebsiella pneumoniae as key associated taxa. Conclusions: This study found that Urumqi-derived isolates are widely distributed across genomic clusters in Xinjiang, with a unique local transmission chain identified, though definitive source attribution requires further geographically balanced sampling. Salmonella enterica carriage exhibited ecological niche synergy with intestinal Enterobacteriaceae, but did not significantly affect gut microbial diversity.