Convergence of multidrug resistance, virulence, and biofilm formation in Salmonella isolates from humans, animals, and food in Xinjiang, China

Salmonella, a major Gram-negative enterobacterial pathogen, is a leading cause of foodborne illnesses worldwide. This study characterizes Salmonella isolates from human, animal, and food sources in Xinjiang, China, by analyzing their biofilm-forming capacity, antimicrobial resistance (AMR), virulence genes, serotypes, and sequence types based on multilocus sequence types (MLST) analysis. A total of 1,446 samples, including rectal swabs from poultry, cattle, sheep, and camels, equine abortion tissues, retail chicken samples, and human fecal specimens from outpatients with acute diarrhea, were collected between 2018 and 2025 in Xinjiang, China. Salmonella was isolated using standard culture methods (pre-enrichment in buffered peptone water, selective enrichment in Rappaport-Vassiliadis and tetrathionate broths, and plating on XLT-4 agar) and was confirmed by PCR (polymerase chain reaction) analysis of the invA gene. Biofilm formation was assessed using the crystal violet staining. Antimicrobial susceptibility was determined by disk diffusion following the CLSI guidelines (2020). Whole-genome sequencing was performed on an Illumina NovaSeq 6000 platform, and bioinformatics analysis was used to identify AMR genes (CARD, ≥ 90% identity, ≥ 80% coverage), virulence factors (VFDB, ≥ 90% identity, ≥ 80% coverage), serotypes (SeqSero2), and sequence types (PubMLST). Forty-nine Salmonella isolates (26 from animals, 23 from humans) were obtained after isolation and confirmation of the invA gene. Of these, 91.8% exhibited strong biofilm-forming capacity. High resistance rates were observed for ampicillin (65.3%), streptomycin (59.2%), tetracycline (49.0%), and trimethoprim-sulfamethoxazole (30.6%), with 48.9% classified as multidrug-resistant (MDR). Analysis of resistance genes indicated high frequencies of blaTEM−1 (51.0%), aph(3’’)-Ib (40.8%), aph(6)-Id (40.8%), and tet(A) (38.8%), with strong concordance between genotypes and phenotypes (e.g., blaTEM−1 with ampicillin resistance; aph(3’’)-Ib/aph(6)-Id with streptomycin resistance). Virulence profiling identified approximately 200 unique genes across eight functional classes, with near-universal presence of iron acquisition genes (e.g., fepG; 98.0%), type III secretion system genes (e.g., sipA, sspA, and invA; 95.9%), and fimbrial adhesion genes (e.g., fimH; 91.8%). Serotyping identified S. Enteritidis (26.5%), S. Typhimurium (16.3%), and S. Agona (16.3%) as the most prevalent serotypes, while MLST analysis showed ST11 (28.6%) as the dominant sequence type, primarily within phylogenetic groups B (44.9%) and D1 (26.5%). The co-occurrence of MDR, diverse virulence factors, and strong biofilm-forming capacities in the Salmonella isolates suggests an increased potential for environmental persistence and zoonotic transmission. These findings highlight significant public health risks and provide critical molecular insights to inform targeted surveillance and control strategies for Salmonella in this understudied region.