Phenotypic and genomic characterization of Salmonella isolates from pre-cooked seasoned chicken: predominant serovars and associations between mobile genetic element and antimicrobial resistance dissemination.

Pre-cooked seasoned chicken has become a mainstream processed poultry product worldwide, yet the pervasive contamination of multidrug-resistant (MDR) Salmonella poses severe threats to public health and food safety. Despite growing market demand, comprehensive surveillance of phenotypic and genomic multidrug resistance dynamics in this commodity remains limited. In this study, 424 commercially available pre-cooked seasoned chicken samples were collected from 12 provincial-level administrative regions across China during 2024-2025. Of 424 samples, 75 were culture-positive for Salmonella (17.69%), yielding 149 isolates. Among all isolates, 77.85% presented resistance to one or more antibiotics, and 45.64% were identified as MDR strains. A dominant resistance pattern (CRO-CFZ-CXM-TET) was shared by 75% (51/68) of MDR isolates, of which 28 (54.9%) were also resistant to ciprofloxacin. Fluoroquinolone intermediate susceptibility was highly prevalent, reaching 73.83% among all isolates. Whole-genome sequencing of 42 representative isolates revealed 15 serovars with corresponding unique sequence types (STs), among which Salmonella Infantis ST32, Salmonella Agona ST13, Salmonella Kentucky ST198 and Salmonella Indiana ST17 were predominant. The chromosomal parC (p.T57S) mutation was identified as a prevalent genetic marker strongly associated with fluoroquinolone intermediate susceptibility. Notably, S. Kentucky and S. Indiana isolates were all MDR strains and harbored significantly higher quantities of antimicrobial resistance genes (ARGs), QRDR mutations and insertion sequences than other serovars. Correlation analysis verified positive associations among resistance genes, insertion sequences and plasmid replicons. Additionally, the evolutionary trajectories of bacterial virulence and drug resistance appeared to be independent of each other. Phylogenetic analysis indicated that S. Indiana has formed regionally endemic MDR clones, while S. Kentucky exhibited cross-regional and widespread dissemination. More importantly, two S. Kentucky isolates recovered from pre-cooked seasoned chicken were genetically closely related to a human clinical strain (with cgSNP distances of 18 and 19), highlighting public health concerns regarding this clone in the commercial food chain. This study characterizes the phenotypic and genomic features of MDR Salmonella in pre-cooked seasoned chicken, contributing baseline data for further surveillance in this product category.