Genomic characterization of the convergence of multidrug resistance and virulence in Salmonella Enteritidis from a broiler slaughterhouse in China.

Salmonella Enteritidis (SE) remains a leading cause of human salmonellosis worldwide, with poultry products serving as a primary transmission vehicle. This study presented a comprehensive genomic characterization of SE isolates from a broiler slaughterhouse in Sichuan Province of China, revealing critical insights into antimicrobial resistance profiles, virulence potential and population structure. Among 175 isolates subjected to antimicrobial susceptibility testing, 98.86% demonstrated multidrug resistance, exhibiting notably high resistance rates to tetracycline (98.29%), sulfisoxazole (97.71%), nalidixic acid (97.14%), ampicillin (96.57%), cefotaxime (94.86%) and ciprofloxacin (94.29%). Whole-genome sequencing was performed on 61 representative isolates, selected to maximum spatial, temporal and phenotypic heterogeneity. The analysis identified a conserved resistance genotype featuring a universal chromosomal gyrA D87G mutation in the quinolone resistance-determining region, alongside a high prevalence of plasmid-borne blaCTX-M-14 (96.72%), fosA3 (96.72%) and tet(A) (98.36%). All sequenced isolates harbored complete virulence determinants, including functional type III secretion systems (T3SS-1 and T3SS-2) and plasmid-borne spvBCR (93.44%) and rck (100%) genes, indicating enhanced systemic pathogenicity. Detailed characterization of representative strain Y9-1T revealed two critical plasmids, including a conjugative IncX1 plasmid co-harboring blaCTX-M-14, fosA3 and qnrS1 within a mobile genetic element-rich region, and an IncFIB(S)/IncFII(S) virulence plasmid carrying spvABCDR and rck genes. Phylogenetic analysis delineated five HierBAPS clades, with most isolates belonging to the globally disseminated Clade 1. In particular, a distinct monophyletic Clade 4 exclusively comprised recent Chinese isolates (2023-2024) characterized by a uniform gyrA D87G and blaCTX-M-14 signature. This study demonstrated the emergence and clonal expansion of a concerning SE lineage within the Chinese poultry sector, characterized by a high-risk convergence of extensive drug resistance, enhanced virulence potential and efficient clonal dissemination. The coexistence of global and locally adapted clones in the slaughterhouse underscored the urgent need for integrated One Health interventions to curb the spread of these high-risk pathogens through the food chain.