Genomic Characterization of a Virulent Multidrug-Resistant Salmonella enterica Serovar Enteritidis Strain Isolated from Meat Rabbits (Oryctolagus cuniculus) in China

Background The rise of virulent, multidrug-resistant Salmonella enterica serovar Enteritidis strains threatens food safety and human health. This study reports the isolation of a Salmonella enterica serovar Enteritidis strain (SE JL228) from a meat rabbit, which was associated with a high-mortality outbreak on a rabbit farm in China in 2018. The objective of this study was to elucidate the genetic characteristics, antimicrobial resistance determinants, metal tolerance mechanisms, and virulence potential of a rabbit-derived strain, thereby providing insights into its implications for both public and animal health. Results This strain exhibited resistance to 13 antibiotics within 8 antimicrobial categories as well as to silver (Ag ⁺ ), copper (Cu ²⁺ ), and tellurium (Te ⁴⁺ ). Additionally, SE JL228 demonstrated high tolerance to the quaternary ammonium compound (QAC) disinfectant. In vitro assays revealed superior invasion of human brain microvascular endothelial cells and enhanced intracellular survival in activated peritoneal macrophages compared to the moderately virulent SE strain LN248. In vivo studies confirmed extensive dissemination in mice, with an LD ₅₀ approximately 68-fold lower than that of LN248. A 4.7-megabase chromosome together with two plasmids—pSE228A (211.4 kb, IncFIB/IncHI2) and pSE228B (54.6 kb, IncN)—was identified through whole-genome sequencing. The genome encoded 17 antibiotic resistance genes (ARGs), 34 virulence factors including an intact spv operon, and heavy metal resistance operons ( copESDBAC , silPABFCRE , terEDCBAZWYX ) alongside a QAC-resistance gene ( qacE ) on pSE228A. Plasmid pSE228A shares near-identical structure with a previously-isolated IncHI2 plasmid, while pSE228B, carrying the transferable bla _TEM−1 gene conferring penicillin resistance, showed limited homology to the known plasmids. Conclusions The rabbit-derived SE JL228 represents a highly virulent, multidrug-resistant, and metal-tolerant pathogen. Its ability to invade brain endothelial cells, survive within macrophages, and disseminate systemically underscores its zoonotic potential. The presence of transferable plasmids encoding both resistance and virulence factors suggests a heightened risk of spread within farm environments and beyond. These findings emphasize the urgent need for enhanced surveillance, prudent antimicrobial use, and effective biosecurity measures to mitigate the emergence and dissemination of such hybrid pathogens.