Genomic and resistome analysis of isolates from retail markets in Yichun city, China.

Nontyphoidal (NTS) causes global outbreaks of foodborne disease. The main source of for humans is animal-borne foods; however, the monitoring of in the food chain via genomic platforms was limited in China. This study evaluated the prevalence, resistome, and virulome diversity of strains identified from pork, retail environment, aquatic products, and poultry eggs of retail markets in Yichun city, Jiangxi province. The overall incidence of was 9.4 %, with a higher contamination rate observed in pork at 13.5 %, followed by the retail environment at 7.69 %. The genomic analysis of the isolates revealed a total of fifteen distinct serovars, with serovar Enteritidis being the most prevalent (64.3 %). The phenotypic resistance analysis conducted by the broth microdilution method, revealed that 81.12 % of the isolates exhibited multidrug resistance (MDR), with high resistance to trimethoprim/sulphonamides (100 %), followed by tetracycline (99.3 %) and streptomycin (99.3 %). Genotypic analysis of antimicrobial resistance identified 80 antimicrobial-resistant genes (ARGs), with , , , , , , , and conferring resistance to different antimicrobial classes, being the predominant ARGs. Additionally, forty ESBL genes, particularly critical genes such as and , were also identified in isolates. The , , and plasmid replicons were widely prevalent and served as significant reservoirs of horizontally acquired foreign genes. Moreover, key virulence genes such as , and were also detected, in addition to pathogenicity islands SPI-1 and SPI-2. This study reveals the prevalence of multidrug-resistant and virulent strains of serovars in the markets of Yichuan city, posing a risk of human infections. The gained knowledge provided essential baseline information that may be utilized for regular tracking of MDR transmission in the food chain to minimize potential future outbreaks.