Discovery, evolution, and environmental co-selection of novel msrA-harboring plasmids in multidrug-resistant Staphylococcus from retail foods.

The escalating prevalence of antimicrobial resistance in food-related pathogens constitutes a critical challenge to global public health and food safety. To elucidate the mechanisms underlying the high erythromycin resistance rate observed in our previous surveillance of Staphylococcus in retail foods, we conducted a comprehensive genomic investigation of msrA-positive Staphylococcus from a nationwide retail food collection in China. We identified 102 msrA-positive isolates, all of which exhibited a multidrug-resistant (MDR) phenotype, with a significantly higher prevalence in aquatic products (13.95%), identifying this food category as a high-risk reservoir for transmitting resistant bacteria to consumers. Genomic typing revealed the dominance of the S. aureus ST15-t085 lineage (58.0%), which exhibited a specific ecological adaptation to retail aquatic products. We characterized 12 novel msrA-harboring plasmids (pMsrA-I to pMsrA-XII), with the dominant Type A plasmids carrying a coupled msrA-mphC cassette that confers synergistic high-level resistance. Structural analysis demonstrated that IS431R serves as a key driver of plasmid evolution, mediating the capture of resistance clusters. Notably, these plasmids also harbor genes conferring tolerance to heavy metals and food preservatives, physically linked to the antimicrobial resistance regions. This genetic linkage suggests that routine disinfection and environmental residues in retail food processing environments likely drive the co-selection of these multidrug-resistant plasmids. Furthermore, these isolates harbored both the plasmids and chromosomal biofilm-associated genes, as well as the neglected enterotoxin gene seh (15.7%), highlights a dual threat of environmental persistence and pathogenicity. These findings underscore the urgent need for targeted surveillance of novel resistance plasmids in the retail food market to mitigate the spread of these multidrug-resistant pathogens.