Characterization of colistin resistance mechanisms development in Salmonella isolates from retail meat in Shanghai, China

Salmonella is a significant foodborne pathogen that threatens food safety. This study aims to characterize the prevalence, genomic profiles and colistin resistance mechanisms of Salmonella isolates obtained from 218 retail meat samples collected between January 2021 and January 2023 in Shanghai, China. Overall, 57 (26.1%, 57/218) Salmonella isolates were obtained, which were classified into 13 serotypes, including Salmonella Enteritidis (n=20) and Salmonella Typhimurium (n=19). Genomic analysis revealed 41 antimicrobial-resistance genes, primarily conferring β-lactams and fluoroquinolones resistance. The antimicrobial resistance profiling showed that six isolates (10.5%, 6/57) were resistant to colistin, and the site-directed mutagenesis and lipid A structure analysis were performed to investigate the resistance mechanism. The results demonstrated that two amino acid substitutions (R93P and L98Q) and a three-amino-acid insertion (138TTL) in PmrB enhanced L-Ara4N production via upregulation of pmrE and pmrK gene expression. The L-Ara4N-modified lipid A ultimately resulted in a 4- to 32-fold increase in colistin MIC (1-8 μg/mL). Gene knockout ( pmrE / pmrK ) in mutants (wt14 PmrB R93P and wt14 PmrB 138TTL insertion ) restored susceptibility to parental MIC levels, confirming pmrE / pmrK -dependent resistance. Together, these results emphasize the widespread prevalence of Salmonella in retail meat in Shanghai and these mutations identified in PmrB are key contributors to colistin resistance. • Higher level Salmonella contamination existed in retail duck than in beef and lamb. • WGS identifies genomic factors associated with fluoroquinolone- and MDR Salmonella. • Substitutions R93P, L98Q and 138TTL insertion in PmrB were novel mutations. • Mutations resulted in colistin resistance by altering lipid A through L-Ara4N. • The mutations might confer colistin resistance through the pmrK and pmrE pathways.