Antimicrobial resistance surveillance and focused comparative genomics of clinical Salmonella isolates from patients with diarrhea in northern Gyeonggi Province, Korea.

We analyzed 320 Salmonella enterica isolates recovered from patients with diarrhea in northern Gyeonggi Province, Korea, between 2015 and 2022. Resistance was most frequent to ampicillin, tetracycline, and nalidixic acid, and 26.6% of isolates exhibited multidrug resistance (MDR). Extended-spectrum cephalosporin-resistant isolates mainly carried blaCTX-M and blaDHA, whereas plasmid-mediated quinolone resistance determinants, such as qnrS and qnrB, were also detected. Mutations in quinolone resistance-determining regions, predominantly gyrA mutations corresponding to the predicted D87N substitution, were frequent. PFGE and MLST supported relatedness within major resistant serotypes; ST34 and ST11 were the most frequent sequence types among the MLST-analyzed isolates. Resistance to nalidixic acid and colistin was significantly higher in S. Enteritidis than in S. I 4,[5],12:i:-, whereas S. I 4,[5],12:i:- showed higher resistance to tetracycline, chloramphenicol, and trimethoprim-sulfamethoxazole (all P < 0.001). Whole-genome sequencing of two representative isolates (GGN-BG-22, ST34; GGN-BG-25, ST11) identified distinct resistance- and virulence-related genomic features, including plasmid-associated resistance determinants. SNP-based phylogenetic analyses using selected publicly available genomes placed these two representative lineages in a broader genomic context. Together, these findings provide regional surveillance-based insights into antimicrobial resistance in clinical Salmonella isolates and focused genomic insights into two clinically relevant lineages.IMPORTANCEMultidrug-resistant Salmonella poses an increasing challenge to both patient care and public health. This study integrates regional antimicrobial resistance surveillance with focused comparative genomic analysis of two representative clinical isolates, providing context for major resistant lineages identified in northern Gyeonggi Province, Korea. Our findings highlight lineage-specific resistance and genomic features and support the continued use of molecular surveillance to monitor high-risk clones and resistance-associated mobile genetic elements in clinical and public health settings.