Genomic Insights into Antimicrobial Resistance and Virulence of Monophasic Salmonella enterica I 4,[5],12:i:- Isolates from Clinical and Environmental Sources in Jeollanam-do, Korea

This study investigated the molecular epidemiology, virulence, antimicrobial resistance, and mobile genetic elements (MGEs) of <i>Salmonella enterica</i> serovar I 4,[5],12:i:- isolates collected in Jeollanam-do, South Korea, between 2021 and 2023. A total of 135 isolates were tested for antimicrobial susceptibility and 14 virulence-associated genes were screened by PCR. Pulsed-field gel electrophoresis (PFGE) assessed clonal relatedness, and whole-genome sequencing (WGS) enabled multilocus sequence typing (MLST), core genome MLST (cgMLST), SNP phylogeny, resistance gene detection, and MGE analysis. Nine virulence profiles (VP1-VP9) were identified. VP1 (74.1%) was strongly associated with multidrug resistance (MDR), while VP2 (14.8%), which carried plasmid-encoded <i>spv</i> genes, remained largely susceptible. Overall, 83.7% of isolates were resistant to at least one antimicrobial, and 65.2% were MDR, with ampicillin and tetracycline consistently forming the backbone of MDR phenotypes. PFGE revealed high genetic diversity, with 72 pulsotypes, yet certain clones (e.g., SMOX01.006, SMOX01.012) were widely distributed and corresponded to VP2 isolates. WGS confirmed two dominant sequence types, ST34 (<i>n</i> = 24) and ST19 (<i>n</i> = 20), with SNP phylogeny showing VP1 isolates mainly clustered with ST34 and VP2 with ST19. Genotype-phenotype concordance showed strong agreement for most antimicrobials, except cefoxitin, ciprofloxacin, amikacin, and trimethoprim/sulfamethoxazole. MGE analysis revealed that <i>tet(B)</i> was consistently associated with ISVsa5, while ISEc59 was linked to multiple resistance genes, though only <i>aac(3)-IV</i> was phenotypically expressed. These findings demonstrate that MDR and virulence gene composition were closely associated with clonal clustering and that MGEs may contribute to resistance gene expression. This study provides a basis for understanding the dissemination of resistant and virulent <i>Salmonella</i> in the region and underscores the need for continuous genomic surveillance.