Genetic Characteristics of Multidrug-Resistant Salmonella Isolated from Poultry Meat in South Korea

Given the lack of genetic characterization data for multidrug-resistant (MDR) <i>Salmonella</i> in South Korean poultry, we analyzed 53 MDR <i>Salmonella</i> strains from 1232 poultry meat samples (723 chicken, 509 duck) using whole-genome sequencing. Five serotypes were identified: <i>S.</i> Infantis (30/53, 56.6%), <i>S.</i> Enteritidis (11/53, 20.8%), <i>S.</i> Virchow (9/53, 17.0%), <i>S.</i> Agona (2/53, 3.8%), and <i>S.</i> Indiana (1/53, 1.9%). Sequence types (STs) included ST32, ST11, ST16, ST13, and ST17, with three major clusters, each having two subclusters. Eight core genome sequence types (cgSTs) were identified: 225993, 2268, 58360, 150996, 232041, 96964, 117577, and 267045. <i>Salmonella</i> Infantis and <i>S.</i> Enteritidis had two (117577, 267045) and three (225993, 2268, 58360) cgSTs, respectively, whereas <i>S.</i> Virchow showed allelic differences in identical cgSTs. The <i>S.</i> Enteritidis subcluster was classified as chicken or duck. Twenty-eight antimicrobial resistance genes (ARGs), 10 plasmid replicons, 11 <i>Salmonella</i> pathogenicity islands (SPIs), and 230 virulence genes were identified, showing distinct profiles by cluster and subcluster. <i>Salmonella</i> Infantis, the primary MDR <i>Salmonella</i>, carried the IncFIB (pN55391) plasmid, 10-11 ARGs, nine SPIs, and approximately 163 virulence genes. Three major MDR <i>Salmonella</i> serotypes (<i>S.</i> Infantis, <i>S.</i> Enteritidis, and <i>S.</i> Virchow) had specific genetic profiles that can inform epidemiological surveillance.