Novel Variants of SCCmec Type IX Identified in Clonal Complex 398 Livestock-Associated Methicillin-Resistant Staphylococcus aureus from Pork Production Systems in Korea

<b>Background/Objectives</b>: The occurrence of novel variants of staphylococcal cassette chromosome <i>mec</i> (SCC<i>mec</i>) in livestock-associated methicillin-resistant <i>Staphylococcus aureus</i> (LA-MRSA) has frequently been reported, posing significant zoonotic concern worldwide. In this study, the occurrence of novel types of SCC<i>mec</i> IX elements was identified in two clonal complex (CC) 398 LA-MRSA strains derived from a pig farm and a slaughterhouse in Korea. <b>Methods</b>: Whole-genome sequence analysis of the two CC398 MRSA-SCC<i>mec</i> IX strains, designated KF1A-1172 and JS1E-122, revealed that these strains are most closely related to previously characterized strains of CC398 LA-MRSA carrying SCC<i>mec</i> V isolated from pig farms in Korea. <b>Results</b>: Further structural analysis of the SCC<i>mec</i> IX in KF1A-1172 and JS1E-122 revealed the presence of multiple <i>ccr</i> gene complexes (<i>ccrA5B3, ccrAB3</i>, and a truncated <i>ccrA1</i>), including <i>ccrA1B1</i> genes for SCC<i>mec</i> type IX. In addition, the pseudo-SCC (ΨSCC) elements, genes associated with the type 1 restriction-modification (RM) system, and zinc resistance gene <i>czrC</i>, were identified in the SCC<i>mec</i> IX. <b>Conclusions</b>: These findings suggest that the multiple recombination events of elements derived from various SCC<i>mec</i> types contributed to the emergence of the novel SCC<i>mec</i> IX variant. The identification of these novel SCC<i>mec</i> IX types in CC398 LA-MRSA also suggests that epidemiological diversification of SCC<i>mec</i> IX in CC398 LA-MRSA is an ongoing event, necessitating continued surveillance on the emergence of novel SCC<i>mec</i> variants. This study is the first to report the complete genome sequences of CC398 MRSA carrying SCC<i>mec</i> IX in Korea.