Novel Variants of SCCmec Type IX Identified in Clonal Complex 398 Livestock-Associated Methicillin-Resistant...

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