Clonal Diversity and Genetic Characteristics of Methicillin-Resistant Staphylococcus aureus Isolates from a Tertiary Care Hospital in Japan

Molecular epidemiological characteristics were investigated for 1,041 isolates of methicillin-resistant Staphylococcus aureus (MRSA) collected in a tertiary care hospital in northern Japan for a 4-year period (2011–2014). Genotypes (staphylococcal cassette chromosome mec [SCC mec ], sequence type, spa , coa , etc.) and the presence of drug resistance/virulence factor genes in the isolates were analyzed by multiplex/uniplex PCR, and PCR-direct sequencing as needed. Among these MRSA, predominant SCC mec type was IIa (87.2%), followed by IV (10.1%) and V (1.2%). The SCC mec IIa-MRSA belonged to coagulase genotype ( coa ) IIa and ST5/ST764, which are known as major health care-associated-MRSA (HA-MRSA) in Japan (New York/Japan clone) and its variant. Panton–Valentine leucocidine (PVL) genes were detected in only five isolates (0.5%) with genotypes ST8-SCC mec IVa/ spa -t008/ coa -IIIa (USA300 clone), ST6-SCC mec IVb, and ST59-SCC mec V (Taiwanese clone). Arginine catabolic mobile element (ACME) type I and II′ were identified in three and five isolates of ST8-SCC mec IVa and ST764-SCC mec IIa MRSA, respectively. PVL−/ACME− isolates were classified into various STs/clonal complexes (CCs), with CC1, CC5, CC8, CC89, and CC121 being common. It was notable that SCC mec IVl was the most common among SCC mec IV subtypes, and was carried by almost half of coa -IIIa isolates (47%, 34/72) without PVL genes, which represented the novel ST8 MRSA clone spreading in Japan ( i.e. , “ST8/CA-MRSA/J”). Uncommon MRSA clones in Japan, ST72-SCC mec IV (South Korean clone), ST398 livestock-associated clone, and ST20 bovine-associated MRSA, were identified. Furthermore, we isolated PVL-negative ST8-SCC mec I/ coa -IIIa and ST81-SCC mec V/ coa -VIIa MRSA, which were considered presumptive novel clones. The present study revealed the genetic diversity of HA-MRSA, including potentially emerging clones of putative different origins.