Complete genome analysis of representative methicillin-resistant Staphylococcus aureus clinical strains prevalent in Korea during 2014-2017

Background: Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen responsible for various clinical infections. The investigation of representative MRSA genomes is important for understanding their molecular epidemiology and genetic evolution, as well as MRSA infections. We characterized the complete genome sequences of representative MRSA clinical strains prevalent in Korea between 2014 and 2017. Methods: Ten representative clinical MRSA strains were selected based on the Staphylococcal Cassette Chromosome mec (SCCmec) type. Complete genomes were generated via hybrid assembly using long- and short-read sequencing. Analyses of resistance and virulence genes, whole-genome alignment, phylogenetic tree construction, and comparative genome hybridization were performed. Results: The average chromosomal lengths were 2.916 Mb in SCCmec II (n = 6), 2.920 Mb in SCCmec IV (n = 2), and 2.777 Mb in SCCmec IVA (n = 2). The number of genome coding sequences ranged from 2,713 to 3,026, with an average of 2,946 in SCCmec II, 3,001 in SCCmec IV, and 2,740 in SCCmec IVA. Only the SCCmec IV and spa t008 strains (n = 2) harbored the Panton–Valentine leukocidin gene, which is rarely detected in Korea. The SCCmec IVA strains of ST72 showed a distinct genetic group compared with other representative SCCmec IV strains, as determined by single-nucleotide polymorphism analysis. Conclusion: In the present study, the complete and gap-filled genome sequences of representative MRSA clones prevalent in Korea were derived and characterized by genome size, virulence, antimicrobial resistance genes, and their evolutionary relationships. Information on these clinical MRSA strains would enhance our understanding of the pathogenicity and molecular epidemiology of Korean MRSA isolates.