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14820,000 deaths per year in the United States1), and about 4,000 in Japan2). Determination of the molec-ular epidemiology of MRSA strains has allowed prediction of their regional spread and the design of effective chemotherapeutic agents against these infectious diseases. Methods of molecular epidemio-logical analyses include multi-locus sequence types (MLST)3); searches and typing of mobile genetic elements, drug-resistance genes and virulence-re-lated genes; and phylogenetic analysis based on single nucleotide polymorphisms (SNPs). Molec-ular epidemiological analyses of MRSA have also included typing of staphylococcal protein A genes based on their polymorphism4) and typing of the staphylococcal cassette chromosome mec (SCCmec), a determinant of resistance to β-lactam antibiotics5).The results of molecular analyses are available as databases listed on websites. One example is PubMLST (https://pubmlst.org)6), a collection of MLST of various microorganisms. The webpage shows lists of bacterial strains and their MLST by countries. Several hundred strains of S. aureus have been identified to date in industrialized coun-tries, with much less information available about S. aureus strains in other regions of the world. For example, as of July 2021 no strain of S. aureus had been isolated in the Republic of Indonesia, although this country has a population of 264 million resi-dents, the fourth highest in the world in 2018, and a gross domestic product based on purchasing power parity of 3.9 trillion dollars, the seventh highest in the world in 2018. Due to its large popu-lation and economic potential, Indonesia can play an important role in the appearance and spread of new molecular types of MRSA strains, similar to other industrialized countries. Therefore, the molec-ular epidemiological analyses of MRSA strains isolated in Indonesia are needed to predict the appearance of MRSA strains. The present study analyzed MRSA strains obtained from the clinical microbiology laboratory at a leading referral hospital in Surabaya City, Jawa Timur, Indonesia. Of these strains, 10 were subjected to whole genome sequencing by employing a next generation sequencer, with analyses showing that these strains varied in sequence types, as defined by MLST, the presence of mobile genetic elements including SCCmec, virulence factors and drug resis-tance genes. The results strongly suggested that these strains had originated in various regions and from various sources throughout the world. Further-more, complete genome sequencing of one of these strains, followed by detailed comparative analyses with a known S. aureus genome, showed that the genome of this MRSA strain underwent rapid alteration after migration into Indonesia. Statement on ethics control and appropriateness of the experiments. All of the methods and the exper-imental protocols employed in this study were performed in accordance with relevant guidelines and regulations and were approved by Juntendo University School of Medicine Research Ethics Committee (permission #2019041). Informed consent was obtained from all participants. Prior to starting this study, all participating researchers had completed an ethics training course provided by Association for the Promotion of Research Integ-rity, Tokyo, Japan. Bacterial isolates and patient characteristics. Single specimens were obtained from 121 patients and grown on mannitol salt agar. Each of these speci-mens yielded a single strain with a yellowish pigment and background, suggesting that they were strains of S. aureus. These strains were subsequently isolated on tryptic soy agar as single colonies. Forty-five of these strains, designated Infectious Diseases Society of America (IDSA) strains, were subjected to Microflex Biotyper matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS)7) and identified by comparison with a database complete as of March 2018 (Bruker, Billerica, MA, USA). Ten of these 45 MRSA strains were selected after categorizing them by patterns of antibiotic resis-tance and clinical features, while omitting strains with the same features. Strain identification was confirmed by sequencing of the 16S ribosomal RNA genes as part of whole genome sequencing.DNA manipulation, genome sequencing, annota-tion, species identification and comparisons with other S. aureus strains. The genomic DNAs of S. aureus strains used in this study were extracted and purified using ISOPLANT II kits (NipponGene, Tokyo, Japan). After preparing libraries with Nextera XT library preparation kits (Illumina), the genomic DNAs were subjected to whole-genome Materials and methods