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Ryotaro SHIMOGAMI6)†, Teruo KIRIKAE3), Keiichi HIRAMATSU7)††5)Faculty of Health Science, Juntendo University, Tokyo, Japan6)Department of Bacteriology, Juntendo University, Tokyo, Japan4)Graduate School of Nursing, Seisen Jogakuin College, Nagano, Japan1)Department of Neurology, Juntendo University School of Medicine, Tokyo, Japan3)Department of Bacteriology, Juntendo University Graduate School of Medicine, Tokyo, Japan2)Department of Medical Microbiology, Airlangga University Faculty of Medicine, Jawa Timur, Indonesia7)Department of Infection Control Science, Juntendo University School of Medicine, Tokyo, JapanFirman SETIAWAN1, 2), Tadashi BABA3, 4), Yuh MORIMOTO3, 5), Yosuke NAKAGAWA6)†, Corresponding author: Tadashi BabaDepartment of Bacteriology, Juntendo University Graduate School of Medicine2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, JapanTEL: +81-3-5802-1041　E-mail: tbaba@juntendo.ac.jp† Undergraduate student of Juntendo University School of Medicine†† Former professor emeritus for Department of Infection Control Science, Juntendo University School of Medicine, deceased June 5th, 2020〔Received　Nov. 7, 2021〕〔Accepted　Jan. 7, 2022〕J-STAGE Advance published date: Apr. 20, 2022Copyright © 2022 The Juntendo Medical Society. This is an open access article distributed under the terms of Creative Commons Attribution License (CC BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original source is properly credited. doi: 10.14789/jmj.JMJ21-0040-OAObjective: Most strains of methicillin-resistant Staphylococcus aureus (MRSA) analyzed to date have been from industrialized countries, with information lacking on the epidemiology of MRSA in other regions of the world. The present study describes the molecular epidemiology of MRSA strains collected at a referral hospital in Surabaya City, Indonesia in 2015-2016. The similarity of strains isolated in Indonesia to known lineages of MRSA was investigated.Materials: Of 45 MRSA strains isolated in Surabaya, 10 were selected by antibiotic resistance patterns and clinical features, while excluding duplicates. Methods: Whole genome sequencing was performed using a next-generation sequencer, and the complete genome sequence of one of these 10 strains was also determined by the PacBio system. The strains were subjected to molecular epidemiological analyses, including the presence of drug-resistance and virulence-related genes, the determination of sequence types and staphylococcal cassette chromosome mec (SCCmec) types and mutual phylogenetic relationships, using standard analytical tools.Results: The molecular types of these MRSA strains showed significant diversity. Complete sequencing of the genome of strain IDSA1 showed that it belonged to the ST239 group, while also having unique mobile genetic elements. Conclusions: Despite the small number of MRSA strains collected in a limited area and over a short period of time, these strains were found to have arisen in many other regions of the world, suggesting that they had migrated into Indonesia through human movement. These strains also showed molecular differentiation after migrating into Indonesia.Key words: Methicillin-resistance Staphylococcus aureus (MRSA), Staphylococcal cassette chromosome mec (SCCmec), Indonesia, Complete genome determinationJuntendo Medical Journal2022. 68(2), 147-156Original ArticlesMolecular Epidemiology and Comparative Genome Analysis of IntroductionStaphylococcus aureus is a microorganism known to cause hospital, community and livestock infec-tions, as well as fatal diseases such as toxic shock, bacteremia, sepsis, necrotizing pneumonia and endocarditis. The emergence of drug-resistance strains of S. aureus, including multidrug-resistant S. aureus (MRSA) has become a worldwide concern, with MRSA infections causing approximately 147Clinically-isolated MRSA Strains in Indonesia