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bacterial strains to be categorized by their genetic lineages, thus determining their phylogenetic rela-tionship. The MLST of the MRSA strains used in this study are summarized in Table 2. This analysis showed 11 strains belonging to as many as five sequence types (ST), indicating marked diversity in their genetic backgrounds. Because MLST anal-ysis shows diversities in limited numbers of house-keeping genes, phylogenetic analyses were performed based on SNPs that covered the entire genome. These analyses revealed large variations in the genomes of these strains, regardless of regional and periodic limitations of the MRSA isola-tion (Figure 1). These results strongly suggest that these MRSA strains were derived from various parts of the world. Overview of the IDSA1 genome and comparison of S. aureus strain TW20 with a similar genetic Figure 1　Whole genome-wide phylogenetic relationship among S. aureus strains isolated at a referral hospital in Surabaya City, Indonesia, during 2015-2016Maximum-likelihood tree based on the mapping of SNPs in the genomes to the reference sequence of S. aureus strain USA30033). The branch length indicates the proportions of SNPs relative to the total 21,646 SNPs in the 14 genomes (refer to the scale bar). The whole genome sequences of the S. aureus strains available in databases and the genomes of the N31527), MW224) and IDSA strains (this study) were subjected to CSI Phylogeny 1.418) using default parameters (minimum depth at SNP positions: 10, relative depth at SNP positions: 10, minimum distance between SNPs: 10, minimum SNP quality: 30, minimum read mapping quality: 25, minimum Z-score: 1.96 while ignoring heterozygous SNPs). The sequence types (ST) of the IDSA strains, determined based on MLST analysis3), are indicated with colored ovals, as are the typical regions and sources of the STs. HA-MRSA, hospital-acquired MRSA; CA-MRSA, community-acquired MRSA; LA-MRSA, livestock-associated MRSA. ST672 is a very rare clone, with only 18 reports; it has been isolated in Australia, India, Iran, Haiti and the USA according to the records in PubMLST6) as of August 25, 2021.background. The analyses above showed that three strains belonged to ST239. Because these strains are resistant not only to penicillin but to cephem, the spread of this lineage could become a public concern in Indonesia. To determine the molecular bases of this lineage, one of these ST239 MRSA strains, IDSA1, was subjected to complete genome determination. The genome of IDSA1 consisted of a single chromosome of 3,096,213 base pairs, with no plasmids. The genome of strain GW20 was highly similar to that of IDSA1, with both classified as ST239 and type-III SCCmec. Despite their common features21), the IDSA1 genome was longer in size than the TW20 genome, which consists of 3,043,210 base pairs, because IDSA1 possesses two more prophages than TW20 (Table 4). ST239 is a hospital-acquired MRSA clone22), observed throughout the world. It is noteworthy that this clone was also found in Indonesia, which is geograph-151