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We report the complete genome sequence of M013, a representative strain of a pvl-positive, sequence type 59-staphylococcal cassette chromosome mec type V (ST59-SCCmec type V) community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) clone in Taiwan. Comparison of M013 with the genomes of two CA-MRSA strains in the United States revealed major differences in the regions covering several genomic islands and prophages.
Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of both hospital- and community-associated (CA) infections worldwide (4, 5, 12). In Taiwan, the majority of MRSA strains belong to four clones, sequence type 239-staphylococcal cassette chromosome mec type III (ST239-SCCmec III), ST5-SCCmec II, pvl-negative ST59-SCCmec IV, and pvl-positive ST59-SCCmec V (3, 8, 9, 14). The predominant CA-MRSA clones in different regions have diverse genetic backgrounds, such as ST8 (USA300) in the United States, ST80 and ST45 in Europe, and ST30 in Asia (4, 5, 12, 13), but most carry SCCmec IV, while ST59-SCCmec V (“Taiwan clone”) predominates in Taiwan (3, 8). We here report the complete genome of M013, a pvl-positive, ST59-SCCmec V MRSA strain isolated in 2002 from a wound specimen of a pediatric outpatient during part of the Taiwan Surveillance of Antimicrobial Resistance surveillance (TSAR) project (2, 11).
Whole-genome sequencing of strain M013 was performed with 454 pyrosequencing technology (10). Genomic shotgun and 8-kb mate-paired libraries were constructed and were sequenced separately following the instruction of the 454 GS Junior instrument (Roche Diagnostics, Indianapolis, IN). A total of 44,248,172 bp in 104,100 reads from the shotgun library and 35,179,404 bp in 99,507 reads from the 8-kb mate-paired library were assembled into 44 contigs using the 454 Newbler (version 2.5; 454 Life Sciences, Branford, CT). Using the connecting pair-end reads, these contigs were clustered into three scaffolds of 2,787,445 bp, 20,601 bp, and 2,840 bp in size. The contigs within each scaffold were manually inspected and reassembled using the Consed program (7). The four gaps were filled by sequencing PCR products using an ABI 3730 capillary sequencer. The assembled genome was validated by the Argus optical mapping system with AflII digestion (OpGen, Madison, WI).
The complete genome of S. aureus strain M013 contains a circular chromosome of 2,788,636 bp and a circular plasmid of 21,675 bp in size. Sequence annotation of the chromosome revealed 2,591 protein-coding genes, among which 75% could be assigned to known functional categories. A total of 74 RNA genes were found on the chromosome, including 16 rRNA and 58 tRNA genes. Genomic islands such as SCCmec, νSaα, νSaβ, and prophage Panton-Valentine leukocidin (PVL) were identified.
The genome of M013 was compared with those of two CA-MRSA strains, FPR3757 (ST8-SCCmec IV, GenBank accession no. NC_007793) and MW2 (ST1-SCCmec IV, accession no. NC_003923) (1, 6). The sequence and order of most of the open reading frames (ORFs) in the genomes of these strains were conserved. The PVL sequence of M013 is distinct from those of FPR3757 and MW2 but showed more than 99% identity to that of a recently identified third type of PVL from ST59 MRSA strains in Japan and Taiwan (15) (GenBank accession no. AP011956). Several accessory elements in FPR3757 and MW2, including genomic islands SaPI5 and νSa3 and prophages ϕSa3usa and ϕSa3, are absent in M013. In addition, the majority of the ORFs in the pathogenicity-related genomic island νSaβ are deleted in the corresponding region of the M013 genome. The genome sequence of M013 will facilitate the investigation of ST59-SCCmec V MRSA to increase our understanding of this unique clone.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession number CP003166 with locus tag M013TW. The version described in this paper is the first version, with accession number CP003166.
We thank Ih-Jen Su and Chung-Ming Chang for their support of this project.
This work was supported by the National Science Council of Taiwan (NSC 100-3111-B-400 −001) and by intramural grants from the National Health Research Institutes (00A1-IDPP01-014 and MG-100-PP-16).