Draft Genome Sequence of Methicillin-Resistant Staphylococcus aureus CUHK_188 (ST188), a Health Care-Associated Bacteremic Isolate from Hong Kong.

We report the draft genome sequence of a methicillin-resistant Staphylococcus aureus strain designated CUHK_188, isolated from a bacteremic patient undergoing treatment at a university teaching hospital in Hong Kong. This strain belongs to sequence type 188 (ST188), with spa type t189 and staphylococcal cassette chromosome mec type V.

GENOME ANNOUNCEMENT

Staphylococcus aureus sequence type 188 (ST188) is a double-locus variant (DLV) of ST1, which includes MW2/USA400, the highly virulent and first known Pantón-Valentine leukocidin (PVL)-positive methicillin-resistant S. aureus (MRSA) strain (1). Methicillin resistance in ST188 has been increasingly described, particularly across the Asia-Pacific region. It has been reported in Hong Kong (2), many provinces of mainland China (3, 4), Korea (5), Malaysia (6), and Taiwan (7). Sporadic cases of community-associated MRSA infection have also been reported in Australia (8). The sequenced strain reported here, CUHK_188, is a health care-associated MRSA strain isolated from a 78-year-old female patient with MRSA bacteremia in a university teaching hospital in 2007. It belongs to spa type t189 and staphylococcal cassette chromosome mec type V (SCCmec V), and it is PVL negative. The multilocus sequence typing (MLST) seven-housekeeping-gene allelic pattern is 3-1-1-8-1-1-1 (ST188), a DLV of ST1 (http://saureus.mlst.net/). However, initial DNA microarray-based typing indicated large differences between ST188 and ST1 (2), suggesting the complex evolutionary processes of the ST188 clone.

We sequenced the CUHK_188 genome using the Ion Torrent platform (Ion PGM Sequencer, Torrent Suite software). A total of 1,236,897,130 bp in 6,438,819 reads was obtained. After quality control performed with PrinSeq (9), the sequence reads were de novo assembled using the Roche GS Assembler software. The CUHK_188 genome was assembled into 41 large contigs (N50, 153,524 bp; largest contig size, 271,458 bp; average length, 68,487 bp). The genome is approximately 2.81 Mb in length, with an average G+C content of 32.7%. The average coverage depth was 440×.

The genome was annotated using NMPDR RAST (10) and Geneious (Biomatters Ltd., New Zealand). A total of 2,700 coding DNA sequences (CDSs), 56 tRNA-coding genes, and 4 rRNA loci were detected, with 53% of the genes assigned to specific subsystem categories by RAST (10). Initial comparative analyses with the ST1 reference genome S. aureus MW2 (11) (accession no. NC_003923) highlighted a number of indels and mobile genetic element (MGE) differences. Of note, the prophage φSa2, which is present in MW2 and harbors the lukSF genes encoding PVL, is absent in CUHK_188. PHAST analysis (12) identified that the genome carries two intact prophage regions and one incomplete prophage region. The first intact prophage region of CUHK_188 shows high similarity with prophage φNM1 and harbors three virulence genes, i.e., homologues of the SAV0866, SAV1978, and SAV0862 genes (13). The second prophage shows high similarity with prophage φNM3 (13) and contains genes that encode modulators of the innate immune responses: staphylokinase (sak), chemotaxis inhibitory protein (chp), and staphylococcal complement inhibitor (scn). Both of these prophages were described in S. aureus strain Newman, which has been shown to play important roles in the pathogenesis of staphylococcal infections (14). The sasX gene, which is linked to the φSPβ-like prophage and enhanced MRSA nasal colonization in the Asian ST239 epidemic clone (15), was absent.

Further studies are under way with the CUHK_188 genome that will advance our understanding of the evolution of this emerging clone in the Asia-Pacific region.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JFFV00000000. The version described in this paper is version JFFV01000000.