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. 2014 Apr 17;2(2):e00255-14. doi: 10.1128/genomeA.00255-14

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

Margaret Ip a,✉, Zheng Wang a, Wai Yip Lam b, Haokui Zhou a, Stephen Tsui b
PMCID: PMC3990744  PMID: 24744328

Abstract

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.

ACKNOWLEDGMENTS

We acknowledge funding support from the Research Fund for the Control of Infectious Diseases, HKSAR (commissioned project no. CU-09­05-01). We also acknowledge the use of the MLST website and database, located at the Imperial College London and funded by the Wellcome Trust.

Footnotes

Citation Ip M, Wang Z, Lam WY, Zhou H, Tsui S. 2014. Draft genome sequence of methicillin-resistant Staphylococcus aureus CUHK_188 (ST188), a health care-associated bacteremic isolate from Hong Kong. Genome Announc. 2(2):e00255-14. doi:10.1128/genomeA.00255-14.

REFERENCES

  • 1. Centers for Disease Control and Prevention 1999. Four pediatric deaths from community-acquired methicillin-resistant Staphylococcus aureus—Minnesota and North Dakota, 1997–1999. JAMA 282:1123–1125. 10.1001/jama.282.12.1123-JWR0922-2-1 [DOI] [PubMed] [Google Scholar]
  • 2. Monecke S, Coombs G, Shore AC, Coleman DC, Akpaka P, Borg M, Chow H, Ip M, Jatzwauk L, Jonas D, Kadlec K, Kearns A, Laurent F, O’Brien FG, Pearson J, Ruppelt A, Schwarz S, Scicluna E, Slickers P, Tan HL, Weber S, Ehricht R. 2011. A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus. PLoS One 6:e17936. 10.1371/journal.pone.0017936 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3. Yu F, Li T, Huang X, Xie J, Xu Y, Tu J, Qin Z, Parsons C, Wang J, Hu L, Wang L. 2012. Virulence gene profiling and molecular characterization of hospital-acquired Staphylococcus aureus isolates associated with bloodstream infection. Diagn. Microbiol. Infect. Dis. 74:363–368. 10.1016/j.diagmicrobio.2012.08.015 [DOI] [PubMed] [Google Scholar]
  • 4. He W, Chen H, Zhao C, Zhang F, Li H, Wang Q, Wang X, Wang H. 2013. Population structure and characterisation of Staphylococcus aureus from bacteraemia at multiple hospitals in China: association between antimicrobial resistance, toxin genes and genotypes. Int. J. Antimicrob. Agents 42:211–219. 10.1016/j.ijantimicag.2013.04.031 [DOI] [PubMed] [Google Scholar]
  • 5. Peck KR, Baek JY, Song JH, Ko KS. 2009. Comparison of genotypes and enterotoxin genes between Staphylococcus aureus isolates from blood and nasal colonizers in a Korean hospital. J. Korean Med. Sci. 24:585–591. 10.3346/jkms.2009.24.4.585 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6. Ghaznavi-Rad E, Nor Shamsudin M, Sekawi Z, Khoon LY, Aziz MN, Hamat RA, Othman N, Chong PP, van Belkum A, Ghasemzadeh-Moghaddam H, Neela V. 2010. Predominance and emergence of clones of hospital-acquired methicillin-resistant Staphylococcus aureus in Malaysia. J. Clin. Microbiol. 48:867–872. 10.1128/JCM.01112-09 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7. Chen FJ, Siu LK, Lin JC, Wang CH, Lu PL. 2012. Molecular typing and characterization of nasal carriage and community-onset infection methicillin-susceptible Staphylococcus aureus isolates in two Taiwan medical centers. BMC Infect. Dis. 12:343. 10.1186/1471-2334-12-343 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8. Nimmo GR, Coombs GW. 2008. Community-associated methicillin-resistant Staphylococcus aureus (MRSA) in Australia. Int. J. Antimicrob. Agents 31:401–410. 10.1016/j.ijantimicag.2007.08.011 [DOI] [PubMed] [Google Scholar]
  • 9. Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863–864. 10.1093/bioinformatics/btr026 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. 10.1186/1471-2164-9-75 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11. Baba T, Takeuchi F, Kuroda M, Yuzawa H, Aoki K, Oguchi A, Nagai Y, Iwama N, Asano K, Naimi T, Kuroda H, Cui L, Yamamoto K, Hiramatsu K. 2002. Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 359:1819–1827. 10.1016/S0140-6736(02)08713-5 [DOI] [PubMed] [Google Scholar]
  • 12. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. 2011. PHAST: a fast phage search tool. Nucleic Acids Res. 39:W347–W352. 10.1093/nar/gkr485 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13. Bae T, Baba T, Hiramatsu K, Schneewind O. 2006. Prophages of Staphylococcus aureus Newman and their contribution to virulence. Mol. Microbiol. 62:1035–1047. 10.1111/j.1365-2958.2006.05441.x [DOI] [PubMed] [Google Scholar]
  • 14. Baba T, Bae T, Schneewind O, Takeuchi F, Hiramatsu K. 2008. Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islands. J. Bacteriol. 190:300–310. 10.1128/JB.01000-07 [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15. Li M, Du X, Villaruz AE, Diep BA, Wang D, Song Y, Tian Y, Hu J, Yu F, Lu Y, Otto M. 2012. MRSA epidemic linked to a quickly spreading colonization and virulence determinant. Nat. Med. 18:816–819. 10.1038/nm.2692 [DOI] [PMC free article] [PubMed] [Google Scholar]

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