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J Med Microbiol 55 (2006), 43-51; DOI: 10.1099/jmm.0.46157-0
© 2006 Society for General Microbiology
ISSN 0022-2615

Methicillin-resistant Staphylococcus aureus genotyping using a small set of polymorphisms

Alex J. Stephens1, Flavia Huygens1, John Inman-Bamber1, Erin P. Price1, Graeme R. Nimmo2, Jacqueline Schooneveldt2, Wendy Munckhof3 and Philip M. Giffard1

1 Cooperative Research Centre for Diagnostics, Queensland University of Technology, GPO Box 2434, Brisbane, Queensland 4001, Australia

2 Queensland Health Pathology Services, Princess Alexandra Hospital, Brisbane, Australia

3 Infection Management Services, Princess Alexandra Hospital and District Health Service, Brisbane, Australia

Correspondence
Philip M. Giffard
p.giffard{at}qut.edu.au

Received 17 May 2005
Accepted 21 September 2005

The aim of this study was to identify a set of genetic polymorphisms that efficiently divides methicillin-resistant Staphylococcus aureus (MRSA) strains into groups consistent with the population structure. The rationale was that such polymorphisms could underpin rapid real-time PCR or low-density array-based methods for monitoring MRSA dissemination in a cost-effective manner. Previously, the authors devised a computerized method for identifying sets of single nucleotide polymorphisms (SNPs) with high resolving power that are defined by multilocus sequence typing (MLST) databases, and also developed a real-time PCR method for interrogating a seven-member SNP set for genotyping S. aureus. Here, it is shown that these seven SNPs efficiently resolve the major MRSA lineages and define 27 genotypes. The SNP-based genotypes are consistent with the MRSA population structure as defined by eBURST analysis. The capacity of binary markers to improve resolution was tested using 107 diverse MRSA isolates of Australian origin that encompass nine SNP-based genotypes. The addition of the virulence-associated genes cna, pvl and bbp/sdrE, and the integrated plasmids pT181, pI258 and pUB110, resolved the nine SNP-based genotypes into 21 combinatorial genotypes. Subtyping of the SCCmec locus revealed new SCCmec types and increased the number of combinatorial genotypes to 24. It was concluded that these polymorphisms provide a facile means of assigning MRSA isolates into well-recognized lineages.

Abbreviations: CA-MRSA, community-acquired MRSA; D, Simpson's index of diversity; MLST, multilocus sequence typing; MRSA, methicillin-resistant Staphylococcus aureus; SLV, single locus variant; SNP, single nucleotide polymorphism; ST, sequence type.

A complete description of the MRSA isolates used in this study is available in Supplementary Table S1 with the online version of this paper.




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