Staphylococcus aureus genotyping using novel real-time PCR formats

Huygens, Flavia, Inman-Bamber, John, Nimmo, Graeme R., Munckhof, Wendy, Schooneveldt, Jacqueline, Harrison, Bruce, McMahon, Jennifer A. and Giffard, Philip M. (2006) Staphylococcus aureus genotyping using novel real-time PCR formats. Journal of Clinical Microbiology, 44 10: 3712-3719. doi:10.1128/JCM.00843-06

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Author Huygens, Flavia
Inman-Bamber, John
Nimmo, Graeme R.
Munckhof, Wendy
Schooneveldt, Jacqueline
Harrison, Bruce
McMahon, Jennifer A.
Giffard, Philip M.
Title Staphylococcus aureus genotyping using novel real-time PCR formats
Journal name Journal of Clinical Microbiology   Check publisher's open access policy
ISSN 0095-1137
Publication date 2006
Sub-type Article (original research)
DOI 10.1128/JCM.00843-06
Open Access Status File (Publisher version)
Volume 44
Issue 10
Start page 3712
End page 3719
Total pages 8
Editor A. B. Orderdonk
Place of publication Washington, DC, United States
Publisher American Society for Microbiology
Collection year 2006
Language eng
Abstract One approach to microbial genotyping is to make use of sets of single-nucleotide polymorphisms (SNPs) in combination with binary markers. Here we report the modification and automation of a SNP-plus-binary-marker-based approach to the genotyping of Staphylococcus aureus and its application to 391 S. aureus isolates from southeast Queensland, Australia. The SNPs used were arcC210, tpi243, arcC162, gmk318, pta294, tpi36, tpi241, and pta383. These provide a Simpson's index of diversity (D) of 0.95 with respect to the S. aureus multilocus sequence typing database and define 61 genotypes and the major clonal complexes. The binary markers used were pvl, cna, sdrE, pT181, and pUB110. Two novel real-time PCR formats for interrogating these markers were compared. One of these makes use of light upon extension (LUX) primers and biplexed reactions, while the other is a streamlined modification of kinetic PCR using SYBR green. The latter format proved to be more robust. In addition, automated methods for DNA template preparation, reaction setup, and data analysis were developed. A single SNP-based method for ST-93 (Queensland clone) identification was also devised. The genotyping revealed the numerical importance of the South West Pacific and Queensland community-acquired methicillin-resistant S. aureus (MRSA) clones and the clonal complex 239 Aus-1/Aus-2 hospital-associated MRSA. There was a strong association between the community-acquired clones and pvl.
Keyword Microbiology
Field Gel-electrophoresis
Q-Index Code C1

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2007 Higher Education Research Data Collection
School of Chemistry and Molecular Biosciences
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Citation counts: TR Web of Science Citation Count  Cited 46 times in Thomson Reuters Web of Science Article | Citations
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Created: Wed, 15 Aug 2007, 10:00:51 EST