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Staphylococcus aureus genotyping using novel Real-Time PCR Formats

Huygens, Flavia, Inman-Bamber, John M., Nimmo, Graeme R., Munckhof, Wendy, Schooneveldt, Jacqueline, Harrison, Bruce, McMahon, Jennifer A., & Giffard, Philip M. (2006) Staphylococcus aureus genotyping using novel Real-Time PCR Formats. Journal of Clinical Microbiology, 44(10), pp. 3712-3719.

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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.

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ID Code: 7673
Item Type: Journal Article
Additional Information: For more information, please refer to the journal’s website (see link) or contact the author Flavia Huygens. Author contact details: f.huygens@qut.edu.au
Additional URLs:
Keywords: Staphylococcus aureus, genotyping, real, time PCR, data
DOI: 10.1128/JCM.00843-06
ISSN: 0095-1137
Subjects: Australian and New Zealand Standard Research Classification > MEDICAL AND HEALTH SCIENCES (110000) > CLINICAL SCIENCES (110300) > Infectious Diseases (110309)
Australian and New Zealand Standard Research Classification > MEDICAL AND HEALTH SCIENCES (110000) > MEDICAL MICROBIOLOGY (110800) > Medical Bacteriology (110801)
Australian and New Zealand Standard Research Classification > AGRICULTURAL AND VETERINARY SCIENCES (070000) > VETERINARY SCIENCES (070700) > Veterinary Microbiology (excl. Virology) (070707)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > MICROBIOLOGY (060500) > Microbial Genetics (060503)
Australian and New Zealand Standard Research Classification > TECHNOLOGY (100000) > MEDICAL BIOTECHNOLOGY (100400) > Medical Biotechnology Diagnostics (incl. Biosensors) (100402)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > MICROBIOLOGY (060500) > Infectious Agents (060502)
Divisions: Current > Research Centres > CRC for Diagnostics
Past > QUT Faculties & Divisions > Faculty of Science and Technology
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2006 American Society for Microbiology
Deposited On: 05 Jun 2007
Last Modified: 29 Feb 2012 23:27

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