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Journal of Clinical Microbiology, August 2006, p. 2728-2732, Vol. 44, No. 8
0095-1137/06/$08.00+0     doi:10.1128/JCM.00376-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

New Staphylococcus aureus Genotyping Method Based on Exotoxin (set) Genes

Division of Infectious Diseases and Immunity, School of Public Health, University of California, Berkeley, California,¹ Department of Tropical Medicine, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil,² Diagnosticos da America S.A., Rio de Janeiro, Brazil,³ Department of Molecular Epidemiology, University of California at San Francisco, San Francisco, California⁴

Received 20 February 2006/ Returned for modification 15 March 2006/ Accepted 4 June 2006

A variety of methods for genotyping Staphylococcus aureus isolates exists: the two most widely used methods are pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Here, we describe a sequence-based genotyping method based on genes encoding S. aureus superantigen-like proteins, which belong to a family of exotoxins called staphylococcal exotoxins. The sequences of PCR-amplified internal fragments of three different set genes (set2, set5, and set7) of 61 well-characterized clinical methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolates and reference strains were compared. Phylogenetic analysis was performed based on single-nucleotide polymorphisms (SNP). The SNP dendrograms of the set gene sequences differentiated the 61 isolates into 22 distinct subgroups, designated exotoxin sequence types (ETST), while the standard seven-gene MLST profiles differentiated the same 61 isolates into 19 subgroups. Of the 19 different MLST subgroups, 16 corresponded to 16 distinct ETST groups. However, three MLST subgroups, ST1, ST30, and ST36, were each further separated into more than one ETST subgroup. The exotoxin-based genotyping method was able to discriminate MRSA and MSSA isolates according to their specific epidemiological characteristics. This SNP analysis of the three set genes is thus equally or more discriminatory than the seven-gene MLST method, providing a good alternative typing tool for a laboratory that has sequencing capability.

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