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Journal of Clinical Microbiology, September 2004, p. 4275-4283, Vol. 42, No. 9
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.9.4275-4283.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Uses of Staphylococcus aureus GeneChips in Genotyping and Genetic Composition Analysis

P. M. Dunman,1,{dagger} W. Mounts,2 F. McAleese,1 F. Immermann,3 D. Macapagal,1 E. Marsilio,4 L. McDougal,4 F. C. Tenover,4 P. A. Bradford,1 P. J. Petersen,1 S. J. Projan,5 and E. Murphy1*

Wyeth Research,1 Biometrics Research,4 Pearl River, New York,3 Wyeth Genomics,2 Protein Technologies, Cambridge, Massachusetts,6 Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia5

Received 28 January 2004/ Returned for modification 26 March 2004/ Accepted 13 May 2004

Understanding the relatedness of strains within a bacterial species is essential for monitoring reservoirs of antimicrobial resistance and for epidemiological studies. Pulsed-field gel electrophoresis (PFGE), ribotyping, and multilocus sequence typing are commonly used for this purpose. However, these techniques are either nonquantitative or provide only a limited estimation of strain relatedness. Moreover, they cannot extensively define the genes that constitute an organism. In the present study, 21 oxacillin-resistant Staphylococcus aureus (ORSA) isolates, representing eight major ORSA lineages, and each of the seven strains for which the complete genomic sequence is publicly available were genotyped using a novel GeneChip-based approach. Strains were also subjected to PFGE and ribotyping analysis. GeneChip results provided a higher level of discrimination among isolates than either ribotyping or PFGE, although strain clustering was similar among the three techniques. In addition, GeneChip signal intensity cutoff values were empirically determined to provide extensive data on the genetic composition of each isolate analyzed. Using this technology it was shown that strains could be examined for each element represented on the GeneChip, including virulence factors, antimicrobial resistance determinants, and agr type. These results were validated by PCR, growth on selective media, and detailed in silico analysis of each of the sequenced genomes. Collectively, this work demonstrates that GeneChips provide extensive genotyping information for S. aureus strains and may play a major role in epidemiological studies in the future where correlating genes with particular disease phenotypes is critical.

* Corresponding author. Mailing address: Wyeth Vaccines Research, 401 N. Middletown Rd., Pearl River, NY 10965. Phone: (845) 602-4411. Fax: (845) 602-5536. E-mail: MurphyE3{at}wyeth.com.

{dagger} Present address: University of Nebraska Medical Center, Omaha, NE 68198.

Journal of Clinical Microbiology, September 2004, p. 4275-4283, Vol. 42, No. 9
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.9.4275-4283.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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