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Journal of Clinical Microbiology, September 2002, p. 3300-3307, Vol. 40, No. 9
0095-1137/02/$04.00+0     DOI: 10.1128/JCM.40.9.3300-3307.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Comparative Assessment of Genotyping Methods for Epidemiologic Study of Burkholderia cepacia Genomovar III

Tom Coenye, Theodore Spilker, Alissa Martin, and John J. LiPuma*

Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109-0646

Received 15 May 2002/ Returned for modification 21 June 2002/ Accepted 30 June 2002

We analyzed a collection of 97 well-characterized Burkholderia cepacia genomovar III isolates to evaluate multiple genomic typing systems, including pulsed-field gel electrophoresis (PFGE), BOX-PCR fingerprinting and random amplified polymorphic DNA (RAPD) typing. The typeability, reproducibility, and discriminatory power of these techniques were evaluated, and the results were compared to each other and to data obtained in previous studies by using multilocus restriction typing (MLRT). All methods showed excellent typeability. PFGE with SpeI was more reproducible than RAPD and BOX-PCR fingerprinting. The discriminatory power of the methods was variable, with PFGE and RAPD typing having a higher index of discrimination than BOX-PCR fingerprinting. In general, the results obtained by PFGE, BOX-PCR fingerprinting, and MLRT were in good agreement. Our data indicate that different genomic-based methods can be used to type B. cepacia genomovar III isolates depending on the situation and the epidemiologic question being addressed. PFGE and RAPD fingerprinting are best suited to addressing small-scale studies (i.e., local epidemiology), whereas BOX-PCR fingerprinting is more appropriate for large-scale studies (i.e., global epidemiology). In this regard, BOX-PCR fingerprinting can be considered a rapid and easy alternative to MLRT.

* Corresponding author. Mailing address: Department of Pediatrics and Communicable Diseases, 8323 MSRB III, Box 0646, 1150 W. Med. Center Dr., Ann Arbor, MI 48109-0646. Phone: (734) 936-9767. Fax: (734) 764-4279. E-mail: jlipuma{at}umich.edu.

Journal of Clinical Microbiology, September 2002, p. 3300-3307, Vol. 40, No. 9
0095-1137/02/$04.00+0     DOI: 10.1128/JCM.40.9.3300-3307.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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