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Journal of Clinical Microbiology, December 2004, p. 5502-5511, Vol. 42, No. 12
0095-1137/04/$08.00+0     DOI: 10.1128/JCM.42.12.5502-5511.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Exploration of Biases That Affect the Interpretation of Restriction Fragment Patterns Produced by Pulsed-Field Gel Electrophoresis

Department of Medicine and Epidemiology,¹ Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California,³ Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota²

Received 24 December 2003/ Returned for modification 10 February 2004/ Accepted 17 August 2004

Pulsed-field gel electrophoresis (PFGE) has been used extensively in epidemiological investigations of bacteria, especially during food-borne outbreaks or nosocomial infections. The relationship between similarities in PFGE patterns and true genetic relatedness is poorly understood. In this study, computer-simulated populations of Escherichia coli isolates were created by mutating the sequence of E. coli K-12 strain MG1655. The simulated populations of isolates were then digested, again through simulation, with different restriction enzymes and were analyzed for their relatedness by different techniques. Errors associated with band determination and band matching were incorporated into the analyses, as both of these error types have been shown to affect PFGE interpretations. These errors increased the apparent similarities of the isolates. The use of multiple enzymes improved the fidelity between the results of PFGE analyses and the true sequence similarities. These findings, when they are combined with results from laboratory studies, emphasize the need for the inclusion of multiple enzymes and additional epidemiological data in order to make more accurate interpretations.