Exploration of biases that affect the interpretation of restriction fragment patterns produced by pulsed-field gel electrophoresis

Randall S. Singer, William M. Sischo, Tim Carpenter

Research output: Contribution to journalArticle

21 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)5502-5511
Number of pages10
JournalJournal of Clinical Microbiology
Issue number12
StatePublished - Dec 1 2004


ASJC Scopus subject areas

  • Microbiology (medical)
  • Microbiology

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