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Journal of Clinical Microbiology, May 2006, p. 1635-1644, Vol. 44, No. 5
0095-1137/06/$08.00+0     doi:10.1128/JCM.44.5.1635-1644.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Comparison of DNA Fingerprinting Methods for Use in Investigation of Type E Botulism Outbreaks in the Canadian Arctic

Daniel Leclair, Franco Pagotto, Jeffrey M. Farber, Brigitte Cadieux, and John W. Austin^*

Bureau of Microbial Hazards, Health Products and Food Branch, Food Directorate, Health Canada, Ottawa K1A 0L2, Canada

Received 27 October 2005/ Returned for modification 18 December 2005/ Accepted 18 February 2006

Pulsed-field gel electrophoresis (PFGE), randomly amplified polymorphic DNA (RAPD) analysis, and automated ribotyping were compared for epidemiological typing of Clostridium botulinum type E using clinical and food isolates associated with four botulism outbreaks occurring in the Canadian Arctic. All type E strains previously untypeable by PFGE, even with the use of a formaldehyde fixation step, could be typed by the addition of 50 µM thiourea to the electrophoresis running buffer. Digestion with SmaI or XhoI followed by PFGE was used to link food and clinical isolates from four different type E botulism outbreaks and differentiate them from among 39 group II strains. Strain differentiation was unsuccessful with the automated ribotyping system, producing a single characteristic EcoRI fingerprint common to all group II strains. RAPD analysis of C. botulinum group II strains was not consistently reproducible with primer OPJ-6 or OPJ-13, apparently discriminating between epidemiologically related strains. A modified PFGE protocol was judged to be the most useful method for typing epidemiologically related C. botulinum type E strains, based on its ability to type all strains reproducibly and with an adequate level of discrimination.

Present address: Public Health Agency of Canada, 100 Colonnade Rd., Ottawa, Ontario K1A 0K9, Canada.

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