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*

Botulism Reference Service,Food Directorate, Health Canada, Tunney’s Pasture, PL 2204A2,
Ottawa, Ontario, Canada K1A 0L2.

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 M 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.

Keywords:Type E Botulism,PFGE,Pulsed-field gel electrophoresis,RAPD,Clostridium botulinum,microorganims,Taxonomy.

E-mail: john_austin@hc-sc.gc.ca