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Journal of Clinical Microbiology, February 2008, p. 431-437, Vol. 46, No. 2
0095-1137/08/$08.00+0     doi:10.1128/JCM.01484-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Comparison of Seven Techniques for Typing International Epidemic Strains of Clostridium difficile: Restriction Endonuclease Analysis, Pulsed-Field Gel Electrophoresis, PCR-Ribotyping, Multilocus Sequence Typing, Multilocus Variable-Number Tandem-Repeat Analysis, Amplified Fragment Length Polymorphism, and Surface Layer Protein A Gene Sequence Typing{triangledown}

George Killgore,1 Angela Thompson,1 Stuart Johnson,2 Jon Brazier,3 Ed Kuijper,4 Jacques Pepin,5 Eric H. Frost,5 Paul Savelkoul,8 Brad Nicholson,6 Renate J. van den Berg,4 Haru Kato,7 Susan P. Sambol,2 Walter Zukowski,2 Christopher Woods,6 Brandi Limbago,1* Dale N. Gerding,2 and L. Clifford McDonald1

Centers for Disease Control and Prevention, Atlanta, Georgia,1 Hines VA Hospital, Hines, Illinois,2 Anarobe Reference Laboratory, National Public Health Service for Wales, Microbiology Cardiff University Hospital of Wales, Cardiff, United Kingdom,3 Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands,4 Department of Microbiology and Infectious Diseases, University of Sherbrooke, Sherbrooke, Quebec, Canada,5 Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, North Carolina,6 Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashimurayama, Tokyo, Japan,7 Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands8

Received 24 July 2007/ Returned for modification 11 September 2007/ Accepted 14 November 2007

Using 42 isolates contributed by laboratories in Canada, The Netherlands, the United Kingdom, and the United States, we compared the results of analyses done with seven Clostridium difficile typing techniques: multilocus variable-number tandem-repeat analysis (MLVA), amplified fragment length polymorphism (AFLP), surface layer protein A gene sequence typing (slpAST), PCR-ribotyping, restriction endonuclease analysis (REA), multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). We assessed the discriminating ability and typeability of each technique as well as the agreement among techniques in grouping isolates by allele profile A (AP-A) through AP-F, which are defined by toxinotype, the presence of the binary toxin gene, and deletion in the tcdC gene. We found that all isolates were typeable by all techniques and that discrimination index scores for the techniques tested ranged from 0.964 to 0.631 in the following order: MLVA, REA, PFGE, slpAST, PCR-ribotyping, MLST, and AFLP. All the techniques were able to distinguish the current epidemic strain of C. difficile (BI/027/NAP1) from other strains. All of the techniques showed multiple types for AP-A (toxinotype 0, binary toxin negative, and no tcdC gene deletion). REA, slpAST, MLST, and PCR-ribotyping all included AP-B (toxinotype III, binary toxin positive, and an 18-bp deletion in tcdC) in a single group that excluded other APs. PFGE, AFLP, and MLVA grouped two, one, and two different non-AP-B isolates, respectively, with their AP-B isolates. All techniques appear to be capable of detecting outbreak strains, but only REA and MLVA showed sufficient discrimination to distinguish strains from different outbreaks.

* Corresponding author. Mailing address: Centers for Disease Control and Prevention, MS 16, 1600 Clifton Rd., Atlanta, GA 30333. Phone: (404) 639-2162. Fax: (404) 639-3822. E-mail: bbl7{at}cdc.gov

{triangledown} Published ahead of print on 26 November 2007.

Journal of Clinical Microbiology, February 2008, p. 431-437, Vol. 46, No. 2
0095-1137/08/$08.00+0     doi:10.1128/JCM.01484-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.



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