Open AccessComparison 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
Author(s) -
George Killgore,
Angela Thompson,
Stuart Johnson,
Jon S. Brazier,
Ed J. Kuijper,
Jacques Pépin,
Éric Frost,
Paul H. M. Savelkoul,
Brad Nicholson,
R.J. van den Berg,
Haru Kato,
Susan P. Sambol,
Walter Zukowski,
Christopher W. Woods,
Brandi Limbago,
Dale N. Gerding,
L. Clifford McDonald
Publication year - 2008
Publication title -
journal of clinical microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.349
H-Index - 255
eISSN - 1070-633X
pISSN - 0095-1137
DOI - 10.1128/jcm.01484-07
Subject(s) - multilocus sequence typing , multiple loci vntr analysis , biology , typing , pulsed field gel electrophoresis , ribotyping , restriction enzyme , genetics , variable number tandem repeat , clostridium difficile , clostridium difficile toxin a , amplified fragment length polymorphism , restriction site , microbiology and biotechnology , polymerase chain reaction , genotype , gene , population , genetic diversity , demography , sociology , antibiotics
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 sevenClostridium difficile typing techniques: multilocus variable-number tandem-repeat analysis (MLVA), amplified fragment length polymorphism (AFLP), surface layer protein A gene sequence typing (slpA ST), 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 thetcdC 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,slpA ST, PCR-ribotyping, MLST, and AFLP. All the techniques were able to distinguish the current epidemic strain ofC. difficile (BI/027/NAP1) from other strains. All of the techniques showed multiple types for AP-A (toxinotype 0, binary toxin negative, and notcdC gene deletion). REA,slpA ST, MLST, and PCR-ribotyping all included AP-B (toxinotype III, binary toxin positive, and an 18-bp deletion intcdC ) 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.