Subtyping of Clostridium difficile polymerase chain reaction (PCR) ribotype 001 by repetitive extragenic palindromic PCR genomic fingerprinting

Molecular Analysis of Clostridium difficile PCR Ribotype 027 Isolates from Eastern and Western Canada

“…The Montreal/Sherbrooke outbreak appears to be the result of a single REP subtype, and while the identical strain was predominant in both Alberta and British Columbia, the composition of circulating PCR ribotype 027 strains in both western regions appears to be more heterogenous. The resolution of PCR ribotype 027 REP subtypes remains more subtle than differences reported among type 001 strains (20). Despite the endemicity of the PCR ribotype 027 clone in the Calgary population, no outbreaks have been noted.…”

“…REP-PCR has recently been put forth as a useful corollary or subtyping methodology for PCR ribotype 001 strains, offering improved strain type resolution over PCR-ribotyping alone (16,20). While PCR-ribotyping and REP-PCR are both based on the differential amplification of bacterial genomic sequences, their coverage and basis for discrimination are fundamentally different.…”

“…REP-PCR was conducted using the same basic reaction volumes and composition as described above for PCR-ribotyping. Heterogenous primers were generated as described previously by Rahmati et al, but thermocycler conditions were modified from previously published reports (16,20). The modified profile is as follows: an initial denaturation cycle of 2 min at 95°C and 3 s at 94°C, followed by 35 cycles of 30 s at 92°C, 1 min at 40°C, and 1 min at 65°C, with a final extension cycle of 8 min at 65°C.…”

Comparative Phylogenomics of Clostridium difficile Reveals Clade Specificity and Microevolution of Hypervirulent Strains

“…Commonly used methods are toxinotyping based upon variations in the PaLoc sequence (28), pulsed-field gel electrophoresis (PFGE) (9), PCR ribotyping (26) and restriction endonuclease analysis (REA) (4). These methods have generally been efficient at grouping strains and in particular have been used to distinguish the recently emerged hypervirulent strains as toxinotype III, North American PFGE type 1, REA group BI, or PCR ribotype 027 (generally referred to as BI/NAP1/027) (20,24,32).…”

An investigation of the subtype diversity of clinical isolates of Irish Clostridium difficile ribotypes 027 and 078 by repetitive-extragenic palindromic PCR

“…PCR amplification between these elements results in DNA amplicons of various sizes and frequencies giving rise to individual rep-PCR profiles. Discrimination of subtypes within ribotypes by rep-PCR Rahmati et al, 2005;Spigaglia & Mastrantonio, 2003), randomly amplified polymorphic DNA techniques (Fawley et al, 2003) and a commercially available semi-automated rep-PCR system (DiversiLab, Bacterial Barcodes; bioMérieux) has been useful for further studying C. difficile epidemiology and these methods have shown good reproducibility for this organism (Healy et al, 2005;Pasanen et al, 2011;Spigaglia & Mastrantonio, 2003).…”