Editorial Commentary: Does Infection With Specific Clostridium difficile Strains or Clades Influence Clinical Outcome?

Abstract

A number of DNA banding–based typing systems for classifying Clostridium difficile isolates have been devised including polymerase chain reaction (PCR) ribotyping, restriction endonuclease analysis (REA), and pulsed-field gel electrophoresis (PFGE) [1–4]. PCR ribotyping was developed in Wales and is commonly used in Europe, whereas REA and PFGE have been used more commonly in North America. In addition, toxinotyping, which is based on amplification of regions within the pathogenicity locus (PaLoc) for toxins A and B, has been used to describe “toxin variant” strains whose PaLoc genes differ from the standard or toxinotype “0” PaLoc to which most PCR ribotypes, REA groups, and PFGE types belong [5]. The aforementioned DNA-banding typing systems are invaluable for discriminating isolates from each other, but do not provide meaningful evolutionary analyses. Multilocus sequence typing (MLST), in which a selected number of housekeeping gene loci (7 in the case of C. difficile) are amplified and sequenced to yield sequence types (STs), can be used to group STs by evolutionary relationships into clades [6]. Members of a clade are considered to be derived from the same common ancestor and can be organized into evolutionary trees using phylogenetic or cladistic analyses. MLST classification of C. difficile clades agrees with previous classification based on DNA microarray comparative genomics and suggests that genotypes clustered by MLST may be an accurate proxy for whole-genome sequencing analysis [7]. STs correlate well with PCR ribotypes; however, as with toxinotyping, the vast majority of STs are clustered in a single clade, clade 1, with only 1 or 2 STs (ribotypes) in each of the remaining 4 clades (Table 1).