Comparison of PCR-ribotyping, arbitrarily primed PCR, and pulsed-field gelelectrophoresis for typing Clostridium difficile

Clostridium difficile is now recognized as the major agent responsible for nosocomial diarrhea in adults. Among the genotyping methods available, arbi trarily primed PCR (AP-PCR), PCR-ribotyping, and pulsed-field gel electroph oresis (PFGE) have been widely used for investigating outbreaks of C. diffi cile infections, However, the comparative typing ability, reproducibility, discriminatory power, and efficiency of these methods have not been fully i nvestigated. We compared the results of three methods-AP-PCR with three dif ferent primers (AP3, AP4, and AP5), PCR-ribotyping, and PFGE (with SmaI end onuclease)-to differentiate 99 strains of C. difficile that had been previo usly serogrouped. Typing abilities were 100% for PCR-ribotyping and AP-PCR with AP3 and 90% for PFGE, due to early DNA degradation in strains from ser ogroup G. Reproducibilities were 100% for PCR-ribotyping and PFGE but only 88% for AP-PCR with AP3, 67% for AP-PCR with AP4, and 33% for AP-PCR with A P5, Discriminatory power for unrelated strains was > 0.95 for all the metho ds but was lower for PCR-ribotyping among serogroups D and C. PCR-based met hods were easier and quicker to perform, but their fingerprints were more d ifficult to interpret than those of PFGE. We conclude that PCR-ribotyping o ffers the best combination of advantages as an initial typing tool for C. d ifficile.