Comparison of arbitrarily-primed polymerase chain reaction, restriction enzyme analysis and pulsed-field gel electrophoresis for typing Clostridium difficile

Three methods of molecular typing of Clostridium difficile [arbitrarily-primed polymerase chain reaction (AP-PCR), restriction enzyme analysis (REA) and pulsed-field gel electrophoresis (PFGE)] were compared using 33 isolates collected during a prospective study of Clostridium difficile transmission. Sixteen isolates (from 13 patients and 3 environmental sites) represented a cluster of C. difficile diarrhea on 2 wards, whereas the other 17 isolates were from sporadic cases of C. difficile diarrhea or asymptomatically colonized patient contacts. Fourteen of the 16 clustered isolates were nontypable by pulsed-field gel electrophoresis because of degradation. All 14 of these isolates were a single strain by REA and AP-PCR; 7 of 17 nonclustered isolates also represented the same strain. The other 12 isolates (2 clustered; 10 nonclustered) were subdivided into 9 subgroups by REA, 10 groups by AP-PCR and 7 subgroups by pulsed-field gel electrophoresis. In one instance, AP-PCR resolved isolates indistinguishable by other methods into different groups. However, the interpretation of AP-PCR patterns was complicated by variable intensity of bands and lack of reproducibility of minor bands. In conclusion, these 3 methods of genotyping yielded comparable results, with AP-PCR showing somewhat greater discriminatory power but lower reproducibility.