Correlation between restriction endonuclease analysis and PCR ribotyping for the identification of Clostridioides (Clostridium) difficile clinical strains

Abstract

Restriction endonuclease analysis (REA) and PCR ribotyping are two typing systems that have been frequently utilized for molecular epidemiologic characterization of Clostridioides (Clostridium) difficile. To correlate typing data obtained from each method, we performed both REA and PCR ribotyping on a large and diverse set of historical and contemporary C. difficile infection clinical isolates. Eighty isolates were selected from each reference laboratory in the United States (Microbiology Reference Laboratory, Hines VA Medical Center) and United Kingdom (Clostridium difficile Network for England and Northern Ireland laboratory, University of Leeds). The 160 isolates were assigned to 82 unique ribotypes and 51 unique REA groups (116 unique REA types). In general, concordance between typing methods was good. Dendrogram analysis of PCR ribotype band patterns demonstrated close genetic relationships among strain types with discordant REA and ribotype assignments. While REA typing was more discriminatory, several REA types in this study were further discriminated by PCR ribotyping, indicating that discriminatory value of these typing methods may be strain dependent. These data will assist with molecular epidemiologic surveillance of strains identified by these two commonly used C. difficile typing systems.

Keywords: Clostridium difficile; Molecular epidemiology; PCR ribotyping; Restriction endonuclease analysis; Typing.

Fig. 1.

PCR ribotyping dendrogram of C. difficile isolates and corresponding REA groups and types. The complete dendrogram has been separated into 6 sections for print (A-F). *Isolates identified by REA group, but specific REA type not assigned (see methods). ˆHistoric BI strains isolated in the late 1980s/early 1990s, well before the BI/NAP1/027 epidemic, which started in the early 2000s. dup-two of the isolates analyzed were blinded duplicates of the same isolate. p- Plasmid accounts for a distinguishing band in the REA pattern of the whole genome HindIII digest.