PCR-based Ribotyping of Clostridium difficile

by Liz Horton, Canon BioMedical on October 15, 2018

Clostridium difficile (C. difficile) is a commonly identified healthcare-associated infection that is sometimes difficult to treat and can in some cases be fatal. The ability to identify and track particular strains during outbreaks is important to understanding the epidemiology. There have been many methods used for typing C. difficile such as pulsed-field gel electrophoresis and restriction endonuclease analysis, but PCR ribotyping has emerged as a simple and cost-effective method. Recent publications reported validation studies using this technique (1, 2).

In a poster presented at the 28th European Congress of Clinical Microbiology and Infectious Diseases in April 2018, Ben Johns, Michael Perry and Trefor Morris from the UK Anaerobe Reference Unit in Cardiff looked at the ability to speed up the PCR step of the C. difficile PCR ribotyping assay by using the NEXTGENPCR thermocycler (3). Using the published assay, which has a 138 minute cycling time (1), and optimizing the protocol for NEXTGENPCR, they reported PCR cycling times of only 21 minutes. The authors validated the results against conventional PCR assays as a reference for the study, looking at 22 ribotypes. They note that additional research is in progress to evaluate NEXTGENPCR in PCR ribotyping against more ribotypes of C. difficile as well as evaluation of the technology for the PCR stage of 16S sequencing.


  1. Fawley, W. N., et al. (2015). Development and validation of an internationally-standardized, high-resolution capillary gel-based electrophoresis PCR-ribotyping protocol for Clostridium difficile. PLoS One, 10(2), e0118150.
  2. Martinson, J. N., et al. (2015). Evaluation of portability and cost of a fluorescent PCR ribotyping protocol for Clostridium difficile epidemiology. Journal of clinical microbiology, JCM-03591.
  3. Johns, B., Perry, M and Morris, T. (2018) Verification of the MBS NextGen PCR instrument for significantly reducing end point PCR cycling times. Poster at the 28th European Congress of Clinical Microbiology and Infectious Diseases.

If you are interested in trying the NEXTGENPCR in your lab, click the link below.