Direct Clostridioides difficile ribotyping from stool using capillary electrophoresis

• Published in: Diagnostic microbiology and infectious disease 2021-03, Vol.99 (3), p.115259-115259, Article 115259
• Main Authors: Lloyd, Colin D., Shah-Gandhi, Binal, Parsons, Brendon D., Morin, Sarah B.N., Du, Tim, Golding, George R., Chui, Linda
• Format: Article
• Language: English
• Subjects: Capillary electrophoresis; Clostridioides difficile; Direct Polymerase Chain Reaction ribotyping; Mixed C. difficile; Quantitative Polymerase Chain Reaction
• ISSN: 0732-8893; 1879-0070
• DOI: 10.1016/j.diagmicrobio.2020.115259

Clostridioides difficile(C. difficile) genotyping is essential for surveillance of emerging strains, transmissions, and outbreak investigations, but culture is lengthy and may not be routinely performed, which necessitates culture-independent genotyping methods. We aimed to develop a direct from stool C. difficile PCR ribotyping algorithm using capillary electrophoresis. Ribotypes were generated directly from 66.8% of stools with 33.2% requiring broth enrichment. 16S and tcdB cycle thresholds (Ct) were significantly lower (P< 0.001) in directly ribotyped stools compared to enriched stools, and Ct correlated with direct ribotyping (area under the curve: 0.97 and 0.96, respectively). Direct and isolate ribotypes were 94.7% concordant. Mixed C. difficile ribotypes were presumptively identified in 14 (7.5%) samples with 12 (6.4%) mixtures confirmed. We have developed a rapid PCR ribotyping algorithm allowing for direct C. difficile genotyping from stool using capillary electrophoresis with occasional detection of mixed C. difficile populations in stool, which is a limitation of conventional isolate genotyping.