Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile

• DOI: 10.3389/fcimb.2021.681518
• Publication Date: 2021-06-01T17:41:46Z
• Authors: Helena M. B. Seth...; Michael Biggel; Tim Roloff; Vladimira Hinic; Thomas Bodmer; Martin Risch; Carlo Casanova; Andreas Widmer; Rami Sommerstein; Jonas Marschall; Sarah Tschudin-Su...; Adrian Egli
• Keywords: Ribotyping; Multilocus sequence typing; Sanger sequencing; Molecular Epidemiology

Clostridioides difficile causes nosocomial outbreaks which can lead to severe and even life-threatening colitis. Rapid molecular diagnostic tests allow the identification of toxin-producing, potentially hypervirulent strains, is critical for patient management infection control. PCR-ribotyping has been used decades as reference standard investigate transmission in suspected outbreaks. However, introduction whole genome sequencing (WGS) epidemiology provides a realistic alternative PCR-ribotyping. In this transition phase it crucial understand strengths weaknesses two technologies, assess their correlation. We aimed ribotype prediction from WGS data, options analysis at different levels analytical granularity. Ribotypes cannot be directly determined short read Illumina sequence data rRNA operons including ribotype-defining ISR fragments collapse assemblies, comparison with traditional results becomes impossible. Ribotype extraction long Oxford nanopore also requires optimization. have compared WGS-based typing nearly 300 clinical environmental isolates Switzerland, addition Enterobase database (n=1778). Our show that while multi-locus type (MLST) often correlates specific ribotype, agreement not complete, some ribotypes resolution insufficient. Using core MLST (cgMLST) analysis, there an improved predicted within clusters, using cutoffs 30-50 allele differences. The exceptions are known complexes such RT078/RT106, where differences cgMLST do reflect segregation. clusters display degrees diversity, could important definition cluster cutoffs. offers ultimate SNP level, enabling exploration patient-to-patient transmission. does sufficiently discriminate prove certainty. discuss associated challenges opportunities switch conventional ribotyping C. .