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

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, which is critical for patient management and infection control. PCR-riboty...

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Autores principales: Seth-Smith, Helena M. B., Biggel, Michael, Roloff, Tim, Hinic, Vladimira, Bodmer, Thomas, Risch, Martin, Casanova, Carlo, Widmer, Andreas, Sommerstein, Rami, Marschall, Jonas, Tschudin-Sutter, Sarah, Egli, Adrian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8204696/
https://www.ncbi.nlm.nih.gov/pubmed/34141631
http://dx.doi.org/10.3389/fcimb.2021.681518
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author Seth-Smith, Helena M. B.
Biggel, Michael
Roloff, Tim
Hinic, Vladimira
Bodmer, Thomas
Risch, Martin
Casanova, Carlo
Widmer, Andreas
Sommerstein, Rami
Marschall, Jonas
Tschudin-Sutter, Sarah
Egli, Adrian
author_facet Seth-Smith, Helena M. B.
Biggel, Michael
Roloff, Tim
Hinic, Vladimira
Bodmer, Thomas
Risch, Martin
Casanova, Carlo
Widmer, Andreas
Sommerstein, Rami
Marschall, Jonas
Tschudin-Sutter, Sarah
Egli, Adrian
author_sort Seth-Smith, Helena M. B.
collection PubMed
description 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, which is critical for patient management and infection control. PCR-ribotyping has been used for decades as the reference standard to investigate transmission in suspected outbreaks. However, the introduction of whole genome sequencing (WGS) for molecular epidemiology provides a realistic alternative to PCR-ribotyping. In this transition phase it is crucial to understand the strengths and weaknesses of the two technologies, and to assess their correlation. We aimed to investigate ribotype prediction from WGS data, and options for analysis at different levels of analytical granularity. Ribotypes cannot be directly determined from short read Illumina sequence data as the rRNA operons including the ribotype-defining ISR fragments collapse in genome assemblies, and comparison with traditional PCR-ribotyping results becomes impossible. Ribotype extraction from long read Oxford nanopore data also requires optimization. We have compared WGS-based typing with PCR-ribotyping in nearly 300 clinical and environmental isolates from Switzerland, and in addition from the Enterobase database (n=1778). Our results show that while multi-locus sequence type (MLST) often correlates with a specific ribotype, the agreement is not complete, and for some ribotypes the resolution is insufficient. Using core genome MLST (cgMLST) analysis, there is an improved resolution and ribotypes can often be predicted within clusters, using cutoffs of 30-50 allele differences. The exceptions are ribotypes within known ribotype complexes such as RT078/RT106, where the genome differences in cgMLST do not reflect the ribotype segregation. We show that different ribotype clusters display different degrees of diversity, which could be important for the definition of ribotype cluster specific cutoffs. WGS-based analysis offers the ultimate resolution to the SNP level, enabling exploration of patient-to-patient transmission. PCR-ribotyping does not sufficiently discriminate to prove nosocomial transmission with certainty. We discuss the associated challenges and opportunities in a switch to WGS from conventional ribotyping for C. difficile.
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spelling pubmed-82046962021-06-16 Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile Seth-Smith, Helena M. B. Biggel, Michael Roloff, Tim Hinic, Vladimira Bodmer, Thomas Risch, Martin Casanova, Carlo Widmer, Andreas Sommerstein, Rami Marschall, Jonas Tschudin-Sutter, Sarah Egli, Adrian Front Cell Infect Microbiol Cellular and Infection Microbiology 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, which is critical for patient management and infection control. PCR-ribotyping has been used for decades as the reference standard to investigate transmission in suspected outbreaks. However, the introduction of whole genome sequencing (WGS) for molecular epidemiology provides a realistic alternative to PCR-ribotyping. In this transition phase it is crucial to understand the strengths and weaknesses of the two technologies, and to assess their correlation. We aimed to investigate ribotype prediction from WGS data, and options for analysis at different levels of analytical granularity. Ribotypes cannot be directly determined from short read Illumina sequence data as the rRNA operons including the ribotype-defining ISR fragments collapse in genome assemblies, and comparison with traditional PCR-ribotyping results becomes impossible. Ribotype extraction from long read Oxford nanopore data also requires optimization. We have compared WGS-based typing with PCR-ribotyping in nearly 300 clinical and environmental isolates from Switzerland, and in addition from the Enterobase database (n=1778). Our results show that while multi-locus sequence type (MLST) often correlates with a specific ribotype, the agreement is not complete, and for some ribotypes the resolution is insufficient. Using core genome MLST (cgMLST) analysis, there is an improved resolution and ribotypes can often be predicted within clusters, using cutoffs of 30-50 allele differences. The exceptions are ribotypes within known ribotype complexes such as RT078/RT106, where the genome differences in cgMLST do not reflect the ribotype segregation. We show that different ribotype clusters display different degrees of diversity, which could be important for the definition of ribotype cluster specific cutoffs. WGS-based analysis offers the ultimate resolution to the SNP level, enabling exploration of patient-to-patient transmission. PCR-ribotyping does not sufficiently discriminate to prove nosocomial transmission with certainty. We discuss the associated challenges and opportunities in a switch to WGS from conventional ribotyping for C. difficile. Frontiers Media S.A. 2021-06-01 /pmc/articles/PMC8204696/ /pubmed/34141631 http://dx.doi.org/10.3389/fcimb.2021.681518 Text en Copyright © 2021 Seth-Smith, Biggel, Roloff, Hinic, Bodmer, Risch, Casanova, Widmer, Sommerstein, Marschall, Tschudin-Sutter and Egli https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cellular and Infection Microbiology
Seth-Smith, Helena M. B.
Biggel, Michael
Roloff, Tim
Hinic, Vladimira
Bodmer, Thomas
Risch, Martin
Casanova, Carlo
Widmer, Andreas
Sommerstein, Rami
Marschall, Jonas
Tschudin-Sutter, Sarah
Egli, Adrian
Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile
title Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile
title_full Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile
title_fullStr Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile
title_full_unstemmed Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile
title_short Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile
title_sort transition from pcr-ribotyping to whole genome sequencing based typing of clostridioides difficile
topic Cellular and Infection Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8204696/
https://www.ncbi.nlm.nih.gov/pubmed/34141631
http://dx.doi.org/10.3389/fcimb.2021.681518
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