Direct Clostridioides difficile ribotyping from stool using capillary electrophoresis

Colin D. Lloyd; Binal Shah-Gandhi; Brendon D. Parsons; Sarah B.N. Morin; Tim Du; George R. Golding; Linda Chui

doi:10.1016/j.diagmicrobio.2020.115259

Direct Clostridioides difficile ribotyping from stool using capillary electrophoresis

Colin D. Lloyd, Binal Shah-Gandhi, Brendon D. Parsons, Sarah B.N. Morin, Tim Du, George R. Golding, Linda Chui

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

Abstract

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.

Original language	English
Article number	115259
Journal	Diagnostic Microbiology and Infectious Disease
Volume	99
Issue number	3
DOIs	https://doi.org/10.1016/j.diagmicrobio.2020.115259
Publication status	Published - Mar 2021
Externally published	Yes

Bibliographical note

Funding Information:
The authors would like to thank Alberta Precision Laboratories-ProvLab for the GeneXpert data, and particular thanks to LeeAnn Turnbull, and Christina Ferrato from ProvLab as well as Tracie Lloyd and Byron Berenger from CLS for assistance in obtaining the stool samples. Lloyd C is supported by a Team Collaborative Research and Innovation Opportunities (CRIO) awarded by Alberta Innovates, and by the Women and Children's Health Research Institute. This WCHRI graduate studentship has been funded through the generous support of the Stollery Children's Hospital Foundation through the Women and Children's Health Research Institute.

Funding Information:
The authors would like to thank Alberta Precision Laboratories-ProvLab for the GeneXpert data, and particular thanks to LeeAnn Turnbull, and Christina Ferrato from ProvLab as well as Tracie Lloyd and Byron Berenger from CLS for assistance in obtaining the stool samples. Lloyd C is supported by a Team Collaborative Research and Innovation Opportunities (CRIO) awarded by Alberta Innovates, and by the Women and Children's Health Research Institute. This WCHRI graduate studentship has been funded through the generous support of the Stollery Children's Hospital Foundation through the Women and Children's Health Research Institute.

Funding Information:
This work was supported by the University of Alberta Hospital Foundation Kaye Fund Award. The funder provided only monetary support.

Publisher Copyright:
© 2020 Elsevier Inc.

ASJC Scopus Subject Areas

Microbiology (medical)
Infectious Diseases

PubMed: MeSH publication types

Journal Article

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.diagmicrobio.2020.115259

Cite this

@article{45165d4d683342229a262695be85f959,

title = "Direct Clostridioides difficile ribotyping from stool using capillary electrophoresis",

abstract = "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.",

author = "Lloyd, {Colin D.} and Binal Shah-Gandhi and Parsons, {Brendon D.} and Morin, {Sarah B.N.} and Tim Du and Golding, {George R.} and Linda Chui",

note = "Funding Information: The authors would like to thank Alberta Precision Laboratories-ProvLab for the GeneXpert data, and particular thanks to LeeAnn Turnbull, and Christina Ferrato from ProvLab as well as Tracie Lloyd and Byron Berenger from CLS for assistance in obtaining the stool samples. Lloyd C is supported by a Team Collaborative Research and Innovation Opportunities (CRIO) awarded by Alberta Innovates, and by the Women and Children's Health Research Institute. This WCHRI graduate studentship has been funded through the generous support of the Stollery Children's Hospital Foundation through the Women and Children's Health Research Institute. Funding Information: The authors would like to thank Alberta Precision Laboratories-ProvLab for the GeneXpert data, and particular thanks to LeeAnn Turnbull, and Christina Ferrato from ProvLab as well as Tracie Lloyd and Byron Berenger from CLS for assistance in obtaining the stool samples. Lloyd C is supported by a Team Collaborative Research and Innovation Opportunities (CRIO) awarded by Alberta Innovates, and by the Women and Children's Health Research Institute. This WCHRI graduate studentship has been funded through the generous support of the Stollery Children's Hospital Foundation through the Women and Children's Health Research Institute. Funding Information: This work was supported by the University of Alberta Hospital Foundation Kaye Fund Award. The funder provided only monetary support. Publisher Copyright: {\textcopyright} 2020 Elsevier Inc.",

year = "2021",

month = mar,

doi = "10.1016/j.diagmicrobio.2020.115259",

language = "English",

volume = "99",

journal = "Diagnostic Microbiology and Infectious Disease",

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AU - Lloyd, Colin D.

AU - Shah-Gandhi, Binal

AU - Parsons, Brendon D.

AU - Morin, Sarah B.N.

AU - Du, Tim

AU - Golding, George R.

AU - Chui, Linda

N1 - Funding Information: The authors would like to thank Alberta Precision Laboratories-ProvLab for the GeneXpert data, and particular thanks to LeeAnn Turnbull, and Christina Ferrato from ProvLab as well as Tracie Lloyd and Byron Berenger from CLS for assistance in obtaining the stool samples. Lloyd C is supported by a Team Collaborative Research and Innovation Opportunities (CRIO) awarded by Alberta Innovates, and by the Women and Children's Health Research Institute. This WCHRI graduate studentship has been funded through the generous support of the Stollery Children's Hospital Foundation through the Women and Children's Health Research Institute. Funding Information: The authors would like to thank Alberta Precision Laboratories-ProvLab for the GeneXpert data, and particular thanks to LeeAnn Turnbull, and Christina Ferrato from ProvLab as well as Tracie Lloyd and Byron Berenger from CLS for assistance in obtaining the stool samples. Lloyd C is supported by a Team Collaborative Research and Innovation Opportunities (CRIO) awarded by Alberta Innovates, and by the Women and Children's Health Research Institute. This WCHRI graduate studentship has been funded through the generous support of the Stollery Children's Hospital Foundation through the Women and Children's Health Research Institute. Funding Information: This work was supported by the University of Alberta Hospital Foundation Kaye Fund Award. The funder provided only monetary support. Publisher Copyright: © 2020 Elsevier Inc.

PY - 2021/3

Y1 - 2021/3

N2 - 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.

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Direct Clostridioides difficile ribotyping from stool using capillary electrophoresis

Abstract

Bibliographical note

ASJC Scopus Subject Areas

PubMed: MeSH publication types

UN SDGs

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