Clostridium difficile : Investigating Transmission Patterns Between Infected and Colonized Patients Using Whole Genome Sequencing
Open accessAbstract
Background: Whole genome sequencing (WGS) studies can enhance our understanding of the role of patients with asymptomatic Clostridium difficile colonization in transmission. Methods: Isolates obtained from patients with Clostridium difficile infection (CDI) and colonization identified in a study conducted during 2006-2007 at 6 Canadian hospitals underwent typing by pulsed-field gel electrophoresis, multilocus sequence typing, and WGS. Isolates from incident CDI cases not in the initial study were also sequenced where possible. Ward movement and typing data were combined to identify plausible donors for each CDI case, as defined by shared time and space within predefined limits. Proportions of plausible donors for CDI cases that were colonized, infected, or both were examined. Results: Five hundred fifty-four isolates were sequenced successfully, 353 from colonized patients and 201 from CDI cases. The NAP1/027/ST1 strain was the most common strain, found in 124 (62%) of infected and 92 (26%) of colonized patients. A donor with a plausible ward link was found for 81 CDI cases (40%) using WGS with a threshold of ≤2 single nucleotide polymorphisms to determine relatedness. Sixty-five (32%) CDI cases could be linked to both infected and colonized donors. Exclusive linkages to infected and colonized donors were found for 28 (14%) and 12 (6%) CDI cases, respectively. Conclusions: Colonized patients contribute to transmission, but CDI cases are more likely linked to other infected patients than colonized patients in this cohort with high rates of the NAP1/027/ST1 strain, highlighting the importance of local prevalence of virulent strains in determining transmission dynamics.
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Some authors set a cut-off of less than or equal to two SNV differences, while others set an ANI value of greater than 98% for isolates to be considered to come from the same natural strain.
“Some authors set a cut-off of less than or equal to two SNV differences [58], while others set an ANI value of greater than 98% [59] for isolates to be considered to come from the same natural strain.”
From Genomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese (2024) · cites this paper as [58]
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“Some authors set a cut-off of less than or equal to two SNV differences [58], while others set an ANI value of greater than 98% [59] for isolates to be considered to come from the same natural strain.”
- Authors
- Kong, L. Y., Eyre, D. W., Corbeil, J., Raymond, F., Walker, A. S., Wilcox, M. H., Crook, D. W., Michaud, S., Toye, B., Frost, E., Dendukuri, N., Schiller, I., Bourgault, A.-M., Dascal, A., Oughton, M., Longtin, Y., Poirier, L., Brassard, P., Turgeon, N., Gilca, R., & Loo, V. G.
- Affiliations
- McGill University Health Centre (CA)
- John Radcliffe Hospital (GB)
- Centre hospitalier universitaire de Québec (CA)
- Centre de recherche CHUQ, Université Laval, Québec City, Québec, Canada
- University of Leeds (GB)
- Université de Sherbrooke (CA)
- University of Ottawa (CA)
- Technology Assessment Unit, Canada
- Division of Infectious Diseases, Jewish General Hospital, Canada
- Jewish General Hospital (CA)
- Hôpital Maisonneuve-Rosemont (CA)
- Institut National de Santé Publique du Québec (CA)
- Corresponding author
- Kong, Ling Yuan
- ORCID
- Venue
- Clinical Infectious Diseases
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-05-28
- Volume
- 68
- Issue
- 2
- Pages
- 204-209
- ISSN
- 1058-4838 (ISSN-L)
- 1537-6591
- PMC
- PMC6321846
- OpenAlex
- W2805150426
- Cited by
- 63
- References
- 24
- Citations by year
- 2026: 1 · 2025: 4 · 2024: 5 · 2023: 15 · 2022: 10 · 2021: 7 · 2020: 10 · 2019: 7 · 2018: 4
- FWCI
- 5.29
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Clinical Infectious Diseases (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Fonds de la recherche en santé du Québec
- Canadian Institutes of Health Research
- Ministère de la Santé et des Services sociaux du Québec
- Institut national de santé publique du Québec
- Health Canada
- Centre hospitalier de l’Université de Montréal
- McGill University Health Centre
- Centre hospitalier universitaire de Québec
- Centre hospitalier universitaire de Sherbrooke
- Topics
- Health Sciences › Medicine › Infectious Diseases › Clostridium difficile and Clostridium perfringens research
- Health Sciences › Medicine › Infectious Diseases › Infection Control in Healthcare
- Health Sciences › Medicine › Infectious Diseases › Antimicrobial Resistance in Staphylococcus
- Keywords
- Clostridium difficile, Clostridium difficile infection, asymptomatic colonization, transmission patterns, whole genome sequencing, pulsed-field gel electrophoresis, multilocus sequence typing, single nucleotide polymorphisms, relatedness
- MeSH terms
- Whole Genome Sequencing, Carrier State, Clostridium Infections, Cross Infection, DNA, Bacterial, Humans, Clostridioides difficile, Genome, Bacterial
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