Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients

Author:

Bansal Saumya1ORCID,Nguyen Jenny P.1,Leligdowicz Aleksandra23ORCID,Zhang Yu4,Kain Kevin C.145,Ricciuto Daniel R.46,Coburn Bryan45

Affiliation:

1. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada

2. University of Toronto, Interdepartmental Division of Critical Care, Toronto, ON, Canada

3. University Health Network, Division of Critical Care Medicine, Toronto, ON, Canada

4. Department of Medicine, University Health Network, Toronto, ON, Canada

5. Department of Medicine, Division of Infectious Diseases, University of Toronto, Toronto, ON, Canada

6. Lakeridge Health, Division of Infectious Diseases, Oshawa, ON, Canada

Abstract

Perturbation of the microbiome has been correlated with various infectious and inflammatory diseases and is common in critically ill patients. Stool is typically used to sample the microbiota in human observational studies; however, it is often unavailable for collection from critically ill patients, reducing its utility as a sample type to study this population. Our research identified alternatives to stool for sampling the microbiota during critical illness. Rectal and naris swabs were practical alternatives for use in these patients, as they were observed to be more reliably obtained than stool, were suitable for culture-independent analysis, and successfully captured within- and between-patient microbiota differences.

Funder

CIHR Foundation Grant

Canada Research Chairs

Publisher

American Society for Microbiology

Subject

Molecular Biology,Microbiology

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