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

ABSTRACT Commensal microbiota are immunomodulatory, and their pathological perturbation can affect the risk and outcomes of infectious and inflammatory diseases. Consequently, the human microbiota is an emerging diagnostic and therapeutic target in critical illness. In this study, we compared four s...

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Autores principales:	Saumya Bansal, Jenny P. Nguyen, Aleksandra Leligdowicz, Yu Zhang, Kevin C. Kain, Daniel R. Ricciuto, Bryan Coburn
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2018
Materias:	16S RNA critical illness human microbiome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b0f36adecc074bf1abe93358ccfc1f4b
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spelling	oai:doaj.org-article:b0f36adecc074bf1abe93358ccfc1f4b2021-11-15T15:24:23ZRectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients10.1128/mSphere.00219-182379-5042https://doaj.org/article/b0f36adecc074bf1abe93358ccfc1f4b2018-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00219-18https://doaj.org/toc/2379-5042ABSTRACT Commensal microbiota are immunomodulatory, and their pathological perturbation can affect the risk and outcomes of infectious and inflammatory diseases. Consequently, the human microbiota is an emerging diagnostic and therapeutic target in critical illness. In this study, we compared four sample types—rectal, naris, and antecubital swabs and stool samples—for 16S rRNA gene microbiota sequencing in intensive care unit (ICU) patients. Stool samples were obtained in only 31% of daily attempts, while swabs were reliably obtained (≥97% of attempts). Swabs were compositionally distinct by anatomical site, and rectal swabs identified within-patient temporal trends in microbiota composition. Rectal swabs from ICU patients demonstrated differences from healthy stool similar to those observed in comparing stool samples from ICU patients to those from the same healthy controls. Rectal swabs are a useful complement to other sample types for analysis of the intestinal microbiota in critical illness, particularly when obtaining stool may not be feasible or practical. IMPORTANCE 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.Saumya BansalJenny P. NguyenAleksandra LeligdowiczYu ZhangKevin C. KainDaniel R. RicciutoBryan CoburnAmerican Society for Microbiologyarticle16S RNAcritical illnesshuman microbiomeMicrobiologyQR1-502ENmSphere, Vol 3, Iss 3 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S RNA critical illness human microbiome Microbiology QR1-502
spellingShingle	16S RNA critical illness human microbiome Microbiology QR1-502 Saumya Bansal Jenny P. Nguyen Aleksandra Leligdowicz Yu Zhang Kevin C. Kain Daniel R. Ricciuto Bryan Coburn Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients
description	ABSTRACT Commensal microbiota are immunomodulatory, and their pathological perturbation can affect the risk and outcomes of infectious and inflammatory diseases. Consequently, the human microbiota is an emerging diagnostic and therapeutic target in critical illness. In this study, we compared four sample types—rectal, naris, and antecubital swabs and stool samples—for 16S rRNA gene microbiota sequencing in intensive care unit (ICU) patients. Stool samples were obtained in only 31% of daily attempts, while swabs were reliably obtained (≥97% of attempts). Swabs were compositionally distinct by anatomical site, and rectal swabs identified within-patient temporal trends in microbiota composition. Rectal swabs from ICU patients demonstrated differences from healthy stool similar to those observed in comparing stool samples from ICU patients to those from the same healthy controls. Rectal swabs are a useful complement to other sample types for analysis of the intestinal microbiota in critical illness, particularly when obtaining stool may not be feasible or practical. IMPORTANCE 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.
format	article
author	Saumya Bansal Jenny P. Nguyen Aleksandra Leligdowicz Yu Zhang Kevin C. Kain Daniel R. Ricciuto Bryan Coburn
author_facet	Saumya Bansal Jenny P. Nguyen Aleksandra Leligdowicz Yu Zhang Kevin C. Kain Daniel R. Ricciuto Bryan Coburn
author_sort	Saumya Bansal
title	Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients
title_short	Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients
title_full	Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients
title_fullStr	Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients
title_full_unstemmed	Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients
title_sort	rectal and naris swabs: practical and informative samples for analyzing the microbiota of critically ill patients
publisher	American Society for Microbiology
publishDate	2018
url	https://doaj.org/article/b0f36adecc074bf1abe93358ccfc1f4b
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Rectal and Naris Swabs: Practical and Informative Samples for Analyzing the Microbiota of Critically Ill Patients

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