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Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients

Ravi, Anuradha, Halstead, Fenella D, Bamford, Amy, Casey, Anna, Thomson, Nicholas M., van Schaik, Willem, Snelson, Catherine, Goulden, Robert, Foster-Nyarko, Ebenezer, Savva, George M. , Whitehouse, Tony, Pallen, Mark J. and Oppenheim, Beryl A. (2019) Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients Microbial Genomics, 5 (9). pp. 1-12.

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Abstract

Among long-stay critically ill patients in the adult intensive care unit (ICU), there are often marked changes in the complexity of the gut microbiota. However, it remains unclear whether such patients might benefit from enhanced surveillance or from interventions targeting the gut microbiota or the pathogens therein. We therefore undertook a prospective observational study of 24 ICU patients, in which serial faecal samples were subjected to shotgun metagenomic sequencing, phylogenetic profiling and microbial genome analyses. Two-thirds of the patients experienced a marked drop in gut microbial diversity (to an inverse Simpson’s index of <4) at some stage during their stay in the ICU, often accompanied by the absence or loss of potentially beneficial bacteria. Intravenous administration of the broad-spectrum antimicrobial agent meropenem was significantly associated with loss of gut microbial diversity, but the administration of other antibiotics, including piperacillin/tazobactam, failed to trigger statistically detectable changes in microbial diversity. In three-quarters of ICU patients, we documented episodes of gut domination by pathogenic strains, with evidence of cryptic nosocomial transmission of Enterococcus faecium . In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species Methanobrevibacter smithii . In conclusion, we have documented a dramatic absence of microbial diversity and pathogen domination of the gut microbiota in a high proportion of critically ill patients using shotgun metagenomics.

Item Type: Article
Divisions : Faculty of Health and Medical Sciences > School of Veterinary Medicine
Authors :
NameEmailORCID
Ravi, Anuradha
Halstead, Fenella D
Bamford, Amy
Casey, Anna
Thomson, Nicholas M.
van Schaik, Willem
Snelson, Catherine
Goulden, Robert
Foster-Nyarko, Ebenezer
Savva, George M.
Whitehouse, Tony
Pallen, Mark J.m.pallen@surrey.ac.uk
Oppenheim, Beryl A.
Date : 17 September 2019
Funders : National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre (NIHR SRMRC), National Institute for Health Research (NIHR), Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC)
DOI : 10.1099/mgen.0.000293
Copyright Disclaimer : © 2019 The Authors. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Uncontrolled Keywords : Intensive care unit; Microbiome; Gut microbiota; Pathogens; Shotgun metagenomics; Antimicrobial resistance; Critical illness; Meropenem
Depositing User : Clive Harris
Date Deposited : 30 Sep 2019 13:22
Last Modified : 30 Sep 2019 13:22
URI: http://epubs.surrey.ac.uk/id/eprint/852838

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