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). ISSN 2057-5858. This article is available to all UHB staff and students using your UHB Open Athens account

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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 . In some patients, we also saw an increase in the relative abundance of apparent commensal organisms in the gut microbiome, including the archaeal species . 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
Additional Information: This article is available to all UHB staff and students using your UHB Open Athens account
Subjects: QW Microbiology. Immunology
Divisions: Clinical Support > Immunology
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Depositing User: Beth Connors
Date Deposited: 29 May 2020 13:50
Last Modified: 29 May 2020 13:50
URI: http://www.repository.uhblibrary.co.uk/id/eprint/3121

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