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Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects

BACKGROUND: The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed “sele...

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Autores principales: Buelow, Elena, Bello González, Teresita d. j., Fuentes, Susana, de Steenhuijsen Piters, Wouter A. A., Lahti, Leo, Bayjanov, Jumamurat R., Majoor, Eline A. M., Braat, Johanna C., van Mourik, Maaike S. M., Oostdijk, Evelien A. N., Willems, Rob J. L., Bonten, Marc J. M., van Passel, Mark W. J., Smidt, Hauke, van Schaik, Willem
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5554972/
https://www.ncbi.nlm.nih.gov/pubmed/28803549
http://dx.doi.org/10.1186/s40168-017-0309-z
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author Buelow, Elena
Bello González, Teresita d. j.
Fuentes, Susana
de Steenhuijsen Piters, Wouter A. A.
Lahti, Leo
Bayjanov, Jumamurat R.
Majoor, Eline A. M.
Braat, Johanna C.
van Mourik, Maaike S. M.
Oostdijk, Evelien A. N.
Willems, Rob J. L.
Bonten, Marc J. M.
van Passel, Mark W. J.
Smidt, Hauke
van Schaik, Willem
author_facet Buelow, Elena
Bello González, Teresita d. j.
Fuentes, Susana
de Steenhuijsen Piters, Wouter A. A.
Lahti, Leo
Bayjanov, Jumamurat R.
Majoor, Eline A. M.
Braat, Johanna C.
van Mourik, Maaike S. M.
Oostdijk, Evelien A. N.
Willems, Rob J. L.
Bonten, Marc J. M.
van Passel, Mark W. J.
Smidt, Hauke
van Schaik, Willem
author_sort Buelow, Elena
collection PubMed
description BACKGROUND: The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed “selective decontamination of the digestive tract” (SDD), is used in some countries where it improves clinical outcome in ICU patients. Yet, the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown. Here, we characterize the composition of the gut microbiota and its antimicrobial resistance genes (“the resistome”) of ICU patients during SDD and of healthy subjects. RESULTS: From ten patients that were acutely admitted to the ICU, 30 fecal samples were collected during ICU stay. Additionally, feces were collected from five of these patients after transfer to a medium-care ward and cessation of SDD. Feces from ten healthy subjects were collected twice, with a 1-year interval. Gut microbiota and resistome composition were determined using 16S rRNA gene phylogenetic profiling and nanolitre-scale quantitative PCRs. The microbiota of the ICU patients differed from the microbiota of healthy subjects and was characterized by lower microbial diversity, decreased levels of Escherichia coli and of anaerobic Gram-positive, butyrate-producing bacteria of the Clostridium clusters IV and XIVa, and an increased abundance of Bacteroidetes and enterococci. Four resistance genes (aac(6′)-Ii, ermC, qacA, tetQ), providing resistance to aminoglycosides, macrolides, disinfectants, and tetracyclines, respectively, were significantly more abundant among ICU patients than in healthy subjects, while a chloramphenicol resistance gene (catA) and a tetracycline resistance gene (tetW) were more abundant in healthy subjects. CONCLUSIONS: The gut microbiota of SDD-treated ICU patients deviated strongly from the gut microbiota of healthy subjects. The negative effects on the resistome were limited to selection for four resistance genes. While it was not possible to disentangle the effects of SDD from confounding variables in the patient cohort, our data suggest that the risks associated with ICU hospitalization and SDD on selection for antibiotic resistance are limited. However, we found evidence indicating that recolonization of the gut by antibiotic-resistant bacteria may occur upon ICU discharge and cessation of SDD. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-017-0309-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-55549722017-08-15 Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects Buelow, Elena Bello González, Teresita d. j. Fuentes, Susana de Steenhuijsen Piters, Wouter A. A. Lahti, Leo Bayjanov, Jumamurat R. Majoor, Eline A. M. Braat, Johanna C. van Mourik, Maaike S. M. Oostdijk, Evelien A. N. Willems, Rob J. L. Bonten, Marc J. M. van Passel, Mark W. J. Smidt, Hauke van Schaik, Willem Microbiome Research BACKGROUND: The gut microbiota is a reservoir of opportunistic pathogens that can cause life-threatening infections in critically ill patients during their stay in an intensive care unit (ICU). To suppress gut colonization with opportunistic pathogens, a prophylactic antibiotic regimen, termed “selective decontamination of the digestive tract” (SDD), is used in some countries where it improves clinical outcome in ICU patients. Yet, the impact of ICU hospitalization and SDD on the gut microbiota remains largely unknown. Here, we characterize the composition of the gut microbiota and its antimicrobial resistance genes (“the resistome”) of ICU patients during SDD and of healthy subjects. RESULTS: From ten patients that were acutely admitted to the ICU, 30 fecal samples were collected during ICU stay. Additionally, feces were collected from five of these patients after transfer to a medium-care ward and cessation of SDD. Feces from ten healthy subjects were collected twice, with a 1-year interval. Gut microbiota and resistome composition were determined using 16S rRNA gene phylogenetic profiling and nanolitre-scale quantitative PCRs. The microbiota of the ICU patients differed from the microbiota of healthy subjects and was characterized by lower microbial diversity, decreased levels of Escherichia coli and of anaerobic Gram-positive, butyrate-producing bacteria of the Clostridium clusters IV and XIVa, and an increased abundance of Bacteroidetes and enterococci. Four resistance genes (aac(6′)-Ii, ermC, qacA, tetQ), providing resistance to aminoglycosides, macrolides, disinfectants, and tetracyclines, respectively, were significantly more abundant among ICU patients than in healthy subjects, while a chloramphenicol resistance gene (catA) and a tetracycline resistance gene (tetW) were more abundant in healthy subjects. CONCLUSIONS: The gut microbiota of SDD-treated ICU patients deviated strongly from the gut microbiota of healthy subjects. The negative effects on the resistome were limited to selection for four resistance genes. While it was not possible to disentangle the effects of SDD from confounding variables in the patient cohort, our data suggest that the risks associated with ICU hospitalization and SDD on selection for antibiotic resistance are limited. However, we found evidence indicating that recolonization of the gut by antibiotic-resistant bacteria may occur upon ICU discharge and cessation of SDD. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40168-017-0309-z) contains supplementary material, which is available to authorized users. BioMed Central 2017-08-14 /pmc/articles/PMC5554972/ /pubmed/28803549 http://dx.doi.org/10.1186/s40168-017-0309-z Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research
Buelow, Elena
Bello González, Teresita d. j.
Fuentes, Susana
de Steenhuijsen Piters, Wouter A. A.
Lahti, Leo
Bayjanov, Jumamurat R.
Majoor, Eline A. M.
Braat, Johanna C.
van Mourik, Maaike S. M.
Oostdijk, Evelien A. N.
Willems, Rob J. L.
Bonten, Marc J. M.
van Passel, Mark W. J.
Smidt, Hauke
van Schaik, Willem
Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
title Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
title_full Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
title_fullStr Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
title_full_unstemmed Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
title_short Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
title_sort comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5554972/
https://www.ncbi.nlm.nih.gov/pubmed/28803549
http://dx.doi.org/10.1186/s40168-017-0309-z
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