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Intensive Care Med. 2018 Aug;44(8):1203-1211. doi: 10.1007/s00134-018-5268-8. Epub 2018 Jun 23.

Pathogen colonization of the gastrointestinal microbiome at intensive care unit admission and risk for subsequent death or infection.

Author information

1
Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical Center, 630 West 168th Street, New York, NY, 10032, USA. def2004@cumc.columbia.edu.
2
Department of Medicine, Columbia University Medical Center, New York, USA.
3
Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, USA.
4
Microbiome and Pathogen Genomics Core, Department of Medicine, Columbia University Medical Center, New York, USA.
5
Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical Center, 630 West 168th Street, New York, NY, 10032, USA.
6
Division of Laboratory Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA.
7
Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, New York, USA.
8
Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, USA.
9
Mailman School of Public Health, New York, USA.

Abstract

PURPOSE:

Loss of colonization resistance within the gastrointestinal microbiome facilitates the expansion of pathogens and has been associated with death and infection in select populations. We tested whether gut microbiome features at the time of intensive care unit (ICU) admission predict death or infection.

METHODS:

This was a prospective cohort study of medical ICU adults. Rectal surveillance swabs were performed at admission, selectively cultured for vancomycin-resistant Enterococcus (VRE), and assessed using 16S rRNA gene sequencing. Patients were followed for 30 days for death or culture-proven bacterial infection.

RESULTS:

Of 301 patients, 123 (41%) developed culture-proven infections and 76 (25%) died. Fecal biodiversity (Shannon index) did not differ based on death or infection (p = 0.49). The presence of specific pathogens at ICU admission was associated with subsequent infection with the same organism for Escherichia coli, Pseudomonas spp., Klebsiella spp., and Clostridium difficile, and VRE at admission was associated with subsequent Enterococcus infection. In a multivariable model adjusting for severity of illness, VRE colonization and Enterococcus domination (≥ 30% 16S reads) were both associated with death or all-cause infection (aHR 1.46, 95% CI 1.06-2.00 and aHR 1.47, 95% CI 1.00-2.19, respectively); among patients without VRE colonization, Enterococcus domination was associated with excess risk of death or infection (aHR 2.13, 95% CI 1.06-4.29).

CONCLUSIONS:

Enterococcus status at ICU admission was associated with risk for death or all-cause infection, and rectal carriage of common ICU pathogens predicted specific infections. The gastrointestinal microbiome may have a role in risk stratification and early diagnosis of ICU infections.

KEYWORDS:

Colonization resistance; Critical care; Microbiome; Mortality; Nosocomial infection; Vancomycin-resistant Enterococcus

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