Clinical and Culture-Based Predictors of Gut Microbiome Alpha Diversity at the Time of ICU Admission.

Abstract

Objectives: Microbiome-based therapies to improve gut colonization resistance are being developed for the ICU, but their efficacy may depend on the baseline gut microbiome at ICU admission. We sought to identify clinical predictors of alpha diversity at ICU admission.

Design: Retrospective reanalysis of a randomized clinical trial (NCT03865706).

Setting: Single-center ICU.

Patients: ICU patients with sepsis as the primary diagnosis who were receiving broad-spectrum antibiotics and could be enrolled within 24 hours of ICU admission.

Interventions: None.

Measurements and main results: Demographic and clinical characteristics for medical ICU patients with sepsis were recorded during a previously published randomized clinical trial. Deep rectal swabs were collected within 24 hours of ICU admission and sequenced to describe alpha diversity (Shannon index) and cultured for vancomycin-resistant Enterococcus (VRE). Patients were organized into tertiles of Shannon diversity (low, middle, high) with a primary outcome of a lower Shannon tertile at ICU admission. Overall, 90 patients were enrolled. The three variables of location before ICU admission (adjusted odds ratio [aOR], 3.54; 95% CI, 1.21-10.3 for ICU transfer vs. emergency department [ED]; aOR, 6.09; 95% CI, 1.89-19.6 for hospital ward vs. ED), prior culture-proven infection within 1 year (aOR, 2.46; 95% CI, 1.02-5.96), and VRE status on ICU admission (aOR, 4.18; 95% CI, 1.44-12.1 for positive vs. negative swab) were sufficient to describe a quasi-linear trend in alpha diversity at ICU admission.

Conclusions: Baseline gut microbiome Shannon alpha diversity at ICU admission could be described with three readily ascertained clinical variables. Our model shows promise as a preliminary framework of factors that collectively best predict baseline alpha diversity at ICU admission and warrants validation in larger independent cohorts.