Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study

Abstract

Background: Host-associated microbial communities have important roles in tissue homeostasis and overall health. Severe perturbations can occur within these microbial communities during critical illness due to underlying diseases and clinical interventions, potentially influencing patient outcomes. We sought to profile the microbial composition of critically ill mechanically ventilated patients, and to determine whether microbial diversity is associated with illness severity and mortality.

Methods: We conducted a prospective, observational study of mechanically ventilated critically ill patients with a high incidence of pneumonia in 2 intensive care units (ICUs) in Hamilton, Canada, nested within a randomized trial for the prevention of healthcare-associated infections. The microbial profiles of specimens from 3 anatomical sites (respiratory, and upper and lower gastrointestinal tracts) were characterized using 16S ribosomal RNA gene sequencing.

Results: We collected 65 specimens from 34 ICU patients enrolled in the trial (29 endotracheal aspirates, 26 gastric aspirates and 10 stool specimens). Specimens were collected at a median time of 3 days (lower respiratory tract and gastric aspirates; interquartile range [IQR] 2-4) and 6 days (stool; IQR 4.25-6.75) following ICU admission. We observed a loss of biogeographical distinction between the lower respiratory tract and gastrointestinal tract microbiota during critical illness. Moreover, microbial diversity in the respiratory tract was inversely correlated with APACHE II score (r = - 0.46, p = 0.013) and was associated with hospital mortality (Median Shannon index: Discharged alive; 1.964 vs. Deceased; 1.348, p = 0.045).

Conclusions: The composition of the host-associated microbial communities is severely perturbed during critical illness. Reduced microbial diversity reflects high illness severity and is associated with mortality. Microbial diversity may be a biomarker of prognostic value in mechanically ventilated patients.

Trial registration: ClinicalTrials.gov ID NCT01782755 . Registered February 4 2013.

Keywords: Critical illness; Gastrointestinal tract microbiota; Microbial diversity; Microbiome; Respiratory tract microbiota.

Fig. 1

Lack of microbial consensus and loss of biogeographical distinction in ICU patients. Principal coordinate analysis (PCoA) ordination using the Bray-Curtis dissimilarity metric between the ICU and healthy cohorts demonstrate that samples collected from the healthy cohort tend to cluster per body sites (PERMANOVA, p < 0.001, R² = 0.529) whereas the samples from different anatomical sites tend to overlap in the ICU cohort (PERMANOVA, p < 0.001, R² = 0.082; a). The ordination plot of group dispersions within body site demonstrates a lack of compositional homogeneity within anatomical sites in the ICU cohort (p < 0.001; b). The overlaying lines on the scatter plot show the median distances between the cluster’s centroid displayed with a black circle and each samples within the group and the interquartile range of each site. UPGMA dendogram showing the Bray-Curtis dissimilarity between specimens displays a perfect segregation of samples in the healthy cohort based on collections sites. This is not observed in the ICU cohort (c)

Fig. 2

Compositional heterogeneity observed within and between anatomical sites in critically ill patients. Taxonomic summaries of the 65 samples included in this study displayed by patients and anatomical sites. Bacterial groups present at less than 5% relative abundance are grouped in the “other” category displayed in gray. Taxonomic groups are labeled according to the highest level resolved if not at the Genus (Order; o_, Family; f_)

Fig. 3

Lower respiratory tract microbial diversity is associated with illness severity in critically ill patients. Correlation analysis using Spearman’s rank correlation coefficient demonstrated an inverse association between APACHE II score and Shannon diversity (r = − 0.46, p = 0.013; a), Simpson diversity (r = − 0.44, p = 0.017; b) and Observed species (r = − 0.31, p = 0.11; c). Correlation matrix of clinical parameters and microbial diversity markers showed only a limited number of significant associations (d). The sizes of the circles are dependent on the correlation coefficient value (r). Comparisons that did not achieve significance are represented with a gray circle. LOS represents the length of stay

Fig. 4

Association between microbial diversity and hospital mortality within ICU samples. Shannon (a) and Simpson diversity (b) of ETA and GA specimens shaded by hospital mortality demonstrates a significant reduction in the ETA Shannon diversity in the patients deceased in the hospital versus patients discharged alive. Kaplan-Meier survival curves displayed by high and low microbial diversity groups (c). The censored (i.e., discharged alive) patients are indicated by ticks marks. The threshold for grouping by diversity was the median value of the Shannon diversity measurements for the 29 samples included in this analysis. Confidence intervals are represented by the blue and red shaded areas. Numbers of patients included in the analysis and censored are shown per group under the Kaplan-Meier curve