Gut Microbiota Predict Enterococcus Expansion but Not Vancomycin-Resistant Enterococcus Acquisition

Abstract

Vancomycin-resistant Enterococcus (VRE) is a leading cause of hospital-acquired infections and continues to spread despite widespread implementation of pathogen-targeted control guidelines. Commensal gut microbiota provide colonization resistance to VRE, but the role of gut microbiota in VRE acquisition in at-risk patients is unknown. To address this gap in our understanding, we performed a case-control study of gut microbiota in hospitalized patients who did (cases) and did not (controls) acquire VRE. We matched case subjects to control subjects by known risk factors and "time at risk," defined as the time elapsed between admission until positive VRE screen. We characterized gut bacterial communities using 16S rRNA gene amplicon sequencing of rectal swab specimens. We analyzed 236 samples from 59 matched case-control pairs. At baseline, case and control subjects did not differ in gut microbiota when measured by community diversity (P = 0.33) or composition (P = 0.30). After hospitalization, gut communities of cases and controls differed only in the abundance of the Enterococcus-containing operational taxonomic unit (OTU), with the gut microbiota of case subjects having more of this OTU than time-matched control subjects (P = 0.01). Otherwise, case and control communities after the time at risk did not differ in diversity (P = 0.33) or community structure (P = 0.12). Among patients who became VRE colonized, those having the Blautia-containing OTU on admission had lower Enterococcus relative abundance once colonized (P = 0.004). Our results demonstrate that the 16S profile of the gut microbiome does not predict VRE acquisition in hospitalized patients, likely due to rapid and profound microbiota change. The gut microbiome does not predict VRE acquisition, but it may be associated with Enterococcus expansion, suggesting that these should be considered two distinct processes.IMPORTANCE The Centers for Disease Control and Prevention estimates that VRE causes an estimated 54,000 infections and 539 million dollars in attributable health care costs annually. Despite improvements in hand washing, environmental cleaning, and antibiotic use, VRE is still prevalent in many hospitals. There is a pressing need to better understand the processes by which patients acquire VRE. Multiple lines of evidence suggest that intestinal microbiota may help some patients resist VRE acquisition. In this large case-control study, we compared the 16S profile of intestinal microbiota on admission in patients that did and did not subsequently acquire VRE. The 16S profile did not predict subsequent VRE acquisition, in part due to rapid and dramatic change in the gut microbiome following hospitalization. However, Blautia spp. present on admission predicted decreased Enterococcus abundance after VRE acquisition, and Lactobacillus spp. present on admission predicted Enterococcus dominance after VRE acquisition. Thus, VRE acquisition and domination may be distinct processes.

Keywords: colonization resistance; hospital-acquired infection; microbiome; vancomycin-resistant Enterococcus.

FIG 1

In hospitalized patients, admission gut microbiota do not predict subsequent VRE acquisition. We used 16S rRNA sequencing to characterize gut bacterial communities in 118 hospitalized patients who tested negative for VRE at admission. We compared admission gut microbiota across 59 matched cases (patients who acquired VRE) and controls (patients who did not acquire VRE). (Left) Visualization of admission gut microbial communities using principal-component analysis. The admission gut communities of cases and controls did not differ in their community composition, either visually or via permutation testing (P = 0.3 by PERMANOVA). (Right) Comparison of average species diversity as measured by Shannon diversity index in admission gut communities. The admission gut communities of cases and controls did not differ in their community Shannon diversity index (P = 0.96 by conditional logistic regression).

FIG 2

After the time at risk, the gut microbiota of cases and controls differ primarily in their relative abundance of Enterococcus. The 10 most abundant bacterial taxa are shown in controls (top) and cases (bottom), at the time of admission (left), and following matched time at risk (right). Cases and controls did not differ in their admission microbiota (left). After the time at risk, the gut microbiota of cases were enriched with Enterococcus relative to control (P < 0.01, mvabund), but otherwise did not differ in their community composition (P > 0.05 for all other taxa, mvabund).

FIG 3

With the exception of Enterococcus, gut communities of VRE-infected and uninfected patients do not differ. When we excluded Enterococcus OTU enriched in VRE-infected patients, we found no remaining difference in bacterial community composition, either visually (principal-component analysis) or via permutation testing (P = 0.12 by PERMANOVA).

FIG 4

Rapid and dramatic change in gut microbiota among hospitalized patients. We calculated the dissimilarity between admission and subsequent (index, time at risk) gut communities in both cohorts with Jaccard distance. Both cases and controls exhibited rapid changes in gut communities during hospitalization, with Jaccard distance changing at an exponential rate. Cases and controls did not differ from each other in temporal disruption of gut microbiota. Dashed lines in the figure represent the 95% confidence interval for predicted mean Jaccard distance (inner ribbon) and predicted Jaccard distance for an individual subject (outer ribbon).

FIG 5

Presence of Blautia species on admission is predictive of decreased Enterococcus abundance at the time of VRE acquisition. A random forest regression model identified seven OTUs present on admission that predicted subsequent relative abundance of Enterococcus spp. Of these, the presence of Enterobacteriaceae spp., Lactobacillus spp., and Blautia spp. were significant predictors of the final relative abundance of Enterococcus spp.. Only Lactobacillus spp. and Blautia spp. remained significant after correcting for multiple testing. Significance was determined using the Mann-Whitney U test controlled for multiple comparisons.