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

Abstract

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.

Keywords: Anti-bacterial agents; Antibiotic prophylaxis; Drug resistance; Intensive care; Microbial; Microbiome.

Fig. 1

Dynamics of gut microbiota composition and diversity in ICU patients and healthy subjects. a Principal component analysis (PCA) of gut microbiota composition of ICU patients. Dashed symbols indicate fecal samples collected after ICU discharge and continued hospitalization in a medium-care ward. Fecal samples that were collected in the first 5 days of ICU hospitalization are indicated by a black line around the symbol. Fecal samples of healthy subjects were collected at two time points with 1-year interval, indicated with black and gray circles, respectively. b Diversity (Shannon index) of the microbiota of ICU patients. Double lines indicate hospitalization in a medium-care ward. c Diversity (Shannon index) of the microbiota of healthy subjects. d Gut microbiota composition of patients and healthy subjects. Stacked bar charts represent the abundance of different major taxa in the gut microbiota of ICU patients and healthy subjects. Among Bacilli, the genus Enterococcus has been highlighted, as SDD has previously been shown to select for colonization with enterococci [36, 37]. Fecal samples that were collected after ICU discharge and during medium-care hospitalization are indicated by gray triangles. Statistically significant differences of the abundance of taxa in the gut microbiota of patients during ICU hospitalization and healthy subjects are indicated in the legend (*q < 0.05; **q < 0.01; ***q < 0.001; Mann-Whitney U test with Benjamini-Hochberg correction for multiple testing)

Fig. 2

Abundance of E. coli in the gut microbiota of ICU patients and healthy subjects. Quantification of E. coli 16S rRNA gene copies relative to total 16S rRNA gene copies, performed by qPCR with three technical replicates. Error bars indicate standard deviation. Samples are ordered by time of sampling during ICU stay. The color coding of the samples is unique for each patient and is identical to Fig. 1. Statistical testing was performed with the Mann-Whitney U test

Fig. 3

Antimicrobial resistance genes present at significantly higher or lower levels in the microbiota of ICU patients, compared to healthy subjects. ARGs that are present at significantly higher (aac(6′)-Ii, ermC, qacA, and tetQ) or lower (catA and tetW) abundance in ICU patients, compared to healthy subjects, are shown. Testing for statistically significant differences was performed by the Mann-Whitney U test, with Benjamini-Hochberg correction for multiple testing (*q < 0.05; **q < 0.01). The horizontal line denotes the median value. The detection limit of the qPCR assay is indicated with the dashed line