Intestinal dysbiosis in carbapenem-resistant Enterobacteriaceae carriers

Infection with Carbapenem-Resistant Enterobacteriaceae (CRE) became an important challenge in health-care settings and a growing concern worldwide. Since infection is preceded by colonization, an understanding of the latter may reduce CRE-infections. We aimed to characterize the gut microbiota after colonization by CRE, assuming that an imbalanced gastrointestinal tract (GIT)-associated microbiota precedes CRE-colonization. We evaluated the GIT-microbiota using 16S rRNA genes sequencing extracted of fecal samples, collected from hospitalized CRE-carriers, and two control groups of hospitalized non-carriers and healthy adults. The microbiota diversity and composition in CRE-colonized patients differed from that of the control groups participants. These CRE-carriers displayed lower phylogenetic diversity and dysbiotic microbiota, enriched with members of the Enterobacteriaceae family. Concurrent with the bloom in Enterobacteriaceae, a depletion of anaerobic commensals was observed. Additionally, changes in several predicted metabolic pathways were observed for the CRE-carriers. Concomitant, we found higher prevalence of bacteremia in the CRE-carriers. Several clinical factors that might induce change in the microbiota were examined and found as insignificant between the groups. CRE-colonized patients have dysbiotic gut microbiota in terms of diversity and community membership, associated with increased risk for systemic infection. Our study results provides justification for attempts to restore the dysbiotic microbiota with probiotics or fecal transplantation.