Intestinal Dysbiosis in Carriers of Carbapenem-Resistant Enterobacteriaceae

Infection with carbapenem-resistant Enterobacteriaceae (CRE) has become 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 in-fections. We aimed to characterize the gut microbiota in CRE carriers, assuming that mi-crobiota alterations precede CRE colonization. We evaluated the gut microbiota using 16S rRNA gene sequencing extracted of fecal samples collected from hospitalized CRE carriers and two control groups, hospitalized noncarriers and healthy adults. The micro-biota diversity and composition in CRE-colonized patients differed from those of the control group participants. These CRE carriers displayed lower phylogenetic diversity and dysbiotic microbiota, enriched with members of the family Enterobacteriaceae . Concur-rent with the enrichment in Enterobacteriaceae , a depletion of anaerobic commensals was observed. Additionally, changes in several predicted metabolic pathways were ob-served for the CRE carriers. Concomitantly, we found higher prevalence of bacteremia in the CRE carriers. Several clinical factors that might induce changes in the microbiota were examined and found to be insignificant between the groups. The compositional and functional changes in the microbiota of CRE-colonized patients are associated with increased risk for systemic infection. Our study results provide justification for attempts to restore the dysbiotic microbiota with probiotics or fecal transplantation. IMPORTANCE The gut microbiota plays important roles in the host's normal func-tion and health, including protection against colonization by pathogenic bacteria. Al-terations in the gut microbial profile can potentially serve as an early diagnostic tool, as well as a therapeutic strategy against colonization by and carriage of harm-ful bacteria, including antibiotic-resistant pathogens. Here, we show that the micro-biota of hospitalized patients demonstrated specific taxa which differed between carriers of carbapenem-resistant Enterobacteriaceae (CRE) and noncarriers. The difference in the microbiota also dictates alterations in microbiome-specific metabolic capabilities, in association with increased prevalence of systemic infection. Reintroducing specific strains and/or correction of dysbiosis with probiotics or fecal transplantation may poten-tially lead to colonization by bacterial taxa responsible for protection against or deple-tion of antibiotic-resistant pathogens.