Alteration of gut microbiota in carbapenem-resistant Enterobacteriaceae carriers during fecal microbiota transplantation according to decolonization periods

Objectives: Fecal microbiota transplantation (FMT) has been suggested as an alternative therapeutic option to decolonize carbapenem-resistant Enterobacteriaceae (CRE). However, the analysis of gut microbiota alteration in CRE carriers during FMT treatments is still limited. Methods: The decolonization of 10 carbapenemase producing-CRE (CP-CRE) carriers was evaluated after FMT using serial consecutive rectal swab culture. The alterations of gut microbiota before and after FMT treatments (56 serial samples) were analyzed by high-throughput sequencing based on 16S rRNA gene. Results: Decolonization rates of CP-CRE carriers after FMT treatments were 40.0%, 50.0%, and 90% within 1, 3, 5 months after initial FMT, respectively. The composition of gut microbiota was significantly changed after FMT treatments, and the diversity of microbiota and the relative abundance of Bacteroidetes significantly increased. However, the alteration of microbiota was different between early decolonization (EDC) group and late decolonization (LDC) group. The convergence of microbiota in carriers to donor were detected only in EDC group within 4 weeks, and genera within Bacteroidetes played keystones in the gut microbiota of EDC before FMT compared to LDC group. The relative abundance of Klebsiella was lower in EDC group than LDC both before and after FMT. Different alterations of gut microbiota between EDC and LDC groups could be due to the difference of gut microbiota before FMT. Conclusions: This study showed that FMT was a potential option for CRE decolonization. The gut microbiota of CRE carriers could be used to predict the timing of decolonization after FMT and determine necessary of repeated FMT.