Background: The role of fecal microbiota transplantation (FMT) for Clostridium difficile infection (CDI) is not well-known.

Purpose: To assess the efficacy, comparative effectiveness, and harms of FMT for CDI.

Data sources: MEDLINE (1980 to January 2015), Cochrane Library, and ClinicalTrials.gov, followed by hand-searching references from systematic reviews and identified studies.

Study selection: Any study of FMT to treat adult patients with CDI; case reports were only used to report harms.

Data extraction: Data were extracted by 1 author and verified by another; 2 authors independently assessed risk of bias and strength of evidence.

Data synthesis: Two randomized, controlled trials (RCTs); 28 case-series studies; and 5 case reports were included. Two RCTs and 21 case-series studies (516 patients receiving FMT) reported using FMT for patients with recurrent CDI. A high proportion of treated patients had symptom resolution; however, the role of previous antimicrobials is unclear. One RCT comparing FMT with 2 control groups (n = 43) reported resolution of symptoms in 81%, 31%, and 23% of the FMT, vancomycin, or vancomycin-plus-bowel lavage groups, respectively (P < 0.001 for both control groups vs. FMT). An RCT comparing FMT route (n = 20) reported no difference between groups (60% in the nasogastric tube group and 80% in the colonoscopy group; P = 0.63). Across all studies for recurrent CDI, symptom resolution was seen in 85% of cases. In 7 case-series studies of patients with refractory CDI, symptom resolution ranged from 0% to 100%. Among 7 patients treated with FMT for initial CDI, results were mixed.

Limitation: Most studies were uncontrolled case-series studies; only 2 RCTs were available for analysis.

Conclusion: Fecal microbiota transplantation may have a substantial effect with few short-term adverse events for recurrent CDI. Evidence is insufficient on FMT for refractory or initial CDI treatment and on whether effects vary by donor, preparation, or delivery method.

Primary funding source: U.S. Department of Veterans Affairs.