Effectiveness and Safety of Colonic and Capsule Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection

Byron P. Vaughn, Monika Fischer, Colleen R. Kelly, Jessica R. Allegretti, Carolyn Graiziger, Juana Thomas, Emma McClure, Amanda J. Kabage, Alexander Khoruts

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


Background & Aims: Fecal microbiota transplantation (FMT) emerged as rescue treatment for multiply recurrent Clostridioides difficile infections (rCDIs) nonresponsive to standard therapy. However, estimation of FMT efficacy varies among different protocols and formulations, while placebo-controlled clinical trials have excluded most rCDI patients because of medical comorbidities. This study aimed to determine the safety and effectiveness of capsule FMT (cap-FMT) and colonoscopy FMT (colo-FMT) for rCDI using standardized products in a large, multicenter, prospective, real-world cohort. Methods: Clinical outcomes and adverse events after FMT performed for rCDI at 6 sites were captured in a prospective registry. FMT was performed using 1 of 2 standardized formulations of microbiota manufactured by the University of Minnesota Microbiota Therapeutics Program, freeze-dried/encapsulated or frozen-thawed/liquid. The FMT administration route was determined by the treating physician. The rCDI cure rate was assessed at 1 and 2 months. Safety data were collected within the first 72 hours and at 1 and 2 months. Logistic regression was used to investigate factors associated with FMT failure. Results: A total of 301 FMTs were performed in 269 unique patients. Two-thirds were cap-FMT. CDI cure rates were 86% (95% CI, 82%–90%) at 1 month and 81% (95% CI, 75%–86%) at 2 months. There was no difference in the 1-month or 2-month cure rate between cap-FMT and colo-FMT. Cap-FMT recipients were older and less likely to be immunosuppressed or have inflammatory bowel disease. Patient factors of older age and hemodialysis were associated with FMT failure by 2 months on multivariate logistic regression. In addition, post-FMT antibiotic use was associated with FMT failure at 2 months. One serious adverse event was related to colonoscopy (aspiration pneumonia), otherwise no new safety signals were identified. Conclusions: Cap-FMT using freeze-dried capsules has a similar safety and effectiveness profile compared with colo-FMT, without the procedural risks of colonoscopy. Although highly effective overall, patient selection is a key factor to optimizing FMT success.

Original languageEnglish (US)
Pages (from-to)1330-1337.e2
JournalClinical Gastroenterology and Hepatology
Issue number5
StatePublished - May 2023

Bibliographical note

Funding Information:
Funding This work was supported by a generous donation from Achieving Cures Together, a nonprofit organization dedicated to advancing microbiome-based research.

Publisher Copyright:
© 2023 AGA Institute


  • Clostridioides difficile Infection
  • Colitis
  • Fecal Microbiota Transplant
  • Microbiome

PubMed: MeSH publication types

  • Multicenter Study
  • Journal Article
  • Research Support, Non-U.S. Gov't


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