Inflammatory Bowel Disease Outcomes Following Fecal Microbiota Transplantation for Recurrent C. difficile Infection

Inflamm Bowel Dis. 2020 Nov 6;izaa283. doi: 10.1093/ibd/izaa283. Online ahead of print.

Jessica R Allegretti 1 2, Colleen R Kelly 3, Ari Grinspan 4, Benjamin H Mullish 5, Jonathan Hurtado 1, Madeline Carrellas 1, Jenna Marcus 1, Julian R Marchesi 5 6, Julie A K McDonald 5 7, Ylaine Gerardin 8, Michael Silverstein 8, Alexandros Pechlivanis 5 9, Grace F Barker 5, Jesus Miguens Blanco 5, James L Alexander 5, Kate I Gallagher 5, Will Pettee 10, Emmalee Phelps 11, Sara Nemes 11, Sashidhar V Sagi 11, Matthew Bohm 11, Zain Kassam 8, Monika Fischer 11


Author information

  • 1Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA.
  • 2Harvard Medical School, Boston, MA, USA.
  • 3Division of Gastroenterology, Alpert Medical School of Brown University, Providence, RI, USA.
  • 4The Henry D. Janowitz Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
  • 5Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
  • 6School of Biosciences, Cardiff University, Cardiff, UK.
  • 7MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK.
  • 8Finch Therapeutics, Somerville, MA, USA.
  • 9Center for Interdisciplinary Research and Innovation, School of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece.
  • 10OpenBiome, Cambridge, MA, USA.
  • 11Division of Gastroenterology, Indiana University School of Medicine, Indianapolis, IN, USA.


Background: Recurrent Clostridioides difficile infection (CDI) in patients with inflammatory bowel disease (IBD) is a clinical challenge. Fecal microbiota transplantation (FMT) has emerged as a recurrent CDI therapy. Anecdotal concerns exist regarding worsening of IBD activity; however, prospective data among IBD patients are limited.

Methods: Secondary analysis from an open-label, prospective, multicenter cohort study among IBD patients with 2 or more CDI episodes was performed. Participants underwent a single FMT by colonoscopy (250 mL, healthy universal donor). Secondary IBD-related outcomes included rate of de novo IBD flares, worsening IBD, and IBD improvement-all based on Mayo or Harvey-Bradshaw index (HBI) scores. Stool samples were collected for microbiome and targeted metabolomic profiling.

Results: Fifty patients enrolled in the study, among which 15 had Crohn's disease (mean HBI, 5.8 ± 3.4) and 35 had ulcerative colitis (mean partial Mayo score, 4.2 ± 2.1). Overall, 49 patients received treatment. Among the Crohn's disease cohort, 73.3% (11 of 15) had IBD improvement, and 4 (26.6%) had no disease activity change. Among the ulcerative colitis cohort, 62% (22 of 34) had IBD improvement, 29.4% (11 of 34) had no change, and 4% (1 of 34) experienced a de novo flare. Alpha diversity significantly increased post-FMT, and ulcerative colitis patients became more similar to the donor than Crohn's disease patients (P = 0.04).

Conclusion: This prospective trial assessing FMT in IBD-CDI patients suggests IBD outcomes are better than reported in retrospective studies.

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