##common.pageHeaderLogo.altText##
DOI:
https://doi.org/10.57187/5144

Original article

Vol. 156 No. 7 (2026)

Efficacy and safety of faecal microbiota transplantation for recurrent Clostridioides difficile infection: a 4-year retrospective study in a Swiss cohort

Cite this as:
Swiss Med Wkly. 2026;156:5144
Published
16.07.2026

Summary

STUDY AIMS: Clostridioides difficile infection (CDI) is associated with high recurrence and mortality. Faecal microbiota transplantation (FMT) is recognised as the most effective treatment for recurrent CDI. However, implementation varies internationally, and real-world data from Switzerland – where FMT is now regulated as a medicinal product – are scarce. Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, established a standardised FMT programme in 2019, yet its outcomes have not previously been reported.

PATIENTS AND METHODS: This retrospective cohort study evaluated all adult patients treated with FMT for recurrent Clostridioides difficile (CDI) infection at CHUV between January 2021 and February 2025. Standardised procedures included strict donor screening, frozen preparation of stool suspensions or capsules, and administration by colonoscopy, jejunostomy, enema or oral capsules. The primary efficacy endpoint was clinical cure, defined as no CDI recurrence at 8 weeks. Adverse events and serious adverse events were recorded prospectively, with causality assessed according to international criteria.

RESULTS: Among the 88 patients who received 100 FMTs, a clinical cure was achieved in 93% of cases after a single treatment, 98% after two and 100% after three. Only three new episodes were reported beyond the 8-week time point. Efficacy was consistent across subgroups, including immunosuppressed individuals. Early gastrointestinal adverse events were mild and transient. Of 24 serious adverse events recorded during follow-up, most were infections or complications related to underlying conditions. Eight deaths occurred during follow-up. Importantly, no serious adverse events or deaths were attributed to FMT.

CONCLUSION: FMT demonstrated a high efficacy and a favourable safety profile for recurrent Clostridioides difficile infection in a real-world Swiss cohort, consistent with international evidence. Standardised donor selection, treatment production and pharmacovigilance were key to maintaining safety. These findings support FMT as a reliable therapeutic option for recurrent Clostridioides difficile infection, including high-risk populations. Further trials are warranted to evaluate earlier use of FMT in the CDI disease course.

References

  1. 1. Barbut F, Bouée S, Longepierre L, Goldberg M, Bensoussan C, Levy-Bachelot L. Excess mortality between 2007 and 2014 among patients with Clostridium difficile infection: a French health insurance database analysis. J Hosp Infect. 2018 Jan;98(1):21–8. 10.1016/j.jhin.2017.07.006
  2. 2. Widmer AF, Frei R, Kuijper EJ, Wilcox MH, Schindler R, Spaniol V, et al. Multicenter Prevalence Study Comparing Molecular and Toxin Assays for Clostridioides difficile Surveillance, Switzerland. Emerg Infect Dis. 2020 Oct;26(10):2370–7. 10.3201/eid2610.190804
  3. 3. van Prehn J, Reigadas E, Vogelzang EH, Bouza E, Hristea A, Guery B, et al.; Guideline Committee of the European Study Group on Clostridioides difficile. European Society of Clinical Microbiology and Infectious Diseases: 2021 update on the treatment guidance document for Clostridioides difficile infection in adults. Clin Microbiol Infect. 2021 Dec;27 Suppl 2:S1–21. 10.1016/j.cmi.2021.09.038
  4. 4. McDonald LC, Gerding DN, Johnson S, Bakken JS, Carroll KC, Coffin SE, et al. Clinical Practice Guidelines for Clostridium difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin Infect Dis. 2018 Mar;66(7):e1–48. 10.1093/cid/cix1085
  5. 5. Ianiro G, Maida M, Burisch J, Simonelli C, Hold G, Ventimiglia M, et al. Efficacy of different faecal microbiota transplantation protocols for Clostridium difficile infection: A systematic review and meta-analysis. United European Gastroenterol J. 2018 Oct;6(8):1232–44. 10.1177/2050640618780762
  6. 6. Quraishi MN, Widlak M, Bhala N, Moore D, Price M, Sharma N, et al. Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection. Aliment Pharmacol Ther. 2017 Sep;46(5):479–93. 10.1111/apt.14201
  7. 7. Cammarota G, Ianiro G, Tilg H, Rajilić-Stojanović M, Kump P, Satokari R, et al.; European FMT Working Group. European consensus conference on faecal microbiota transplantation in clinical practice. Gut. 2017 Apr;66(4):569–80. 10.1136/gutjnl-2016-313017
  8. 8. Cammarota G, Ianiro G, Kelly CR, Mullish BH, Allegretti JR, Kassam Z, et al. International consensus conference on stool banking for faecal microbiota transplantation in clinical practice. Gut. 2019 Dec;68(12):2111–21. 10.1136/gutjnl-2019-319548
  9. 9. Sokol H, Galperine T, Kapel N, Bourlioux P, Seksik P, Barbut F, et al.; French Group of Faecal microbiota Transplantation (FGFT). Faecal microbiota transplantation in recurrent Clostridium difficile infection: Recommendations from the French Group of Faecal microbiota Transplantation. Dig Liver Dis. 2016 Mar;48(3):242–7. 10.1016/j.dld.2015.08.017
  10. 10. Mullish BH, Merrick B, Quraishi MN, Bak A, Green CA, Moore DJ, et al. The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridioides difficile infection and other potential indications: second edition of joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines. Gut. 2024 Jun;73(7):1052–75. 10.1136/gutjnl-2023-331550
  11. 11. Benech N, Cassir N, Alric L, Barbut F, Batista R, Bleibtreu A, et al.; French Faecal Transplant Group (GFTF). Impact of Clinical and Pharmacological Parameters on Faecal Microbiota Transplantation Outcome in Clostridioides difficile Infections: Results of a 5-Year French National Survey. Aliment Pharmacol Ther. 2025 Jan;61(1):159–67. 10.1111/apt.18330
  12. 12. Terveer EM, Vendrik KE, Ooijevaar RE, Lingen EV, Boeije-Koppenol E, Nood EV, et al. Faecal microbiota transplantation for Clostridioides difficile infection: Four years’ experience of the Netherlands Donor Feces Bank. United European Gastroenterol J. 2020 Dec;8(10):1236–47. 10.1177/2050640620957765
  13. 13. Kelly CR, Yen EF, Grinspan AM, Kahn SA, Atreja A, Lewis JD, et al. Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry. Gastroenterology. 2021 Jan;160(1):183–192.e3. 10.1053/j.gastro.2020.09.038
  14. 14. Kassam Z, Dubois N, Ramakrishna B, Ling K, Qazi T, Smith M, et al. Donor Screening for Fecal Microbiota Transplantation. N Engl J Med. 2019 Nov;381(21):2070–2. 10.1056/NEJMc1913670
  15. 15. Rossier L, Matter C, Burri E, Galperine T, Hrúz P, Juillerat P, et al. Swiss expert opinion: current approaches in faecal microbiota transplantation in daily practice. Swiss Med Wkly. 2023 Aug;153(8):40100. 10.57187/smw.2023.40100
  16. 16. GUIDE TO THE QUALITY AND SAFETY OF TISSUES AND CELLS FOR HUMAN APPLICATION. COUNCIL OF EUROPE; 2023.
  17. 17. Rakotonirina A, Galperine T, Allémann E. Fecal microbiota transplantation: a review on current formulations in Clostridioides difficile infection and future outlooks. Expert Opin Biol Ther. 2022 Jul;22(7):929–44. 10.1080/14712598.2022.2095901
  18. 18. Kelly CR, Fischer M, Allegretti JR, LaPlante K, Stewart DB, Limketkai BN, et al. ACG Clinical Guidelines: Prevention, Diagnosis, and Treatment of Clostridioides difficile Infections. Am J Gastroenterol. 2021 Jun;116(6):1124–47. 10.14309/ajg.0000000000001278
  19. 19. Ianiro G, Masucci L, Quaranta G, Simonelli C, Lopetuso LR, Sanguinetti M, et al. Randomised clinical trial: faecal microbiota transplantation by colonoscopy plus vancomycin for the treatment of severe refractory Clostridium difficile infection-single versus multiple infusions. Aliment Pharmacol Ther. 2018 Jul;48(2):152–9. 10.1111/apt.14816
  20. 20. Peery AF, Kelly CR, Kao D, Vaughn BP, Lebwohl B, Singh S, et al.; AGA Clinical Guidelines Committee. Electronic address: clinicalpractice@gastro.org. AGA Clinical Practice Guideline on Fecal Microbiota-Based Therapies for Select Gastrointestinal Diseases. Gastroenterology. 2024 Mar;166(3):409–34. 10.1053/j.gastro.2024.01.008
  21. 21. Harris PA, Taylor R, Minor BL, Elliott V, Fernandez M, O’Neal L, et al.; REDCap Consortium. The REDCap consortium: building an international community of software platform partners. J Biomed Inform. 2019 Jul;95:103208. 10.1016/j.jbi.2019.103208
  22. 22. European Medicines Agency. ICH E2A Clinical safety data management: definitions and standards for expedited reporting - Scientific guideline. [Internet]. 1995 [cited 2025 Oct 27]. Available from: https://www.ema.europa.eu/en/ich-e2a-clinical-safety-data-management-definitions-standards-expedited-reporting-scientific-guideline
  23. 23. American Gastroenterological Association. AGA: American Gastroenterological Association. Fecal Microbiota Transplant National Registry [Internet]. 2017 [cited 2025 Oct 27]. Available from: https://cdn.clinicaltrials.gov/large-docs/55/NCT03325855/Prot_000.pdf
  24. 24. von Elm E, Altman DG, Egger M, Pocock SJ, Gøtzsche PC, Vandenbroucke JP; STROBE Initiative. The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. J Clin Epidemiol. 2008 Apr;61(4):344–9. 10.1016/j.jclinepi.2007.11.008
  25. 25. Minkoff NZ, Aslam S, Medina M, Tanner-Smith EE, Zackular JP, Acra S, et al. Fecal microbiota transplantation for the treatment of recurrent Clostridioides difficile (Clostridium difficile). Cochrane Database Syst Rev. 2023 Apr;4(4):CD013871. 10.1002/14651858.CD013871.pub2
  26. 26. Benech N, Cassir N, Alric L, Barbut F, Batista R, Bleibtreu A, et al.; French Faecal Transplant Group (GFTF). Impact of Clinical and Pharmacological Parameters on Faecal Microbiota Transplantation Outcome in Clostridioides difficile Infections: Results of a 5-Year French National Survey. Aliment Pharmacol Ther. 2025 Jan;61(1):159–67. 10.1111/apt.18330
  27. 27. Vaughn BP, Fischer M, Kelly CR, Allegretti JR, Graiziger C, Thomas J, et al. Effectiveness and Safety of Colonic and Capsule Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection. Clin Gastroenterol Hepatol. 2023 May;21(5):1330–1337.e2. 10.1016/j.cgh.2022.09.008
  28. 28. Hvas CL, Dahl Jørgensen SM, Jørgensen SP, Storgaard M, Lemming L, Hansen MM, et al. Fecal Microbiota Transplantation Is Superior to Fidaxomicin for Treatment of Recurrent Clostridium difficile Infection. Gastroenterology. 2019 Apr;156(5):1324–1332.e3. 10.1053/j.gastro.2018.12.019
  29. 29. Quraishi MN, Widlak M, Bhala N, Moore D, Price M, Sharma N, et al. Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection. Aliment Pharmacol Ther. 2017 Sep;46(5):479–93. 10.1111/apt.14201
  30. 30. Pomares Bascuñana RÁ, Veses V, Sheth CC. Effectiveness of fecal microbiota transplant for the treatment of Clostridioides difficile diarrhea: a systematic review and meta-analysis. Lett Appl Microbiol. 2021 Aug;73(2):149–58. 10.1111/lam.13486
  31. 31. Tariq R, Pardi DS, Bartlett MG, Khanna S. Low Cure Rates in Controlled Trials of Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection: A Systematic Review and Meta-analysis. Clin Infect Dis. 2019 Apr;68(8):1351–8. 10.1093/cid/ciy721
  32. 32. Tixier EN, Verheyen E, Ungaro RC, Grinspan AM. Faecal microbiota transplant decreases mortality in severe and fulminant Clostridioides difficile infection in critically ill patients. Aliment Pharmacol Ther. 2019 Nov;50(10):1094–9. 10.1111/apt.15526
  33. 33. Jaber MR, Olafsson S, Fung WL, Reeves ME. Clinical review of the management of fulminant clostridium difficile infection. Am J Gastroenterol. 2008 Dec;103(12):3195–203. 10.1111/j.1572-0241.2008.02198.x
  34. 34. Terveer EM, van Beurden YH, Goorhuis A, Seegers JF, Bauer MP, van Nood E, et al. How to: establish and run a stool bank. Clin Microbiol Infect. 2017 Dec;23(12):924–30. 10.1016/j.cmi.2017.05.015
  35. 35. Drekonja D, Reich J, Gezahegn S, Greer N, Shaukat A, MacDonald R, et al. Fecal Microbiota Transplantation for Clostridium difficile Infection: A Systematic Review. Ann Intern Med. 2015 May;162(9):630–8. 10.7326/M14-2693
  36. 36. Drekonja DM, Shaukat A, Huang Y, Zhang JH, Reinink AR, Nugent S, et al. A Randomized Controlled Trial of Efficacy and Safety of Fecal Microbiota Transplant for Preventing Recurrent Clostridioides difficile Infection. Clin Infect Dis. 2025 Feb;80(1):52–60. 10.1093/cid/ciae467
  37. 37. Saha S, Mara K, Pardi DS, Khanna S. Long-term Safety of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection. Gastroenterology. 2021 May;160(6):1961–1969.e3. 10.1053/j.gastro.2021.01.010
  38. 38. Berry P, Tariq R, Pardi DS, Khanna S. Effectiveness and Safety of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection in Immunocompromised Patients. Clin Gastroenterol Hepatol. 2025 Aug;•••: 10.1016/j.cgh.2025.06.043
  39. 39. Merrick B, Allen L, Masirah M Zain N, Forbes B, Shawcross DL, Goldenberg SD. Regulation, risk and safety of Faecal Microbiota Transplant. Infect Prev Pract. 2020 Sep;2(3):100069. 10.1016/j.infpip.2020.100069
  40. 40. Bleibtreu A, Kapel N, Galperine T; French Group of Faecal Microbiota Transplantation. Drug-Resistant Bacteremia after Fecal Microbiota Transplant. N Engl J Med. 2020 May;382(20):1961. 10.1056/NEJMc2002496
  41. 41. Marcella C, Cui B, Kelly CR, Ianiro G, Cammarota G, Zhang F. Systematic review: the global incidence of faecal microbiota transplantation-related adverse events from 2000 to 2020. Aliment Pharmacol Ther. 2021 Jan;53(1):33–42. 10.1111/apt.16148
  42. 42. Baunwall SM, Andreasen SE, Hansen MM, Kelsen J, Høyer KL, Rågård N, et al. Faecal microbiota transplantation for first or second Clostridioides difficile infection (EarlyFMT): a randomised, double-blind, placebo-controlled trial. Lancet Gastroenterol Hepatol. 2022 Dec;7(12):1083–91. 10.1016/S2468-1253(22)00276-X
  43. 43. ClinicalTrials.gov. [Internet]. Bethesda (MD): National Library of Medicine (US). 2000 Feb 29 -. Identifier: NCT05266807, Fecal Microbiota Transplantation in Clostridioides Difficile Infection First Episode and First Recurrence (FENDER) [Internet]. [cited 2025 Oct 27]. Available from: https://clinicaltrials.gov/study/NCT05266807?cond=Fecal%20microbiota%20transplantation%20versus%20vancomycin%20or%20fidaxomicin%20in%20Clostridioides%20difficile%20infection&rank=1

Most read articles by the same author(s)