What is the role of Fecal Microbiota Transplantation (FMT) in treating recurrent Clostridioides difficile (C. difficile) infection?

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Last updated: September 26, 2025View editorial policy

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Role of Fecal Microbiota Transplantation (FMT) in Treating Recurrent Clostridioides difficile Infection

FMT should be offered to all patients with two or more recurrences of C. difficile infection, and should be considered for patients with a first recurrence or as an adjunct to antibiotics in refractory CDI. 1

Indications for FMT in C. difficile Infection

Primary Indications

  • Recurrent CDI: Strongly recommended after two or more recurrences 1
  • First recurrence: Consider FMT, especially in patients with risk factors for further episodes 1
  • Refractory CDI: Consider as an adjunct to antibiotics when standard treatment fails 1

Special Considerations

  • Severe/fulminant CDI: Consider FMT earlier than after second recurrence when patients are not responding to antibiotic therapy 1
  • Initial CDI: FMT is not recommended as initial treatment; antibiotics alone are preferred 1

Pre-FMT Management

  1. Antibiotic treatment:

    • Administer appropriate antibiotics for CDI for at least 10 days prior to FMT 1
    • Maintain a minimum washout period of 24 hours between last antibiotic dose and FMT 1
  2. Patient preparation:

    • Bowel lavage recommended prior to lower GI route FMT (polyethylene glycol preferred) 1
    • Consider bowel lavage prior to upper GI route FMT 1
    • For upper GI administration, consider proton pump inhibitor the evening before and morning of delivery 1

Administration Routes

Lower GI Route

  • Colonoscopic administration: Recommended where appropriate 1
    • Consider preferential delivery to cecum or terminal ileum for highest efficacy 1
  • Enema: Use when colonoscopy or flexible sigmoidoscopy not possible 1
  • Post-administration: Consider single dose of loperamide following lower GI delivery 1

Upper GI Route

  • Administration methods: Via nasogastric, nasoduodenal, nasojejunal tube, or upper GI endoscopy 1
  • Volume restriction: No more than 100 mL should be administered to upper GI tract 1
  • Cautions: Use with caution in patients at risk of regurgitation or with swallowing disorders 1
  • Additional medications: Consider prokinetics prior to FMT via upper GI route 1

Capsulized FMT

  • Offers a promising alternative administration method 1
  • Should follow standardized protocols 1

Donor Selection and Screening

  1. Donor preference:

    • Use FMT from universal donors in preference to related donors 1
    • When possible, source FMT from a centralized stool bank 1
  2. Donor screening:

    • Mandatory screening by questionnaire and personal interview 1
    • Blood and stool testing for transmissible diseases 1
    • Periodic rescreening of donors (at least every 4 months) 1

FMT Preparation and Storage

  1. Preparation method:

    • Frozen FMT is preferable to fresh preparations 1
    • Both aerobic and anaerobic processing methods are acceptable 1
    • Add cryoprotectant such as glycerol to frozen FMT products 1
  2. Storage:

    • Store frozen FMT at -70°C for up to 12 months 1
    • Previously recommended maximum shelf life was 6 months at -80°C 1

Post-FMT Management

  1. Follow-up:

    • Follow patients for at least 8 weeks to establish efficacy and monitor adverse events 1, 2
    • Do not routinely test for C. difficile toxin after FMT 1, 2
    • Consider testing only if persistent symptoms or suspected relapse 1, 2
  2. Management of FMT failure:

    • Offer additional FMT after initial FMT failure 1
    • Consider investigation for alternative causes of symptoms in non-responders 1

Special Patient Populations

  1. Immunosuppressed patients:

    • FMT should be offered with caution to immunosuppressed patients 1
    • For patients at risk of severe infection if exposed to EBV or CMV, use donors negative for these viruses 1
  2. Patients with IBD:

    • FMT should be offered to those with recurrent CDI and IBD 1
    • Counsel patients about small risk of IBD exacerbation after FMT 1
  3. Other comorbidities:

    • Do not refuse or delay FMT due to recipient risk factors (e.g., age over 75) 1
    • Exception: Known anaphylactic food allergy 1

Efficacy and Safety

  • Efficacy: FMT has cure rates approaching 90% for recurrent CDI 3
  • Safety: Inform patients about potential short-term adverse events, particularly self-limiting GI symptoms 1
  • Serious adverse events: Rare but patients should be informed 1

Emerging Evidence

Recent research suggests FMT may be beneficial even earlier in the course of CDI, with one study showing 90% resolution in patients with first or second CDI episodes treated with FMT compared to 33% with standard vancomycin alone 4. This suggests the potential for expanding FMT indications to earlier in the disease course.

References

Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

Guideline

Management of Clostridioides difficile Infection

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

Research

Fecal Microbiota Transplantation.

Clinics in colon and rectal surgery, 2023

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

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