Fecal Microbiota-Based Therapies for Select Gastrointestinal Diseases

Publication Date: February 20, 2024
Last Updated: April 26, 2024

Summary of Recommendations

In immunocompetent adults with recurrent C difficile infection, the AGA suggests the use of fecal microbiota–based therapies upon completion of standard of care antibiotics over no fecal microbiota–based therapies. (C, L )
The following considerations are specific to immunocompetent adult patients with nonsevere, nonfulminant recurrent CDI in the outpatient setting:

Diagnosis of recurrent CDI:
  • A CDI diagnosis requires acute-onset, clinically significant, new-onset diarrhea (eg, 3 or more unformed stools in 24 hours) and highly sensitive (nucleic acid amplification or glutamate dehydrogenase) in combination with highly specific (toxin enzyme immunoassay) testing plus improvement of diarrhea with C difficile–directed antibiotics. A positive nucleic acid amplification test alone in the appropriate clinical context is also reasonable for making a CDI diagnosis.
  • Recurrent CDI is typically defined as clinically significant diarrhea with a confirmatory positive test within 8 weeks of completing antibiotics for CDI.
  • In patients who develop recurrent diarrhea after treatment for CDI, it is important to consider not only CDI recurrence, but also alternative diagnoses, especially if there are atypical symptoms, such as diarrhea alternating with constipation or no response in diarrheal symptoms to treatment with vancomycin or fidaxomicin.

When to consider fecal microbiota–based therapies:
  • Fecal microbiota–based therapies include conventional FMT, fecal microbiota live-jslm and fecal microbiota spores live-brpk.
  • Prevention with fecal microbiota–based therapies can be considered in patients after the second recurrence (third episode) of CDI or in select patients at high risk of either recurrent CDI or a morbid CDI recurrence. Select use includes patients who have recovered from severe, fulminant, or particularly treatment-refractory CDI and patients with significant comorbidities.
  • Careful consideration before proceeding with fecal microbiota–based therapies is recommended in patients who require frequent antibiotics or long-term antibiotic prophylaxis, because ongoing antibiotics may diminish the efficacy of such therapy.

How to administer fecal microbiota–based therapies:
  • Fecal microbiota–based therapies should be given upon completion of a course of standard of care antibiotics for recurrent CDI. The fecal microbiota–based therapies are to prevent recurrence, not for CDI treatment.
  • Suppressive anti-CDI antibiotics (eg, vancomycin) should be used to bridge standard of care antibiotics until fecal microbiota–based therapies are given.
  • Ideally, antibiotics for CDI should be stopped 1–3 days before conventional FMT to allow adequate time for antibiotics to wash out of the system.16 If a bowel purge is given, FMT can be given 1 day after stopping antibiotics. If no bowel purge is given, 3 days off antibiotics is recommended to allow clearance of oral antibiotics. Rarely, patients will recur rapidly (within 1–2 days of stopping CDI antibiotics), this risk needs to be considered when determining an individual treatment window. When administering fecal microbiota spores live-brpk and fecal microbiota live-jslm, refer to the manufacturer package insert for instructions.
  • Conventional FMT should be performed with appropriately screened donor stool.17,18
  • Conventional FMT can be delivered via multiple routes. There is insufficient evidence to recommend a specific route.

Alternatives to fecal microbiota–based therapies:
  • A vancomycin taper, tapered-pulsed fidaxomicin, or bezlotoxumab are reasonable alternative therapies to prevent recurrent CDI in patients who are not interested in fecal microbiota–based therapies.



Fecal Microbiota-Based Therapies for Select Gastrointestinal Diseases

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