Infections & antibiotics

Treating C. difficile when you already have colitis

Which antibiotic, and for how long. Whether your inflammatory bowel disease drugs stop while you take it. What happens if it comes back — and the transplant that treats the infection but not the disease.

3 min read4 sources

Being treated for this while you have inflammatory bowel disease means two decisions at once. What to give for the infection, and what to do about the drugs you are already on. They are separate questions, and the second has the less settled answer.

Which antibiotic

Two drugs carry the recommendations. American and European guidelines both name them as the preferred agents for an initial episode. Metronidazole is now an alternative, for when the others are unavailable — a demotion, and a fairly recent one.

Vancomycin

by mouth, 125 mg four times daily for 10 days
for inflammatory bowel disease, the practice update advises it over metronidazole

Fidaxomicin

200 mg twice daily for 10 days
now prioritised over vancomycin for an initial episode
reduces recurrence risk at 28 days by roughly 10 to 15 percent

The reason fidaxomicin is preferred is recurrence rather than cure. Both clear the infection; one of them is less likely to have it come back within the month.

There is a second way of giving fidaxomicin, used where recurrence is the main worry. It is called an extended-pulsed course: 200 mg twice daily on days 1 to 5, then one dose every other day from day 7 to day 25. The same drug, spread thinner and longer — not a different treatment.

Do your usual drugs stop?

The instinct is that immunosuppression should pause while an infection is treated. The guidance is more careful than that. Clinicians may postpone escalation of steroids and other immunosuppressive agents during acute infection, until treatment for the infection has been started. Past that, the decision to withhold or continue should be individualised. There is insufficient robust literature to build a firm recommendation on.

If it comes back

Recurrence is more likely with inflammatory bowel disease than without: 32 percent against 24 percent in the RECIDIVISM study. It is a question worth having an answer to in advance, rather than during.

The answer that has guidelines behind it is a faecal microbiota transplant. For immunocompetent adults with recurrent infection, the American Gastroenterological Association suggests faecal microbiota-based therapies on completion of standard-of-care antibiotics, over not using them. That is a conditional recommendation, on low certainty evidence. The practice update is more direct for this group: clinicians should offer a referral for the transplant to inflammatory bowel disease patients with recurrent infection. Cure after a single transplant commonly ranges from 74 to 84 percent, rising to approximately 90 percent with repeat administration.

Where this came from

Oral vancomycin 125 mg four times daily for 10 days and fidaxomicin 200 mg twice daily for 10 days, and extended-pulsed fidaxomicin at 200 mg twice daily on days 1 to 5 then every other day from day 7 to day 25; that American and European guidelines now prioritise fidaxomicin over vancomycin for an initial episode, reducing recurrence at 28 days by roughly 10 to 15 percent; the RECIDIVISM recurrence figures; that evidence on immunosuppression is mixed and guidelines recommend individualised risk assessment; the multicentre study showing reduced adjusted odds of death, sepsis and colectomy within 90 days among those escalated after antibiotics were started; transplant cure of 74 to 84 percent after one administration and approximately 90 percent with repeats; the 22.7 percent and 4.6 percent figures for inflammatory bowel disease worsening after transplant.
Seguiti C, Tettoni E, Pezzuto E, et al., “Clostridioides difficile Infection in Special Populations: Focus on Inflammatory Bowel Disease — A Narrative Review from Pathogenesis to Management”, Biomedicines, 2025;13(11):2702
That clinicians should consider treating C. difficile infection in inflammatory bowel disease with vancomycin instead of metronidazole; that profuse diarrhoea, severe abdominal pain, a markedly increased peripheral blood leukocyte count or other evidence of sepsis warrant hospitalisation; that escalation of steroids and other immunosuppressive agents may be postponed until therapy for the infection has been initiated, while the decision to withhold or continue should be individualised given insufficient robust literature; that clinicians should offer a referral for faecal microbiota transplantation to inflammatory bowel disease patients with recurrent infection.
Khanna S, Shin A, Kelly CP, “Management of Clostridium difficile infection in inflammatory bowel disease”, American Gastroenterological Association Clinical Practice Update, 2017
That in immunocompetent adults with recurrent C. difficile infection the AGA suggests faecal microbiota-based therapies on completion of standard-of-care antibiotics, a conditional recommendation on low certainty evidence; and that the same guideline suggests against conventional faecal microbiota transplantation for ulcerative colitis, Crohn’s disease and pouchitis except in the context of clinical trials, each conditional and on very low certainty evidence.
Peery AF, Kelly CR, Kao D, Vaughn BP, Lebwohl B, Singh S, Imdad A, Altayar O, “AGA Clinical Practice Guideline on Fecal Microbiota–Based Therapies for Select Gastrointestinal Diseases”, Gastroenterology, 2024;166(3):409–434
That both the American and European guidelines recommend fidaxomicin or vancomycin as the preferred agents for an initial episode, with metronidazole relegated to alternative status when other options are unavailable.
Jones J, Pradhan A, Pizzuti ME, Bland CM, Bookstaver PB, “Is Three Company or a Crowd? Comparing and Contrasting U.S. and European Clostridioides difficile Clinical Practice Guidelines”, Antibiotics, 2022;11(9):1247