Risk of Clostridium difficile Infection with Systemic Antimicrobial Therapy Following Successful Fecal Microbiota Transplant: Should We Recommend Anti-Clostridium difficile Antibiotic Prophylaxis?

  • Jessica R. AllegrettiEmail author
  • Dina Kao
  • Emmalee Phelps
  • Brandi Roach
  • Justin Smith
  • Vincent C. Ganapini
  • Zain Kassam
  • Huiping Xu
  • Monika Fischer
Original Article



The risk of a new Clostridium difficile infection (CDI) after FMT is unknown if non-CDI antibiotics are required. It is uncertain if anti-CDI prophylaxis or probiotics would reduce risk. We therefore aimed to compare the risk of CDI with and without antibiotic exposure and the benefit of concomitant anti-CDI antibiotic or probiotic prophylaxis.


This is a multicenter retrospective study carried out at three large FMT referral centers of patients who underwent FMT for recurrent CDI. Patients were assessed for antibiotic use, as well as concomitant use of prophylactic anti-CDI antibiotics or probiotics. Time to CDI recurrence after FMT was evaluated using the Kaplan–Meier method.


A total of 404 patients were included: 63% were females, with a mean age of 61.3 ± 18.8 years. Mean length of post-FMT follow-up was 18.1 ± 11.9 months (range 2.2–45.2). Among the entire cohort 8.1% (n = 33) experienced a CDI recurrence. Overall, 111 patients (27.4%) used a non-CDI antibiotic, of which 16.2% (n = 18) experienced a CDI recurrence. Patients who used non-CDI antibiotics were more likely to develop CDI (HR 8.44, 95% CI 4.21–16.93, p < 0.001). The risk of CDI recurrence was not different between patients who received anti-CDI antibiotic prophylaxis to those who did not (HR = 1.88, 95% CI 0.72–4.86, p = 0.2); however, probiotic prophylaxis was associated with a greater risk of CDI recurrence (HR = 2.65, 95% CI 1.02–6.86, p = 0.045).


Non-CDI antibiotic use was not uncommon after successful FMT and significantly increased the risk of a new episode of CDI. In this study, we found that the prophylactic use of anti-CDI antibiotics or probiotics was not protective.


Fecal microbiota transplantation Clostridium difficile infection Systemic antibiotic C. difficile recurrence prevention FMT 


Author’s contribution

JRA, DK, and MF initiated the study concept and design; participated in acquisition, analysis, and interpretation of the data; and critically revised the manuscript. JRA drafted the manuscript. VCG, EP, JS, and BR participated in acquisition and interpretation of the data. HX performed data analysis, interpretation of data, and critical revision of the manuscript. ZK contributed to the interpretation of data and critical revision of the manuscript.

Compliance with ethical standards

Conflict of interest

ZK is employed by and has equity in Finch Therapeutics Group. JRA and MF consult for Finch Therapeutics. No other conflicts of interest to report for any authors relevant to the work presented in this manuscript.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Jessica R. Allegretti
    • 1
    Email author
  • Dina Kao
    • 2
  • Emmalee Phelps
    • 3
  • Brandi Roach
    • 2
  • Justin Smith
    • 2
  • Vincent C. Ganapini
    • 3
  • Zain Kassam
    • 5
  • Huiping Xu
    • 4
  • Monika Fischer
    • 3
  1. 1.Division of GastroenterologyBrigham and Women’s HospitalBostonUSA
  2. 2.Division of Gastroenterology, Zeidler Ledcor CentreUniversity of AlbertaEdmontonCanada
  3. 3.Division of Gastroenterology and HepatologyIndiana UniversityIndianapolisUSA
  4. 4.Department of Biostatistics, The Richard M. Fairbanks School of Public Health and School of MedicineIndiana UniversityIndianapolisUSA
  5. 5.Finch Therapeutics GroupSomervilleUSA

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