Fecal microbiota transplantation (FMT)

Policy context

Fecal microbiota transplantation (FMT) is a procedure whereby donor fecal matter is placed into a patient's gastrointestinal system in order to recolonize it with normal gut bacteria that have been killed or suppressed. Primary use is to treat individuals with difficult to treat infections caused by Clostridium difficile (C. difficile). Frozen stool from healthy donors is transplanted to the infected individual's bowel to restore the normal balance of bacteria in the gut. Concerns are considered medium for safety, high for efficacy, and low for cost-effectiveness.

Status: Decision completed

Primary criteria ranking

  • Safety = Medium
  • Efficacy = High
  • Cost = Low

Assessment timeline

  • Draft key questions published: May 3, 2016
  • Public comment period: May 4 to 17, 2016
  • Final key questions published: June 6, 2016
  • Draft report published: August 18, 2016
  • Public comment period: August 19 to September 19, 2016
  • Final report published: October 14, 2016
  • HTCC public meeting: November 18, 2016


Clostridium difficile infections have become increasingly common in the US in recent years. The number of diagnoses doubled between the years 2001 and 2005,3 and it is currently estimated that C. difficile infects nearly 500,000 people and causes 15,000 deaths every year in the US, 80% of which occur in persons aged 65 years and older.6,7 At the same time, infections have become more severe and difficult to treat, and the FDA currently recognizes C. difficile infections as one of the highest drug-resistant threats in the US.6 The condition typically impacts older persons, particularly those who are hospitalized or in nursing home facilities, although younger persons are also at risk. The bacteria spread via fecal-to-mouth transmission, and infections most commonly impact patients who have received recent treatment with antibiotics (which disrupts the normal gut flora) and were exposed to the bacteria.3 Other risk factors include hospitalization, older age, proton pump inhibitor use, immunosuppression, and chronic kidney disease.3,5 Upon colonization of C. difficile in the colon, toxin is produced and leads to inflammation.3 Symptoms include severe diarrhea, fever, and abdominal pain; if inadequately treated, dehydration, kidney failure, and death may result.3,7 The infection is typically treated with the antibiotics metronidazole, vancomycin, or fidamoxin, with metronidazole and vancomycin being first-line antibiotics, vancomycin used for more severe illness, and fidamoxin typically reserved for recurrent infection.3 However, approximately 20% to 60% of patients have recurrence after antibiotic treatment,5,7,8 and those who develop multiple recurrences become increasingly resistant to antibiotic treatment.3

Fecal microbiota transplantation (FMT) is a treatment alternative for C. difficile infections, particularly those that are recurrent or resistant to standard antibiotic therapy.3,5 Although this treatment has been used for centuries, it has only recently to gained traction in the medical community.5 Infusion of feces from a healthy donor into the gastrointestinal tract of the infected person is thought to restore normal gut flora, which will aid in elimination of C. difficile.3,5 Prior to infusion, the donor feces is screened for transmissible diseases (e.g., HIV, hepatitis, etc.).2 Transplantation can be performed via nasogastric tube, colonoscopy, or enema; and fecal material may be either fresh or frozen.2,4,9,11 It has been suggested that FMT is an effective treatment for C. difficile infections, and that the majority of patients recover after only one procedure.2,4,5 Other conditions for which FMT use is being explored are varied, and include inflammatory bowel disease, ulcerative colitis, and Crohn's disease.4 However, while current FDA regulations permit use of FMT for treating C. difficile infections that have not responded to standard antibiotic therapy, use of FMT for any other indication requires submittal and approval of an IND (investigational new drug) application to the FDA.1,10

The primary aim of this assessment is to systematically review and synthesize evidence on the efficacy, safety, and cost-effectiveness of FMT for C. difficile infections and inflammatory bowel disease.