Doctor, Medical Attention, Patient Care, Medical Guidelines
The updated rules are expected to redefine and bring much-needed standardization for FMT procedures.

The Food and Drug Administration (“FDA”) has recently set guidelines on an increasingly common medical treatment: fecal microbiota transplants, or FMTs. The recent announcement comes after a patient died in June after receiving an FMT that contained drug-resistant bacteria.1 Unfortunately, up until this point, there have not been any designated procedures for screening donor fecal matter; FMT procedures are simply considered a “practice of medicine,” a designation that empowers doctors to make the best possible treatment plan for patients on a case-by-case basis. The new guidelines formalize a procedure to screen donor stool for any drug-resistant bacterium. 

Fecal microbiota transplants have been frequently used in the United States since the 1950s when doctors began transplanting the stool of healthy donors2 into patients infected with the life-threatening bacterium C. difficile. Donors are often individuals that the patient is close with, either a family member or caregiver, as their microbiome is likely to be closest to the patient’s own. Patients who have been treated with extensive antibiotics are at the highest risk for a C. difficile infection. As a patient takes consecutive courses of antibiotics, the “good” bacteria present in their digestive tract can be attacked in the process, leaving the patient susceptible to an overpopulation of C. difficile and potentially life-threatening health issues.

A healthy person has a wide range of microbiota present in their lower intestine (Figure 1). Transplanting stool that hosts a healthy and diverse range of microbiota into a sick patient can help repopulate the patient’s weakened microbiome with healthy bacteria. Doctors have found this treatment to be incredibly beneficial, with high success rates. The treatment gained popularity around the country, even though there were few clinical trials to conclusively state the efficacy of the FMT. 

Intestine Diagram, C Difficile, FMT, Health
Figure 1: Illustration of the effects of C. difficile infection and improvement following an FMT.3

As interest in the microbiome has increased, both in the medical field and in the collective health consciousness, studies have been conducted to prove the effectiveness of FMT to treat C. difficile. A study published in January 2013 in the New England Journal of Medicine showed FMT as such a successful tool in treating C. difficile that researchers stopped including new patients in the trial due to the concern that it would be unethical to have a control group that did not receive the treatment. Even so, by that point, FDA had yet to set any guidelines for doctors using FMT. Of course, many doctors already make a point to check donor stool for pathogens and choose healthy donors. The assumption was, generally, that if the donor was healthy, their stool was most likely healthy as well. 

In the month after the FMT treatment of C. difficile article had been published in the New England Journal of Medicine,  FDA stepped in for the first time. A workshop was held to decide how to best proceed with FMT, which concluded that the procedure would best operate under a drug designation. This would have allowed FDA to move the treatment through an approval process, but it would also bar the “drug” from being used outside of clinical trials.4 Many healthcare providers immediately pushed back, worried that their patients could lose access to a life-saving treatment that had been successfully utilized in mainstream medicine for over fifty years. There was further concern that designating FMT as a drug could eventually make it prohibitively expensive for low income or uninsured patients in need.

After the pushback, FDA moderately amended its decision. Instead, the agency decided to allow “enforcement discretion,” which enables doctors to use FMT outside of clinical trials for patients with C. difficile infections that did not resolve through the use of standard antibiotic treatment. This allowed doctors to continue to use a life-saving treatment but also gave FDA a way to keep track of the increasingly growing field of microbiome interventions. 

Now, with FDA’s latest announcement of guidelines around FMT, numerous concerns arise for both health care practitioners and for the general public. The death of a patient this June marks a new development in the long history of FMT. The increasing threat of drug-resistant bacteria–so-called “superbugs,”–looms large in all aspects of medicine. With these new screening protocols in place, FMT continues to move towards becoming a more regulated, controlled, and perhaps safer procedure. 

As modern medicine’s understanding of the importance of microbiome health expands, it remains to be seen if drug companies will find a way to monetize FMT as a drug. The increasing FDA involvement will put the therapy through rigorous clinical trials to better understand the ways by which the treatment can be made safer and more efficient. Even if a treatment has a history of success, there is always room for improvement. The introduction of screening to donor stool for drug-resistant bacteria could end up being just as important as the introduction of screening blood donations for hepatitis B or HIV. 


  1. Center for Biologics Evaluation and Research. “Safety Communication on Use of FMT and MDROs.” U.S. Food and Drug Administration. FDA, June 13, 2019.
  2.  American Gastroenterological Association. Accessed October 1, 2019.
  3.  American Gastroenterological Association. Accessed October 1, 2019.
  4.  “Fecal Microbiota Transplantation.” IDSA Home. Accessed October 1, 2019.



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