The Efficacy and Safety of Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection: Current Understanding and Gap Analysis
Mark H. Wilcox,1,2 Barbara H. McGovern,3, and Gail A. Hecht4,5
1 Department of Microbiology, Old Medical School, Leeds Teaching Hospitals NHS Trust, Leeds, UK, 2 University of Leeds, Leeds, UK, 3 Seres Therapeutics, Medical Affairs, Cambridge, Massachusetts, USA, 4 Department of Medicine, Division of Gastroenterology, Loyola University Chicago, Chicago, Illinois, USA, and 5 Department of Microbiology and Immunology, Loyola University Chicago, Chicago, Illinois, USA The leading risk factor for Clostridioides
Abstract: The leading risk factor for Clostridioides (Clostridium) difficile infection (CDI) is broad-spectrum antibiotics, which lead to low microbial diversity, or dysbiosis. Current therapeutic strategies for CDI are insufficient, as they do not address the key role of the microbiome in preventing C. difficile spore germination into toxin-producing vegetative bacteria, which leads to symptomatic disease. Fecal microbiota transplant (FMT) appears to reduce the risk of recurrent CDI through microbiome restoration. However, a wide range of efficacy rates have been reported, and few placebo-controlled trials have been conducted, limiting our understanding of FMT efficacy and safety. We discuss the current knowledge gaps driven by questions around the quality and consistency of clinical trial results, patient selection, diagnostic methodologies, use of suppressive antibiotic therapy, and methods for adverse event reporting. We provide specific recommendations for future trial designs of FMT to provide improved quality of the clinical evidence to better inform treatment guidelines.
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The US Food and Drug Administration (FDA) yesterday issued a safety alert about the potential risk of serious, even life-threatening, infections linked to fecal microbiota transplantation (FMT) after six patients were infected with diarrhea-causing Escherichia coli following the procedure. March 13, 2020
According to the alert, two patients developed enteropathogenic E coli (EPEC) infections, and four developed Shiga toxin–producing E coli (STEC), after receiving FMT for Clostridoides difficile infection. Four of the six patients required hospitalization.
“FDA is informing patients and healthcare providers of the potential risk of transmission of pathogenic bacteria by FMT products and the resultant serious adverse reactions that may occur,” the agency said. “Patients considering FMT for the treatment of C. difficile infection should speak to their health care provider to understand the associated risks.”
STEC is a pathogenic form of E coli that causes abdominal pain, bloody diarrhea, vomiting, and mild fever. EPEC generally doesn’t cause any symptoms, but some strains can cause diarrhea.
Change in screening protocols
The stool used in the procedures all came from Boston-based OpenBiome, the country’s largest stool bank. The company said in a press release yesterday that the cases are the first reports of likely transmission of pathogens by FMT involving stool that came from OpenBiome, which has shipped more than 50,000 FMT treatments to physicians since 2013.
The patients who developed the infections received FMT product prepared from three OpenBiome donors. The two patients who developed EPEC infections were treated with stool from two donors, and the six STEC patients received stool from one donor. OpenBiome says all unused material from the donors has been destroyed.
The FDA says bacterial isolates from the patients’ stools are not yet available to determine if the STEC or EPEC organisms are genetically identical to the organisms from the stool donors—a finding that would confirm that the donor stool was the source of the infection.
In response to the safety alert, OpenBiome says it is immediately implementing changes to its screening program in collaboration with the FDA.
While the company has previously screened donor samples for STEC via enzyme immunoassay, and says the donor involved in the STEC cases tested negative at all screens, OpenBiome will add polymerase chain reaction (PCR) testing for STEC to its screening process. PCR tests on retained donor samples conducted after Openbiome was notified of the infections were found to be positive for STEC.
The retained stool samples from the donors linked to the EPEC infections were found to be positive for EPEC upon further testing from OpenBiome. The company says it has not previously screened donors for EPEC, a position based on international and national guidelines, but will immediately implement EPEC screening by PCR into its donor screening protocol.
“In addition to updating and implementing STEC and EPEC screening into our quality and safety protocols, OpenBiome is also working with FDA to implement retrospective screening of units to ensure that available material meets these new standards,” the company said.
After reporting the infections to the FDA, OpenBiome received information that two additional FMT recipients who received stool from the donor linked to the STEC infections had died. The company said in an update today that the treating clinician for one of the patients determined that the patient had died from underlying cardiac causes, and testing for STEC was not performed. In the second case, testing of donor material was negative for STEC.
“Therefore, it was determined that the death was unrelated to STEC,” the company said.
FMT safety issues
FMT has been found in several studies to be a highly effective treatment for recurrent C difficile infections that aren’t responding to antibiotics, and at least 10,000 FMT procedures for recurrent C difficile are performed each year. FMT is also being investigated for treating other conditions in more than 300 trials.
The idea behind the procedure is to introduce healthy bacteria from a donor into the gut microbiome of a sick recipient and restore the balance between good and bad bacteria.
But this is the second safety alert issued by the FDA regarding FMT. In June 2019, the agency warned of the potential for dangerous infections after two FMT patients developed drug-resistant bloodstream infections and one died, and the agency halted a number of FMT trials until additional screening measures could be put in place. A subsequent paper in the New England Journal of Medicine revealed that the two patients, both of whom were enrolled in clinical trials at Massachusetts General Hospital in Boston, had extended-spectrum beta-lacatamase (ESBL)-producing E coli in their blood.
The two patients had both received stool from Mass General that came from the same donor. While the hospital had screened the stool for C difficile and the presence of drug-resistant pathogens by the hospital, it had not screened it for ESBL-producing E coli. The authors of the paper could not conclusively attribute the infections to FMT, but suspected the patients likely acquired the pathogen from the procedure.
Important Safety Alert Regarding Use of Fecal Microbiota for Transplantation and Risk of Serious Adverse Reactions Due to Transmission of Multi-Drug Resistant Organisms
The Food and Drug Administration (FDA) is informing health care providers and patients of the potential risk of serious or life-threatening infections with the use of fecal microbiota for transplantation (FMT). The agency is now aware of bacterial infections caused by multi-drug resistant organisms (MDROs) that have occurred due to transmission of a MDRO from use of investigational FMT.
Summary of the Issue
Two immunocompromised adults who received investigational FMT developed invasive infections caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E.coli). One of the individuals died.
FMT used in these two individuals were prepared from stool obtained from the same donor.
The donor stool and resulting FMT used in these two individuals were not tested for ESBL-producing gram-negative organisms prior to use. After these adverse events occurred, stored preparations of FMT from this stool donor were tested and found to be positive for ESBL-producing E. coli identical to the organisms isolated from the two patients.
Information for Health Care Providers and Patients
In July 2013, FDA issued guidance stating that it intends to exercise enforcement discretion under limited conditions regarding the IND requirements for the use of FMT to treat Clostridium difficile (C. difficile) infection in patients who have not responded to standard therapies. The guidance states that FDA intends to exercise enforcement discretion provided that the treating physician obtains adequate consent for the use of FMT from the patient or his or her legally authorized representative. The consent should include, at a minimum, a statement that the use of FMT to treat C. difficile is investigational and a discussion of its potential risks. FDA is informing members of the medical and scientific communities and other interested persons of the potential risk of transmission of MDROs by FMT and the resultant serious adverse reactions that may occur.
Patients considering FMT to treat C. difficile infection should speak to their health care provider to understand the potential risks associated with the product’s use.
Additional Protections for Investigational Use of FMT
Because of these serious adverse reactions that occurred with investigational FMT, FDA has determined that the following protections are needed for any investigational use of FMT:
Donor screening with questions that specifically address risk factors for colonization with MDROs, and exclusion of individuals at higher risk of colonization with MDROs.
MDRO testing of donor stool and exclusion of stool that tests positive for MDRO. FDA scientists have determined the specific MDRO testing and frequency that should be implemented.
Reporting Adverse Event
FDA encourages all health care providers administering FMT products to report suspected adverse events to the FDA at 1-800-FDA-1088 or http://www.fda.gov/medwatch.
June 13, 2019