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Fecal microbiota transplantation overview addresses use in recurrent C. difficile

November 20, 2023

The gut microbiota has far-reaching impact on health and disease. Disturbances in the composition of microbial communities have been associated with a broad array of autoimmune, metabolic, cardiovascular and gastrointestinal disorders.

Thus, it is not surprising that in the past two decades, there has been an explosion of interest and research into the gastrointestinal microbial environment and potential ways of manipulating that environment.

A new AAP clinical report provides an overview of fecal microbiota transplantation (FMT) in the treatment of Clostridioides difficile infection (CDI). The report also explores the future of FMT in treating other conditions to help pediatricians provide guidance to families seeking FMT for a child.

The report Fecal Microbiota Transplantation: Information for the Pediatrician, from the Section on Gastroenterology, Hepatology and Nutrition and Committee on Infectious Diseases, is available at and will be published in the December issue of Pediatrics.

What is FMT?

FMT typically is defined as the transfer of stool from a “healthy” donor to another individual with the intent of restoring the recipient’s imbalanced microbiome to a “healthy” one to improve symptoms or cure a disease. Fecal material can be delivered in a variety of ways to the upper or lower gastrointestinal tracts. Donors need to undergo a rigorous screening process to evaluate risk of infectious diseases and history of chronic disorders.

Institutional and third-party stool banks in the United States facilitate a cost-effective, standardized and traceable process for the collection, storage and distribution of feces from screened healthy donors who are unknown to the recipient. Stool banks typically operate under the regulatory authority of the Food and Drug Administration.

Most FMTs are performed by gastroenterologists, but infectious disease specialists also perform this procedure.

Accepted CDI treatment

CDI is a major cause of hospital-associated diarrhea and is the most common infectious cause of antibiotic-associated diarrhea. The condition has been identified in children hospitalized with complex chronic conditions.

CDI is a serious public health challenge with an estimated annual burden of hundreds of thousands of cases. The incidence continues to rise in the community setting.

Although symptoms resolve in most patients, up to 30% of individuals treated for CDI experience a recurrence after discontinuation of C. difficile-directed antibiotic therapy. In those with a recurrence, the rates of further occurrences can be as high as 65%, which led to the need for alternative therapies.

In the last several decades, randomized, controlled trials, large observational studies and registries have established that FMT is 80% to 90% effective in curing CDI in adults and has a significant advantage over vancomycin and fidaxomicin.

Although there are no controlled trials in children, a large, multicenter pediatric cohort has established CDI cure rates similar to those of adults.

Is FMT safe?

Safety remains a key concern for FMT. Infectious short-term adverse reactions have been quite rare even for immunocompromised individuals. However, it’s not known whether transferring the microbiome from one individual to another will lead to long-term adverse effects.

Lack of access to a provider who performs FMT, cost and a growing preference to manage conditions at home have led individuals to perform FMTs on themselves or their children using information from the internet or social media. In these do-it-yourself (DIY) cases, recipients typically receive stool from a known donor. People may believe that FMT is “safe” because they view it as more “natural” than medications.

A clear risk in performing DIY procedures is that the donor is not screened rigorously for chronic conditions and communicable diseases.

Other microbiota-based therapies

Inspired by the success of FMT for CDI, pharmacologic alternatives to FMT have been developed. These therapeutics are well-defined mixtures of selected microorganisms designed according to their proposed roles in the microbiota against CDI.

It is anticipated that these laboratory-derived microbiota therapeutics will enable research on conditions other than CDI, given mounting evidence that alterations in microbial composition may play a role in obesity, metabolic syndrome, autism spectrum disorder, Crohn’s disease, ulcerative colitis and reduction of intestinal multidrug-resistant bacteria.

At this time, however, data are insufficient to recommend FMT for any of these indications in clinical practice, and FMT use for conditions other than CDI should be limited to the research setting.

Key points for pediatricians

  • FMT is a viable alternative for children with moderate to severe or recurrent CDI.
  • It is recommended that children be referred to centers experienced in performing this procedure.
  • DIY FMT should not be performed in children for safety reasons.
  • The field of microbial therapies is advancing quickly and includes the development of commercial products for the treatment of CDI.

Dr. Oliva-Hemker is the lead author of the clinical report. She is a former member of the AAP Section on Gastroenterology, Hepatology and Nutrition Executive Committee.

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