The clinical use of fecal microbiota for transplantation (FMT) has the potential to transmit monkeypox virus, according to the Food and Drug Administration (FDA).

The FDA is alerting health care providers and patients about the potential risk and the need for additional safety protections after recent studies showed the presence of monkeypox virus DNA in rectal swabs and/or stool samples from infected individuals. 

In a retrospective study published in Nature Medicine, researchers detected positive samples of monkeypox virus DNA in rectal swabs from 3 asymptomatic individuals, including 2 individuals who had viable monkeypox virus isolated from rectal swabs. While the risk of transmission is unknown, study data suggest that monkeypox virus may be transmitted through FMT products.

FMT is an experimental therapy used in patients with Clostridioides difficile infection that has not responded to standard treatments. Studies have suggested that the use of fecal microbiota collected from healthy individuals can restore intestinal flora in patients with refractory C. difficile infection.

To reduce the risk of monkeypox virus transmission and serious adverse events, the FDA has determined that additional protections are needed for any investigational use of FMT, whether used as part of a study under an Investigational New Drug Application (IND) on file with the FDA or otherwise, if it involves stool donated on or after March 15, 2022. 

These protections include identifying donors who are at high risk for monkeypox, may currently be infected, or were recently infected. Investigators should develop criteria for exclusion of donors and donor stool based on donor screening.

Additionally, patients should be informed about the potential for transmission of monkeypox virus through FMT, including FMT prepared from stool obtained from donors who were asymptomatic for monkeypox. At this time, there is limited information on the availability and sensitivity of direct testing of stool for monkeypox virus.

The FDA encourages all health care providers and patients to report suspected adverse events related to FMT products to the MedWatch Adverse Event Reporting program.


  1. Safety alert regarding use of fecal microbiota for transplantation and additional safety protections pertaining to monkeypox virus. News release. US Food and Drug Administration. Accessed August 23, 2022.
  2. De Baetselier I, Van Dijck C, Kenyon C, et al. Retrospective detection of asymptomatic monkeypox virus infections among male sexual health clinic attendees in Belgium. Nat Med. Published online August 12, 2022. doi:10.1038/s41591-022-02004-w