One person has died after receiving a fecal transplant containing drug-resistant bacteria, the Food and Drug Administration announced Thursday.

The FDA is warning health care providers that the use of the so-called fecal microbiota for transplantation (FMT) can lead to serious or life-threatening infections.

Two patients with weakened immune systems who received FMT from the same donor developed serious infections, the FDA said. One patient died.

The FDA noted that the donor stool had not been tested for the drug-resistant bacteria, called extended-spectrum beta-lactamase (ESBL)-producing E. coli, prior to the transplantation. After the illnesses and death occurred, however, a stored preparation of the donor stool was tested, and found to be positive for the identical strain of bacteria found in the two patients.

The FDA statement does not specify why the patients received the fecal transplants. However, the procedure is most commonly used to treat a difficult-to-treat bacterial infection called C. difficile, which causes severe diarrhea.

C. diff infections kill 29,000 Americans a year and make 450,000 sick in the United States alone, according to the Centers for Disease Control and Prevention.

No standardized protocol

The treatment involves obtaining stool from a healthy donor, and transplanting a processed version of that stool into the patient. The collection of bacteria found in the healthy stool — called the microbiota — repopulate the colon of the patient, and essentially crowd out the infectious bacteria.

While the FDA offers guidance on the procedure, there is not a standardized protocol for what infectious agents donors and their stool should be tested for, said Dr. Sahil Khanna, a gastroenterologist at the Mayo Clinic who performs fecal transplants.

In response to the two cases, the FDA said that protections, including screening donors and stool for multi-drug resistant bacteria, are needed.

Khanna called the patient death from a fecal transplant "heartbreaking." He told NBC News that Mayo Clinic was not involved with the two cases described by the FDA.

To Khanna's knowledge, this is the first report of a death linked to FMT.

"When we talk about FMT for treating C. diff, we say it has the potential to save lives," he said. Indeed, a small study published last year in the New England Journal of Medicine found that FMT works as well as antibiotics to treat the condition.

The use of fecal transplants for C. diff is a relatively new procedure — Mayo Clinic started performing them in 2012 — and the long-term risks and benefits are still unknown, Khanna said. In 2017, the American Gastroenterological Association started a registry that aims to track 4,000 patients for a decade after receiving FMT to study the short- and long-term effects.

Khanna said that he hopes to get more details about the two patients, including why the procedure was performed and how immunocompromised they were. Many clinical trials looking at FMT for C. diff specify that immunocompromised patients should not be included, he added.

"It's very important to do a good job of counseling patients" about the risks and benefits of FMT, Khanna said.

FOLLOW NBC HEALTH ON TWITTER & FACEBOOK