The bacteria that cause C. diffLois S. Wiggs / CDC

For the past several years, the U.S. Food and Drug Administration has been trying to figure out how to regulate human feces.

Fecal transplants are an almost miraculously effective cure for a gut infection called C. diff. The microbes in the stool of a healthy donor repopulate the gut microbiome of a sick patient. But some of those microbes could be dangerous. This month, hypothetical concerns became real when the FDA issued a warning: An immunocompromised patient died after acquiring drug-resistant bacteria from a stool donor.

The death was the first of its kind ever recorded, out of tens of thousands of fecal transplants, and it could very well become a flash point in the battle over regulation. “This is an unintended consequence that the FDA’s really been waiting for, because they’ve had concerns for a long time,” said Colleen Kraft, a microbiologist at Emory University. Kraft spoke on a panel at Aspen Ideas: Health, which is co-hosted by the Aspen Institute and The Atlantic.

The FDA’s concerns have been evident since it originally proposed to regulate fecal transplants like drugs. Back in 2013, the agency suggested that doctors performing the procedure would need to file an Investigational New Drug Application—a step that critics said would be so burdensome that it would prevent doctors from offering the life-saving procedure and drive desperate patients to do it themselves with a blender and enema bottle.

“I have at least three more patients in the process of preparing for [a] self-administered fecal transplant at home,” a doctor wrote in 2013. “These patients are highly motivated, know the data on effectiveness, and won’t be told no!”

Backlash was so fierce to the FDA’s suggestion that the agency backed off a month later, saying that it would exercise “enforcement discretion” while working toward a final decision on how to regulate fecal transplants. This essentially gave doctors the go-ahead to keep doing that they’re doing—until something changes.

But now, the newly reported death will likely lead to a clampdown on donors, Kraft told me. The donor for the patient who died was carrying an antibiotic-resistant bacterium called extended-spectrum beta lactamase–producing Escherichia coli, which normally does not sicken healthy people but can be fatal in patients with already weakened immune systems, such as in this recent case.

The role of this bacterium doesn’t come as a huge surprise. OpenBiome, a nonprofit stool bank, already screens for ESBL-producing E. coli along with other antibiotic-resistant bacteria. But individual doctors can still rely on a relative of a patient or find other donors outside of stool banks, and screening practices differ. (OpenBiome did not provide the sample in the fatal case, and the FDA has not made public any further information about the donor or where the procedure was done.)

The FDA is expected to issue its final guidance on fecal transplants very soon. The decision will clear up whether the agency considers fecal transplants to be like drugs; human tissue, such as blood and organs; or an altogether new category of its own.

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