Two patients contracted severe infections, and one of them died, from fecal transplants that contained drug-resistant bacteria, the Food and Drug Administration reported on Thursday.

As a result, the agency is halting a number of clinical trials until the researchers conducting them can demonstrate that they have procedures in place to screen donated stool for dangerous organisms, said Dr. Peter Marks, director of the agency’s Center for Biologics Evaluation and Research. In an interview, he did not specify how many trials would be suspended, but said it was “not just a few.”

Fecal transplants have come into increasing use to treat severe intestinal disorders, particularly an infection caused by a bacterium called Clostridium difficile, which can be deadly and tends to occur in hospitalized patients who have been heavily treated with antibiotics. The idea behind the transplants is to use stool from a healthy donor to restore the normal balance of bacteria and other organisms in the intestine, the microbiome.

In some cases, the transplants have worked quickly and saved the lives of patients who were wasting away with uncontrollable diarrhea. But the procedure is not approved by the F.D.A. and is considered experimental.