For those battling the dangerous and tenacious intestinal infection caused by the bacteria Clostridium difficile, fecal transplants are a relatively new treatment option. For the procedure, doctors transfer fecal matter from a healthy person into someone with a "microbiome" that is off balance.

Although the transplant has shown promise for treating C. difficile and other health issues, federal health officials recently announced that a patient died after receiving the procedure and another is seriously ill. Because of the possibility of serious infections linked to the procedure, the U.S. Food and Drug Administration (FDA) has issued a warning "to alert all health care professionals who administer FMT [fecal microbiota transplant] about this potential serious risk so they can inform their patients," said Peter Marks, M.D., director of FDA’s Center for Biologics Evaluation and Research, in a news release.

“While we support this area of scientific discovery, it’s important to note that FMT does not come without risk," Marks said.

How fecal transplants are used

The debilitating C. difficile infection usually occurs after someone has taken common antibiotics that kill normal gut bacteria. If the person is then exposed to C. difficile, which is commonly found in many hospitals, the infection can take hold. Characterized by profuse diarrhea, uncontrollable vomiting and high fever, the infection often does not respond to antibiotics.

With the emergence of increasingly toxic strains of the bacteria, a growing number of people are falling victim to the infection. More than 300,000 patients in American hospitals contract C. difficile each year, and researchers estimate that the total number of cases, in and out of hospitals, may be 3 million. It kills 14,000 people annually in the United States.

Fecal transplants have been used by doctors to treat C. difficile for years, and those who perform the treatment say that it is highly effective, but until recently, there have been no controlled studies confirming its success.

“Those of us who do fecal transplant know how effective it is,” Dr. Colleen R. Kelly, a gastroenterologist with the Women’s Medicine Collaborative in Providence, Rhode Island, told The New York Times. “The tricky part has been convincing everybody else.”

A 2013 study, conducted in the Netherlands, was published in the New England Journal of Medicine. It found that fecal transplants cured what had been recurring infections in 15 of 16 participants, whereas antibiotics cured only seven of 26 patients in two comparison groups.

The senior author of the study, Dr. Josbert Keller, a gastroenterologist at the Hagaziekenhuis hospital in The Hague, was inspired to conduct the research after performing the transplant for a number of people, with a stunning success rate.

“After the first four or five patients, we started thinking, ‘We can’t go on doing this kind of obscure treatment without evidence,’” Keller told The New York Times. “Everybody is laughing about it.”

The researchers had intended to continue the study with more people, but determined that the success was so great that it would be unethical to continue allowing the antibiotic groups to suffer. It’s assumed that the treatment works by restoring the gut’s normal system of bacteria.

And now what you’ve been waiting for: the gory details. Stool from a healthy, disease-free donor is diluted with a saline solution and then delivered to the intestinal tract by means of an enema, a colonoscope or a tube through the nose into the stomach.

Eventually, it’s hoped that researchers will be able to isolate the specific bacteria — of the thousands found in feces — are responsible for killing the infection. It may then be possible to create products that contain the correct bacteria.

Editor's note: This story was originally published in January 2013 and has been updated with new information

FDA issues warning about fecal transplants
Fighting C. difficile with antibiotics is often a losing battle, but fecal transplant is novel treatment with FDA warning.