Researchers from the Henry Ford Hospital found that 43 of 49 patients recovered swiftly after treatment and had no adverse complications from C diff infection three months later.
C diff or Clostridium difficile occurs in patients taking antibiotics, and can spread from person-to-person contact or from touching contaminated equipment and objects like door knobs.
Patients with a C diff infection are typically treated with the antibiotics metronidazole or vancomycin.
However, surgery could be required to remove the infected part of the intestines.
In its study, Henry Ford treated patients between May 2010 and June 2012 with a therapy called intestinal microbiota transplantation (IMT), using donated stool from a healthy family member.
Mayur Ramesh, a Henry Ford Infectious Diseases physician and senior author of the study, said the treatment, while appearing unconventional, has striking results.
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"More than 90 per cent of the patients in our study were cured of their C diff infection," Ramesh said in a statement.
"This treatment is a viable option for patients who are not responding to conventional treatment and who want to avoid surgery," Ramesh added.
Ramesh said the healthy stool, when mixed with warm tap water and administered, helps to re-establish the normal intestinal flora in the patient's gastrointestinal tract.
Intestinal flora is healthy bacteria that stimulates the immune system and aids the digestion and absorption of food.
"Patients who receive treatment through a nasogastric tube don't taste or smell the stool mixture as it's administered. Patients often resume their diet within a couple hours and are feeling better within 24 hours," he said.
Of the 49 patients, 43 fully recovered, four died of causes unrelated to C diff, one had intestinal surgery and one had no improvement.
The study will be presented at the annual Infectious Diseases Society of America meeting in San Diego.