It's unnerving, it's invasive and it's extremely awkward to talk about, but a controversial procedure being performed at St. Joseph's Hospital in Hamilton is saving lives.

Dr. Christine Lee has been giving fecal transplants in Hamilton since 2008.

The treatment, used to treat C. difficile, involves introducing stool from a healthy donor into an infected patient's bowel, usually through an enema.

Lee, the medical director of infection prevention and control at St. Joseph's Hospital, started using the procedure to treat C. difficile cases in patients who weren't responding to regular therapy.

"We were running out of options," she said. So fecal transplants were implemented — and they have had a staggering effectiveness rate of around 90 per cent.

Proponents say it works because so-called "good bacteria" from the healthy donor's feces kills the "bad" bacteria in patients who have recurring infection and where antibiotics haven't been effective.

Growing acceptance

Lee has performed the procedure on more than 120 patients in Hamilton. "Unfortunately it's not widely offered, but it is becoming more recognized as a treatment procedure," she said.

Having another person's stool injected into your colon probably doesn't sound like anyone's idea of a good time — but Lee's patients haven't complained.

"By the time they come to me, they're desperate," she said. "They know they're either going to die or lose their colon."

"Many patients are elderly and having diarrhea for weeks to months."

The procedure takes less than five minutes to perform, and patients don't complain of any discomfort, Lee says. Health care workers at the hospital volunteer as donors, as they can easily be fully screened and tested.

C. difficile is a debilitating bacterial infection in the bowel, often caught by elderly or frail patients while they are in hospital. Patients can develop symptoms like fever, diarrhea, abdominal cramps, and inflamed colons.

Though it can be kept in check by good bacteria in the bowel, problems can arise when the superbug is treated by antibiotics such as vancomycin. The antibiotics sometimes wipe out the good bacteria but fail to completely kill the C. difficile — leaving enough of it that it later flourishes again.

"If you wipe out the normal bacteria by taking an antibiotic, then this bug overgrows and it releases a toxin which causes severe diarrhea," Dr. Mike Silverman, an internal medicine specialist from Ajax, Ont., told CBC News.

According to him, the diarrhea can become chronic day after day and month after month. "It's painful, people can't get on with their lives … and if doctors can't keep a patient hydrated and nourished, it can be deadly."

That's why Lee is so keen to advocate the procedure for cases in Hamilton.

"For patients who are not responding to normal treatment, this should really be considered," she said.

But she does so with a caution towards proper, rigorous screening.

"I would hate to see individuals trying to do this at home."