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Dr. Jeanne Keegan-Henry is pictured in a laboratory in Burnaby General Hospital in Burnaby, British Columbia on April 16, 2014.Ben Nelms/The Globe and Mail

Since Fraser Health scrapped a pilot project last spring that would have provided fecal transplants at two Lower Mainland hospitals, at least one patient got so sick with C. difficile that part of her bowels needed to be surgically removed.

Health Canada's continued position of restricting fecal transplants to clinical trials – and Fraser Health's decision to spike the program – means many patients are being denied what could be a life-saving treatment, says Jeanne Keegan-Henry, a Burnaby physician who championed the pilot project until feedback from the federal department resulted in Fraser Health putting it on hold.

"Fraser Health tried really hard to get this flying because they thought it could save lives," Dr. Keegan-Henry said Monday in an interview. "Because they thought it could save lives and it made sense from any point of view that we could all think of … nobody who is a scientist and a clinician is claiming any more that fecal transplants are not a good idea."

On Friday, Surrey Memorial Hospital informed staff that the hospital is experiencing "unprecedented" congestion due to high volumes of patients with C. difficile and other infections of influenza, CPE (carbapenemase-producing enterobacteriaceae) bacteria and respiratory conditions. At least three patients had C. difficile, which prompted the hospital to declare an outbreak and trigger infection-control protocols, which included enhanced cleanings and the grouping together of C. difficile patients.

While that outbreak is relatively minor and was quickly contained, the return of the potentially deadly superbug – whose symptoms include abdominal pains, fever, loss of appetite and nausea – highlights the difficult position that doctors backing the therapy find themselves in. A fecal transplant – often given like an enema – transfers feces from a healthy person into a sick one and is thought to work by reintroducing "good" bacteria. Several studies, including one from the renowned Mayo Clinic, have shown the quick and inexpensive therapy to have a 90-per-cent cure rate.

Health Canada declined to make a spokesperson available for an interview on Monday. In an e-mailed statement, spokesman Eric Morrissette said the department considers fecal therapy to be a drug and, as with all new drugs, must go through a series of controlled clinical trials as part of a research phase.

"The active ingredient is not the feces itself but rather the human microbiota contained in the feces," Mr. Morrissette wrote. "Researchers are just beginning to understand the important role that human microbiota (meaning bacteria that colonize the skin, gut and other tissue surfaces) appear to play with respect to human health."

There are currently six clinical trials for fecal therapies that have been authorized by Health Canada.

Authorities have wrestled with the question of how to regulate fecal transplants.

In March, 2014, the National Institute for Health and Care Excellence (NICE), which provides quality guidelines for the National Health Service in Britain, issued a directive that fecal transplants were "safe and effective enough for doctors to use it with normal safeguards in place, but should only be considered for people who experience persistent C. difficile infections and in whom antibiotics have failed."

In announcing the new guideline, a NICE spokesman said the transplant procedure "doesn't sound pleasant, but the evidence shows that it is safe and effective for four in five people with recurrent C. difficile infections."

Dr. Keegan-Henry, now semi-retired, said she has given up the fight to launch a project at Fraser Health and would be unwilling to participate in a clinical trial even if the health authority were to launch one.

"It is ethically unsupportable," she said, adding that a 2013 trial reported in the New England Journal of Medicine was halted after early results indicated a markedly higher success rate for fecal therapy over conventional antibiotics.

"How could I justify running another trial, where you are saying to people, 'You are at death's door, there's a 50-50 chance I'll give you a placebo.' How could I do that?"

In the U.S., the Food and Drug Administration classifies fecal microbiota transplant, or FMT, as an investigational drug – which typically requires an Investigational New Drug application, or IND. But in 2013, the FDA said it would use "enforcement discretion" for doctors using the procedure to treat patients with recurrent C. difficile, clearing the way for them to provide fecal transplants as long as they obtained patients' informed consent that the process was investigational.

In 2012, eight physicians at Burnaby Hospital signed a letter asserting that 84 patients had died – and hundreds more had suffered serious complications – after outbreaks of C. difficile at the hospital between 2009 and mid-2011. The doctors criticized the health authority's infection and control programs, saying infection rates were two or three times the national average.