Jacques Lapointe said in a report that the failure to take basic precautions while cleaning up the waste of patients infected with the bacteria was part of "a poor culture of infection prevention" at the Cape Breton District Health Authority.
"Cleaning (bedpans) in a separate location from patient rooms is a basic infection prevention and control practice which helps to limit the spread of disease," says the report.
The audit cites poor handwashing practices, staff using high-pressure water sprays that splashed germs around, and one instance of an infected female patient rolling her wheelchair into communal areas of a hospital.
The hospital in Glace Bay and the Cape Breton Regional Hospital in Sydney had deadly outbreaks of the bacteria last year.
The first outbreak of patients suffering the painful intestinal cramps and diarrhea that come with the illness happened at both facilities in February 2011. The second outbreak occurred on two units at the Cape Breton Regional Hospital in December 2011 and lasted until February.
The health authority says that four patients died due to the illness in the first outbreak, and one death occurred in the second outbreak.
Lapointe's report looked at the hospital procedures from April 2009 until June 2011 and relied heavily on two reports done by the Health Department's infection prevention and control unit.
The auditor says he's concerned that lax procedures, such as the failure to clean bedpans in a separate room, were identified in the first outbreak, yet staff went back to doing the same things in the months that followed.
"Poor practices which were corrected during the original outbreak and then relapsed may have contributed to the second outbreak," says the report.
The health authority says in the report that three of the patients infected with C. difficile in the second outbreak at the Cape Breton Regional Hospital were in one room. A spokesman for the health district said in an email that one of those patients died from C. difficile after becoming ill.
Lapointe had harsh words for hospital managers at a news conference.
"Cape Breton's leadership needs to demonstrate leadership by acting quickly and decisively to address these issues," he said.
John Malcom, who retires this week as the district's chief executive, said the hospital has accepted and adopted the auditor's recommendations, and he has personally apologized to the families of the patients.
"We acknowledge that C. difficile got a hold of our facilities for a variety of reasons including the overuse and misuse of antibiotics, and the fact that our cleaning practices were not effective," he said in a telephone interview.
"We accept and have acknowledged our failures here and have apologized and expressed our sorrow to the families."
He said the families reactions have ranged from anger to acceptance that the hospital has done its best to reform its practices, which includes hiring more staff to oversee infection prevention.
Malcom said the hospital should have done an internal report on the outbreaks and then ensured that all staff were aware of the new cleaning practices that were recommended.
The report also directs some criticism at the Health Department, saying it should have done more to ensure that its recommendations were followed up after the first outbreak.
"Three years after establishing Infection Prevention and Control Nova Scotia, the department ... is not adequately monitoring infection prevention and control practices in Nova Scotia hospitals," wrote Lapointe.
Andrew Younger, the Liberal party's health critic, slammed the government for failing to follow up.
"We need to have answers on why the Department of Health isn't ensuring compliance in all of these district health authorities," he said.
Lapointe also noted there is no provincial surveillance system for hospital acquired infections.
Health Minister Maureen MacDonald said her department will make it mandatory for health districts to report infections to the province's infection prevention unit, adding that legislation was brought in several weeks ago requiring mandatory reporting.
"We recognize we need to improve the accountability of the district health authorities to the Department of Health and we've moved in that direction," she said.