Government labs, including the one in Winnipeg handling samples of swine flu, struggle to keep track of viruses and bacteria, a recent audit found.

The Public Health Agency of Canada document warns weak controls at federal facilities could allow harmful pathogens to go missing, or be used for less-than-scientific purposes.

“The tracking systems and processes currently in use have difficulty accounting for pathogens cultivated in the laboratory environment,” the audit says.

The agency’s findings earlier this year came as scientists at Winnipeg’s National Microbiology Laboratory were testing hundreds of samples of what now is known as the H1N1 flu virus.

Part of the problem, the audit found, is that each lab has its own way of taking stock of its germs.

“Some facilities incorporate a mixture of manual and electronic recording or tracking systems,” the audit says, “which could result in a pathogen being misplaced or become the subject of unauthorized activity.”

Theft of 'safe' Ebola from Winnipeg lab

Such was the case earlier this year when 22 vials of biological material went missing from the National Microbiology Laboratory. A former researcher at the lab swiped vials containing safe traces of the Ebola gene in January.

But officials only became aware the vials were missing in May when U.S. authorities arrested the former employee at the Manitoba-North Dakota border.

Konan Michel Yao, 42, pleaded guilty on May 22 in a Grand Forks, N.D. courtroom to a charge of "failure to present merchandise for inspection."

He was sentenced to 17 days in jail but received credit for time already served. He was also fined $500 US.

The vials apparently went unnoticed for so long because there are tens of thousands of them containing non-infectious material in the laboratory’s refrigerators and freezers.

The head of the lab, Dr. Frank Plummer, said at the time that high-level pathogens are subject to rigorous inventory and the workers who handle them are under strict security. But security isn’t as tight for non-infectious materials.

Tracking standards for pathogens needed: PHAC

The PHAC audit, dated June 25, says labs are following biosafety guidelines — but that those measures “could be enhanced.”

“Further study is required to ensure that samples [pathogens] destined for the laboratory environment are rigorously tracked from the time they are delivered to PHAC until they are transferred or destroyed,” it says.

The audit recommended the agency come up with a standard way of tracking and accounting for pathogens.

It also found the agency needs to do a better job making sure workers are assigned the proper levels of access to restricted areas and classified information.

“While there is considerable rigour in the process to control access, there is no evidence to indicate that … access levels assigned to individuals continue to be correct, and that the number of active access keys or cards corresponds to the number of individuals requiring access to any one facility.”

The PHAC didn’t respond to requests for comment.

The National Microbiology Laboratory has played a lead role in testing for the swine flu virus. Scientists at the Winnipeg lab were the first to map out sample H1N1 viruses from Canada and Mexico.

The agency’s auditors also visited the Laboratory for Foodborne Zoonoses (diseases which can jump between humans and animals) in Guelph, Ont., and two satellite labs in Alberta and Quebec.