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Ottawa has finally named a new chief public health officer after leaving the country's most important public health post vacant for nearly 16 months.

The Public Health Agency of Canada announced Wednesday that it has elevated Gregory Taylor, the former deputy chief public officer, to the top job, effective immediately.

Dr. Taylor had been serving in the role on an interim basis since his predecessor, David Butler-Jones, suffered a stroke in May of 2012. Dr. Butler-Jones formally resigned in June 2013.

Since then, the Public Health Agency of Canada (PHAC) and its 2,500 staff have been without a permanent leader, a void that prompted critics to accuse Stephen Harper's government of giving short shrift to public health. The agency has a $600-million annual budget.

Now that Dr. Taylor officially has the job, he is keen to focus on keeping Ebola out of Canada, improving the overall health of Canadians and preparing for future public-health challenges, such as those that could accompany climate change.

"I have to start thinking about the next 10 years and the next decade and training and being prepared ... for those things that we don't know are going to happen yet," he said in an interview Wednesday. "For example, with some of the climate change things happening, we have West Nile virus in Canada, we have Lyme disease that's spreading. So we're not sure what's going to happen down the road."

Dr. Taylor earned his MD at Dalhousie University in Halifax and joined Health Canada's Laboratory Centre for Disease Control, one of the forerunners to PHAC, in 1995.

He rose up the ranks at PHAC to become second-in-command under Dr. Butler-Jones, the first person to hold a job that was created after the SARS crisis in 2003.

After Dr. Butler-Jones's stroke, the chief public health officer's role was divided on a temporary basis between Dr. Taylor and an assistant deputy minister, a system that Dr. Taylor called an effective stopgap. His new contract is a five-year deal.

While the chief public health officer's job went unfilled, some critics complained it was poorly paid and came with too short a government leash to attract top-shelf candidates.

The pay scale for the chief public health officer is $195,599 to $231,924. Dr. Taylor's precise salary was not disclosed.

But Dr. Taylor said the paycheque is not what motivates him to work in public health.

"If I was going in for the salary I'd have done dermatology or I'd have done plastic surgery or something like that. You don't get the opportunity to influence the health of an entire country," he said. "My salary is fine. I'm quite happy with the salary. I think it's been overplayed."

As for suggestions he would be under the thumb of the Harper government, Dr. Taylor said he has always been free to speak his mind in the past and does not expect that to change now. He dismissed suggestions that PHAC would be better off as a fully independent agency, rather than part of Health Canada.

"I can give you a hard example," he said.

When Alberta announced in January that a Canadian woman had become the first North American to die of H5N1 flu after returning from China, he recommended officials make public details about the flights she had been on.

"We gave the flight numbers, the dates, etc. That was direct policy advice that I gave that was taken. I think, if anything, being within government makes us stronger," he said. "I've never been told what to say ... that's not been my experience whatsoever."

Another of Dr. Taylor's priorities is filling the top job at Canada's National Microbiology Lab, the Winnipeg facility that has recently gained worldwide renown for its work on Ebola treatments and vaccines.

The NML's highly respected scientific director, Frank Plummer, stepped down in March for health reasons.

There have also been concerns raised about the pay for that job, which ranges between $132,600 and $155,900.

Dr. Taylor said PHAC has a short list of candidates it intends to start interviewing next week. More than 20 people applied, he said.

He hopes to name Dr. Plummer's replacement by the end of October.