Ottawa, Listeria, Genome Sequencing, and some pretty pictures. What more could you want?

Recently, I found myself in Ottawa, a city best known as Canada’s capital, and notorious for being picturesque, quiet, and freezing cold half of the year. It’s also a city I’ve spent surprisingly little time in, given that my salary is currently funded by an agency headquartered there, and that I grew up only a couple of hours’ drive away. Ottawa is also full of attractive buildings, including some in an endearing Gothic style of architecture that appears to particularly nice effect in the post-dawn light of a winter morning.

Parliament’s East Block and the National War Memorial.

However, I was really there for a workshop about the food-borne pathogen, Listeria monocytogenes, jointly hosted by Genome Canada and the Canadian Food Inspection Agency. The session brought together scientists from a truly astonishing diversity of government agencies, the private sector, NGO’s, and academia, for a day of facilitated discussion. And with good reason – Listeria “mono”, as the experts frequently call it, can make you very sick – with a reported mortality (yes, I did say “mortality”, as in “kills you”) of 20-30% in some cases. It was also the cause of death of twenty-two people during a 2008 outbreak traced to cold cuts produced in Toronto by Maple Leaf Foods, which you can read about here. One of the speakers outlined in a very nice talk the extensive testing and monitoring now undertaken by the company, as a direct result of that tragic event.

Suburban Ottawa, from the air. It looks cold, because it is cold.

Listeriosis is still a potential problem for the food industry, and recent outbreaks of other pathogenic bacteria in Germany and the United States have focused attention in this country back on this unpleasant bug. The meeting was framed around the application of new genomic technologies (primarily “next-generation”, or high-throughput, genome sequencing) to the detection and typing of the various Listeria species and sub-strains, which explains my presence. Currently, detection is by well established microbiological methods (homogenize, culture, plate, select and/or screen), a point that was reinforced in talks by a number of speakers from both government and industry.

But the real eye-opener for a somewhat up-to-date molecule hacker like myself was the description of current methods for species and strain identification. The state of the art is chopping up the bacterial chromosome with a restriction enzyme, followed by fragment separation on a pulsed-field gel to form a diagnostic pattern of large DNA fragments. And while this has been effective, resulting in the establishment of very useful reference databases, I couldn’t help but feel a little déja vu. The last time I ran a pulsed-field gel was in 1996. When ten years later I suggested to some colleagues at my current place of work that they could use this approach to sort out some thorny mapping issues in ugly regions of the human genome, I was almost laughed out of the room. This is old, old technology.

Another speaker from a nearby university outlined a more modern method using multiplexed simple sequence repeat markers (also referred to as “short tandem repeats”, or STR’s, or by older folks such as myself as “microsatellites”). These are tiny bits of repeating DNA sequences that in humans vary between individuals, and in Listeria vary between strains. It’s a symptom of the state of the testing industry that some in the audience seemed skeptical of this “new technology”, while others muttered darkly about how they were doing this in the mid-1990’s. Not naming any names, of course.

But that’s par for the course in a highly-regulated industry, and even modern hospital laboratory diagnostics are not fully caught up to the advances in “research world” – as well they shouldn’t be. It takes time to translate cutting-edge approaches into robust and validated clinical tests, and even longer to have them broadly adopted by agencies with limited budgets, differing regulatory requirements, potentially complicated funding and reimbursement schemes, and varying mandates. But there were encouraging talks too, emphasizing that some of our government agencies, in particular the National Microbiology Laboratory of the Public Health Agency of Canada, have been using high-throughput sequencing for research projects, and were in fact a very early adopter of the technology. Notably, NLM sequenced the H1N1 viral genome in response to the 2009 influenza outbreak, and continues to apply it to various other projects within their mandate. One point of this workshop was to bring other centres with considerable capacity and expertise, such as the Genome Canada Science and Technology Innovation Centres, to the table, and to identify research gaps, industry needs, and potential synergies between the various stakeholders. As a side benefit, I learned a lot about an organism I was only passingly familiar with. And in all of this, I’d say the meeting, as a start, was a success.

This photograph of the Rideau Falls was a success, too. It’s the first time I’ve done a long-exposure shot of moving water. Taken long after dark in freezing cold weather, using a tripod borrowed from my good friend Markus.