The mysteries of microbiology: Q&A with Professor Allison McGeer

Thursday, November 7, 2013
Prof. Allison McGeer
LMP Prof. Allison McGeer

As a microbiology and infectious disease consultant at Mount Sinai Hospital, the Department of Laboratory Medicine and Pathobiology’s (LMP) Professor Allison McGeer (MSc, MD, FRCPC) uses her background in research every day. She attended the University of Toronto for both her Master’s degree in biochemistry and her Medical Degree. She also completed a fellowship in hospital epidemiology at Yale New Haven Hospital. 

An expert during the 2003 SARS outbreak in Toronto, she is a highly-respected global authority on microbiology and infectious disease. This past summer she travelled to the Arabian Peninsula to study the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Along with international collaborators, she published a study in the New England Journal of Medicine which examined a hospital outbreak of the new virus in Saudi Arabia.

How did you become interested in microbiology and infectious diseases? I came into this area from biochemistry, and I was already familiar with and liked working in the lab. I had a Master’s degree and I’d worked for a couple of years in research, so it wasn’t difficult. I don’t know when it became microbiology and infectious diseases as opposed to something else, but I’m very happy with my current position.  

What do you like most about working in this area? The first thing that I like is the element of knowing that the microbial world is always going to be out there ahead of us. We’re always playing catch-up, and no matter how much we know about what’s going on, something new is always going to happen.

The second thing is that in laboratory medicine you can take what you’re learning and make it work better for patients today. I’m less likely to be working on things that will revolutionize patient care 30 years from now, but I can take care of patients on a day-to-day basis and prevent illnesses.

What is life like as a microbiologist and infectious disease expert? You have to like chaos. When new things happen, your day gets rearranged. For about six to eight weeks, from the beginning of May to June 2013, I only worked on MERS. When you’re dealing with outbreaks that may have global implications, time is limited and you want to get the information as fast as you can. My day job is about preventing infections at Mount Sinai. My research job is partly about managing outbreaks and partly about preventing infections.

Instead of spending your time tied to a lab bench repeating experiments, you spend your time tied to your computer searching for different data or looking at data in different ways to try to understand it. It’s a good and a bad thing. You can carry your entire research lab on your computer.

What did you do during the investigation of the MERS outbreak in the hospital in Saudi Arabia? Some of my work was about painstaking patient chart review. I looked at the air supply, how it moved through the hospital and whether it had the potential to be contaminated. I also looked at the food and water supply. The virus could have also come from plants that people brought in. It’s about systematically and broadly looking at how this event could have happened, where the virus originated, how it could have spread, and then looking at the geography to try to sort out what actually happened.

How do you identify the source of an outbreak? In the case of MERS, it’s a coronavirus and the big reservoir for coronaviruses appears to be bats. So it looks like bats may be the beginning. And then there’s quite a lot of evidence now that indicates camels have been infected from bats. It’s still not clear whether there’s another host between camels and people, or whether camels are actually a host. Those studies are difficult to do and it’s hard work. Someone told me an interesting story about an outbreak of Leptospirosis, which people contract from infected rats and occasionally from contaminated water in the Indian sub-continent. The source turned out to be Pepsi—the cans were being stored upright in warehouses and the rats were running across them and peeing on top of the cans. When people opened their can and drank their Pepsi, they got a dose of Leptospirosis. So that’s a nice example of how hard it is to figure out what the common route of transmission is.

What are the challenges of your job? The good and the bad thing about infectious diseases is that there is no end to it. We now know a lot about the structure of the genetic material of a lot of organisms. However, we don’t know a lot about their ecology.  The prevention of infections in the future is not going to be about vaccines, it’s going to be about manipulating your normal flora to keep the pathogens away. You can see that there’s an enormous amount of potential from what we might understand about the interaction of different microbes.  I think the really interesting work in the next 50 years is going to be about understanding the relationship between the ecology of the microbial and human world and how changing that ecology influences risk.

In 2003, you contracted SARS. Are you concerned about risks of your job? On the scale of things, healthcare workers in general are at pretty low risk. Am I aware of the risk? Yes, absolutely. Do I worry enough about it to try to protect myself? Sure. Does it worry me in the basic sense that I would like to do something else? No. The truth of the matter is that although the job I do has risks, it’s much safer than other jobs in this world. Riding my bike to work in downtown Toronto is probably more dangerous than anything I do at work. It’s a risk I live with and recognize but it’s not so big that it makes a difference to my life.

What would your advice be for graduate students? No matter what you’re doing in university or in medicine, trying different things is important. You never know what you’re going to like until you’ve tried it out. And that process of trying to figure out how to get into people’s labs and spend time doing different things is important. If you’re in a lab, you should be spending the time out of the lab thinking about whether you’re interested in the epidemiology or the business aspect of things.

You should also be doing what you love. I think there are people who know what they want to do and where they want to go and they’re willing to put up with not enjoying themselves for a couple of years to get there. But there are so many opportunities out there and good things sometimes come from unexpected places. It’s a rare occasion when doing something that you’re not really interested in doing, or not having fun doing for any length of time, is a good thing for people to do. You need to work on finding what you really like doing and then doing that because there’s endless opportunity. You’re going to spend a lot of time at work. You’ve got to enjoy it!