Decoding bacterial defence systems and building a future in biochemistry | Co-operative Education

Sam Fairburn (they/them) is a fourth-year Biochemistry student in the Faculty of Science. Sam shares their diverse co-op experiences across government, industry and academic fields. They also discuss their most recent work term where they had the opportunity to contribute to the discovery of novel phage defence genes.

Sam's co-op journey

Work term one: Sam began their co-op journey at in Ottawa, working as a toxicology lab assistant. Their research involved studying the expression of specific genes across rats, mice and humans and how that expression was affected by different toxicants.

Work term two: For their next term, Sam joined , a company in Toronto focused on water toxicity testing for nuclear waste. They conducted acute and chronic toxicity tests in water samples using live-animal specimens.

Work term three: Sam’s third co-op was at the University of ��ݮ��Ƶ, where they worked in Dr. John Honek’s lab. Their research centered on the attachment of oxidative enzymes to an agarose polymer, with the goal of applying these systems to bioremediation.

Sam Fairburn smiling in a white lab coat and glasses

Work term four: For their most recent co-op term, Sam worked at the Department of Biochemistry at the University of Toronto, in . Their project focused on bacteriophages, viruses that infect bacteria and how Vibrio parahaemolyticus, a species of marine bacteria, encode natural defense systems against these phages.

Q&A with Sam

Sam Fairburn smiling in front of their research poster

What did you work on during your most recent co-op?

“The specific region that we were looking at in the Vibrio parahaemolyticus genome was called the integron. Essentially, Vibrio are able to incorporate free DNA fragments that exist in the environment into their genome at the integron.”

“That’s how things like antibiotic resistance and phage defence spread so quickly across different strains of bacteria.”

“The lead of the project, Dr. Landon Getz, did a lot of bioinformatics work before I got there. He identified the individual genes in the Vibrio integron and cloned a lot of those into E. coli and Vibrio expression systems.”

“During my co-op, they were at the tail end of the cloning process, and I focused on testing each of those genes for their ability to make bacteria resistant to specific phages. We tested a total of 57 genes from the integron against a collection of bacteriophages.”

“A lot of the work was phage spotting, which is a technique where you make a lawn of bacteria on a petri plate, then pipette a small amount of diluted phage, usually a serial dilution, onto it. You're looking for the formation of plaques, which are clearings in the lawn where cells have died because they've been infected by phage.”

“If the gene you insert into the bacteria confers resistance, the bacteria will be able to grow even where phage has been spotted.”

“We also did some growth curve analysis, where we used absorbance to monitor bacterial growth over time, with and without phage infection, to see how the phage was killing the cells.”

“It was a really fun experience. It was the first project I was on that and I could see the whole process from start to finish. We submitted it for publication in July 2024 and it got published in January 2025.”

What did you enjoy about the work?

“I really like research in general. I enjoy forming a question and then doing experiments to answer it.”

“It was also exciting because antibiotic resistance is a growing problem in medicine. More and more people are getting infections with bacteria that can’t be treated. The same goes for bacteria infecting the aquaculture industry.”

“So, working on something that could potentially lead to alternate treatment options is really rewarding. It’s good to know that I might be making a difference.”

Do you have any advice for other co-op students?

“I’d say don’t get discouraged if your first job, or even your first couple of jobs, aren’t exactly what you are looking for.”

“I can say without a doubt that my last co-op was the best one overall. I had the best time there and everyone was so nice.”

“So, just don’t get discouraged if the first thing you try isn’t what you want to end up doing. That’s what co-op is for, trying different things and figuring out what fits.”

Sam Fairburn smiling in a black graduation gown

Was there anything about the culture or how the work was done that made your last co-op stand out?

“Everything seemed very organized and there was a clear structure for how things were done.”

“The lab setting was pretty big. Currently, I think they have about 16 people, so it’s a busy place. You’re held more accountable for things, whereas in some of the smaller labs I’d been in, things could kind of fall through the cracks.”

“I liked being part of a bigger team where you could ask questions, bounce ideas off people and have a collaborative research environment.”

What's next for you?

“I’m returning to the Maxwell lab this summer. We’re going to be continuing our work with Vibrio parahaemolyticus and hopefully will be isolating some new bacteriophages to be able to screen for broader resistance. I’ll also be starting a direct-entry PhD program in Biochemistry at the University of Toronto in September.”