The next infectious disease threat may not be one that public health laboratories already know how to find.
Vancouver-based BugSeq is building genomic tools designed to help clinical and public health laboratories identify pathogens, track outbreaks, and understand antimicrobial resistance. With support from Genome BC—including one project also funded by Genome Canada—the biotechnology company is advancing two technologies with significant commercial and public health potential.
The first applies artificial intelligence to the growing challenge of antimicrobial resistance. By analyzing the complex interactions among genes and mutations, BugSeq aims to help healthcare providers predict whether bacteria will resist a particular antibiotic and move more quickly toward personalized treatment.
The second uses pathogen-agnostic metagenomic sequencing to detect respiratory threats without searching for one predetermined virus. Unlike targeted diagnostic tools, the technology can identify unexpected or novel pathogens in a sample, potentially giving health authorities more time to contain emerging outbreaks. BugSeq’s platform is already being deployed within public health laboratories across Canada.
Both projects build on BugSeq’s broader ambition to make genomic analysis faster, more accurate, and easier to incorporate into routine laboratory workflows. They also reinforce the company’s roots in British Columbia, where collaborations with Providence Health Care, Vancouver Coastal Health, and the BC Centre for Disease Control have contributed to more than a dozen peer-reviewed publications.
Techcouver spoke with Nick Gauthier, Head of Scientific Affairs at BugSeq, about the connection between the two projects, how AI can strengthen antimicrobial-resistance prediction, and why metagenomic sequencing could make Canada more resilient against future public health threats.
Genome BC chose to support two very different BugSeq projects. What connects them strategically, and what do they say about where BugSeq sees the biggest opportunities in genomics over the next few years?
NG: BugSeq has built a comprehensive suite of bioinformatics tools that empowers clinical and public health microbiology laboratories to track pathogens, antimicrobial resistance, and outbreaks in their healthcare systems. As more labs adopt genomic techniques to gain insight into circulating pathogens, BugSeq aims to strategically grow both the breadth of our offering and build on the accuracy of our workflows to meet our users’ needs. Both the Genome Canada and Genome BC funded project to validate and pilot a pathogen-agnostic genomic workflow to strengthen Canadian biosecurity, as well as the Genome BC project to build new tools to track and characterize antibiotic resistance will help BugSeq achieve our strategic goal of accelerating the adoption of genomics in clinical and public health microbiology.
Antimicrobial resistance is often described as a “silent pandemic.” Why is it such an urgent challenge, and how can AI help clinicians choose the right antibiotic before resistance has a chance to develop?
NG: Antimicrobial resistance is an increasing burden on our healthcare system. A recent Public Health Agrency of Canada report outlined that in 2018, 26% of bacterial infections were resistant to frontline antibiotics. That number is expected to grow to 40% by 2050. Part of the problem is that we are having difficulty developing new drugs to match the pace that bacteria are developing resistance. The genetic mechanisms that drive antimicrobial resistance are becoming increasingly complex. Part of why machine learning helps healthcare providers derive insight from genomic data is that it can elucidate the complex interaction between different genes and mutations that contribute to a bacteria being resistant to a given antibiotic. Genomic workflows could also enable faster results that traditional phenotypic testing, facilitating personalized therapy faster than conventional workflows. AI tooling can also allow us to derive insights from emerging mechanisms of resistance that have yet to be annotated in public databases.
Your respiratory surveillance platform uses metagenomic sequencing rather than targeting a specific virus. What advantages does that give public health labs when they’re trying to detect new variants—or entirely new pathogens?
NG: One of the challenges for healthcare systems attempting to react to an emerging infectious disease outbreak is that we currently rely on targeted diagnostics and surveillance tools that are designed to only detect a narrow range of pathogens. Metagenomic sequencing can enable us to more quickly identify and respond to public health threats because it is a pathogen-agnostic technology, meaning that it can identify whether a novel pathogen is present in a given sample. Having this technology as part of our public health surveillance network may dramatically increase our capacity to rapidly respond to public health threats, and hopefully contain them before widespread outbreaks occur.
The platform is already being deployed in public health laboratories across Canada. What have you learned from working with those labs, and how important is it to build tools that fit seamlessly into existing public health workflows?
NG: Public health laboratories are increasingly using genomics techniques as part of their workflows to track and respond to infectious diseases. As these laboratories continue to broaden their adoption of new genomics workflows, it is critical that we are able to provide them with rapid, actionable, and accurate bioinformatic analysis to serve their growing needs. Part of what makes BugSeq unique is that we work with and collaborate very closely with our users to tailor our workflows, ensuring that their needs are being met.
Genome BC’s investment is also about strengthening British Columbia’s life sciences sector. How has building BugSeq in Vancouver shaped the company, and what advantages does the province offer for scaling genomics companies?
NG: BugSeq is proud to be founded in British Columbia and have strong working relationships with our clinical and public health partners in BC. Through growing BugSeq as a BC-based company, we have helped improve clinical care and public health in the province through longstanding collaborations with BC healthcare institutions including Providence Healthcare, Vancouver Coastal Health, and the BC Centre for Disease Control. These collaborations have led to over a dozen peer-reviewed publications leveraging BugSeq’s workflows for applied clinical and public health microbiology research. A recent example included an in-depth analysis by Providence Healthcare to identify a clonal cluster of multi-drug resistant Shigella sonnei in people experiencing homelessness in Vancouver using BugSeq’s antimicrobial resistance and outbreak analysis tools (Stefanovic et al. 2024).
If we’re having this conversation again two years from now, what outcomes would you hope these Genome BC-funded projects have delivered—for BugSeq, for healthcare providers, and ultimately for patients?
NG: In the next two years, we hope to see the technological advancements from these projects translate into routine clinical workflows in laboratories across Canada. As an end goal to our antimicrobial resistance project, we are planning to deploy this technology to multiple clinical laboratories in BC and internationally, and obtain comprehensive feedback on both the accuracy of the software and how these institutions intend to leverage this technology in their clinical workflows. Ultimately, BugSeq’s goal is that our platform will help reduce translational barriers to drive broad adoption of genomics technology used to tailor antimicrobial therapy for patients and reduce the burden of antibiotic resistance on the Canadian healthcare system. Finally, we hope that expanding access to validated metagenomic sequencing workflows leveraging BugSeq’s bioinformatic workflows in Canadian public health laboratories will improve resiliency in our capacity to respond to emerging pathogens.
The post With Genome BC Support, BugSeq Advances Genomic Tools for Emerging Pathogens and Drug Resistance appeared first on Techcouver.com.
With Genome BC Support, BugSeq Advances Genomic Tools for Emerging Pathogens and Drug Resistance was first posted on August 4, 2026 at 6:00 am.
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