Grant: DRA : Canada Graduate Research Scholarship - Doctoral Program (CGRS D)

Respiratory infections are a leading cause of hospitalizations in Canada; however, current testing to identify causative organisms is limited. Patients with complications or pre-existing conditions experience treatment delays because routine tests are often unable to pinpoint a cause of infection. I propose a sequencing-based test, Rapid Agnostic Pathogen IDentification metagenomic Next generation sequencing (RAPID-mNGS), to identify all potential disease-causing organisms in patients' respiratory specimens. To accomplish this, my PhD research project has three aims. First, I will optimize RAPID-mNGS to detect viruses, bacteria, fungi and parasites; second, I will work with three public health laboratories in BC and Manitoba to measure test performance using clinical samples (validation); and third, I will determine the benefits and risks of using RAPID-mNGS in a real-world setting. RAPID-mNGS, previously shown to detect RNA viruses, has now been optimized for higher accuracy. Steps have been added in the test to process DNA alongside RNA, enabling successful detection of bacteria. RAPID-mNGS expansion will continue to detect fungi and parasites; after which, it will be validated using respiratory specimens over the course of two flu seasons at three laboratories. The analysis of data generated from sequencing will be done in collaboration with a commercial partner (BugSeq), which offers a user-friendly platform to identify organisms efficiently. Lastly, interviews with public health decision-makers in BC will be conducted to assess the possibility of integrating RAPID-mNGS into routine diagnostics for respiratory infections. My doctoral research will improve infectious disease diagnostic testing in Canada, especially in cases where routine tests are negative. RAPID-mNGS has the potential to not only improve current testing, but also to identify new disease-causing organisms and strengthen Canada's readiness for future epidemics and pandemics.