Prospective evaluation of the ONETest™ targeted metagenomic platform to identify respiratory tract pathogens for precise diagnosis and clinical trial recruitment

Challenge: Respiratory tract infections (RTI) are a leading cause of morbidity, mortality, and hospitalizations globally. Yet, many cases of RTI still go undiagnosed and RTI is often treated empirically because the etiologic agent(s) is unidentified. The current diagnostic approach is complex and often takes days to weeks. It may also fail to detect a broad spectrum of pathogens as well as to determine whether identification reflects colonization versus true infection for certain agents. Thus, there is urgent need for innovative diagnostic technologies for RTI.

Solution: The team developed the ONETest™, a next-generation sequencing (NGS)-based end-to-end platform for the diagnosis and surveillance of infectious diseases. The ONETest™ can target any arbitrary set of pathogens and produce comprehensive genomic information about them, in a sensitive and time-efficient manner. Here, the team proposes a prospective clinical study to interrogate a broad range of samples collected during routine clinical care from ~1,000 patients diagnosed with RTI. The spectrum of specimens will allow to expand the evaluation the ONETest™ to test upper and lower RTIs for viral, bacterial and fungal pathogens. Results will be compared to conventional protocols. Additionally, samples from healthy individuals will also be profiled for their respiratory flora.

Expected achievements/Impact: The objective of the study is to provide key insights using sequence data, which are not generated by conventional methods, to achieve a better understanding of the current epidemiological landscape of RTI. It is expected that, at completion, the project will lead to a clinically annotated targeted metagenomic database comprised of respiratory samples from patients with RTI and healthy participants. Such data and tools have applications both in the biopharmaceutical R&D sector and in clinical practice. While improving patient management, ONETest™ could also serve as a companion diagnostic tool for clinical drug trials.

Principal Investigator:

Mohammad A. Qadir
Fusion Genomics


Samira Mubareka 
Sunnybrook Research Institute


Ongoing Project
$ 1,287,067 / 1 year


Supported by CQDM through:
• Merck Canada• BL-NCEAnd by co-funding partners• Fusion Genomics