Development of genome database for nanopore sequence to support food safety inspection (pilot part 3, Staphylococcus aureus)

Funding period: 2022–2025
Leads: Oliver Lung and Peter Kruczkiewicz
Total GRDI funding: $117,000

The mandate of the Canadian Food Inspection Agency's National Centre for Foreign Animal Disease includes diagnostic testing, surveillance testing, developing diagnostic tests and providing scientific advice on responses to transboundary, emerging and re-emerging high-consequence diseases that affect animal health. High-throughput sequencing (HTS) is currently the only available method that allows unequivocal accurate identification and comprehensive genomic characterization of known, novel and unexpected pathogens. HTS can provide the high-resolution information needed for source-tracking and genomic epidemiology.

Since the centre's genomics unit inception, it has experienced a substantial increase in demand for high-throughput sequencing. The centre must invest in developing and deploying new HTS technologies and methods to scale and improve sequencing operations in order to meet the rising standards and expectations for current and future animal health investigations.
Adaptive sampling is a new sequencing technology for Oxford Nanopore sequencers that can substantially reduce the cost and turnaround time of HTS of known, novel and unexpected viruses. This is achieved by reducing or eliminating the need for expensive and time-consuming laboratory-based enrichment.

This project will establish new laboratory and bioinformatics protocols for adaptive sampling, which will reduce or eliminate the costs for capture probe enrichment and reduce the turnaround time from a week to as short as a few hours.