Next generation sequencing, direct detection and genotyping of fungi, bacteria and nematodes in the agri-food system


  1. Levesque, A.
  2. Chen, W.
  3. Hambleton, S.
  4. Seifert, K.
  5. Adam, Z.
  6. Bilodeau, G.
  7. Cullis, J.
  8. Demeke, T.
  9. Dumonceaux, T.
  10. Gagnon, M.-C.
  11. Graefenhan, T.
  12. Kawchuk, L.
Corporate Authors
Defence Research and Development Canada, Centre for Security Science, Ottawa ON (CAN);Agriculture and Agri-Food Canada, Ottawa ON (CAN)
This project engaged Agriculture and Agri-Food Canada (AAFC) and first responders, the Canadian Food Inspection Agency (CFIA) and the Canadian Grain Commission (CGC) to deliver on a collection of sub-projects unified by the technology of Next Generation Sequencing (NGS). The objectives focused on developing innovative methods to counter threats from fungal, bacterial and nematode pathogens. The outputs covered the full spectrum of Technology Readiness Levels (TRL). For example, de novo sequencing was accomplished for some high risk microbes for which there were no genomics data available (TRL1) and some tests developed from the genomics data were used by Canadian first responders to resolve trade disputes, and were either used or are currently being evaluated by first responders in other countries (>TRL7). The genomes and transcriptomes of high risk plant and animal / human pathogens found on crop commodities and in agro-ecosystems were sequenced. DNA and RNA from multiple strains of high profile pathogenic species were processed for NGS from the following genera: Arcobacter, Ditylenchus, Globodera, Pantoea, Pectobacterium, Penicillium, Phytophthora, Puccinia, Ralstonia, Streptomyces, Synchytrium, and Tilletia. Reductions in sequencing costs over the time span of the project and an in-kind contribution for genomics and for data analysis infrastructure installed mid-project, allowed us to increase the number of strains processed for full genome sequencing to more than four

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genotyping;sequencing;PCR;genomics;bioinformatics;diagnostics tools
Report Number
DRDC-RDDC-2015-C148 — Contract Report
Date of publication
01 Apr 2015
Number of Pages
Electronic Document(PDF)

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