Alternative Strategies for determination of biosecurity risk using high throughput sequencing (enterobacteriaceae & Xylella) (5yr)

Biosecurity outcome

• More robust risk assessments of exotic organisms and more rapid, cost-effective clearance of imported horticultural plants by the MPI. This will be achieved by providing new knowledge of pathogen evolution/biology as well as molecular diagnostics tools and new bioinformatics pipelines (e.g. for delta bit score or metagenomics analysis) to define the pathogenicity, host range and/or aggressiveness of individuals within multiple key pathogen groups. The pipelines and diagnostic protocols will be used on cultured organisms as well as on imported plant material directly. Ultimately, the knowledge, pipelines and diagnostic protocols will be incorporated into revised testing procedures for importation of high-risk plant material (e.g. Prunus) where existing costs are highest

Science outcome

• Broadened understanding of the genome-wide changes (and associated diagnostic signatures) in multiple key bacterial pathogen groups (e.g. enterobacteriaceae or Xylella), which enable individuals to emerge to cause disease on plant hosts;
• Establish whether metagenomics can be used to incorporate the benefits of genomics and metabarcoding to simultaneously enhance the specific detection of pathogens directly from plant material and identify genetic traits associated with risk (and management options).

Key end users/stakeholders

Implementation:   MPI PHEL will make formal submissions to the MPI Plant Imports team to incorporate previously developed ‘risk-based’ molecular diagnostics into testing of imported plant material. Use of the new bioinformatics pipelines or molecular diagnostics successfully developed in this project will also be proposed to the MPI Plant Imports team in line with MPI requirements for altering existing diagnostic protocols.