early and accurate detection of bacterial pathogens
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biosecurity built on science
Early and accurate detection of bacterial pathogens
Rachel MannResearch Scientist DEDJTR
Plant Biosecurity Cooperative Research Centre
biosecurity built on science
Project TeamPBCRC 2156 - Deployment of Validated Genome-Informed Bacterial Diagnostics KSU: James Stack, Grethel Busot, Mohammed Arif PFR-NZ: Grant Smith, Sarah Thompson, Rebekah Frampton, Kerry Sullivan DEDJTR VIC - AgriBio: Brendan Rodoni, Rachel Mann, Jason Shiller DPI NSW: Toni Chapman PHD students: Jacqui Morris, Rebecca Roach
biosecurity built on science
What is the problem?
For most plant pathogenic bacteria, accurate, rapid, low cost tools are not currently available (Palacio-Bielsa et al. 2009)
Accurate, rapid, low cost tools for detecting exotic plant pests are the foundation for:- secure border protection- rapid response to incursions- large-scale active surveillance programs
Correct identification is critical- Identification failures result in inappropriate responses- False negative, false positive
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During the 1997 fire blight incursion a false positive result from samples in the Adelaide
Botanical Gardens caused the shut down of trade
biosecurity built on science
What is the problem? In particular, we are designing detection tools to differentiate
at sub-specific levels. For example:- Xanthomonas citri pv. citri, Citrus Canker (not in Australia) from X. citri
pv. malvacearum, bacterial wilt of cotton (in Australia)- Pseudomonas syringae pv. actinidiae (Psa) high virulence strains (not
in Australia) from low virulence strains (in Australia)- Candidatus liberibacter solanacearum haplotypes
The best way to identify new diagnostic targets is by comparing the genomes of these populations of bacteria and identifying DNA targets specific to each group
Genome-informed diagnostic design
biosecurity built on science
What are we doing about it?
Using genome-informed diagnostic design to improve detection of exotic phytopathogenicbacteria that pose a significant threat to Australian Agriculture.
Relevant pathogens:
FireblightErwinia amylovora
Zebra ChipCandidatus Liberibactersolanacearum
Citrus CankerXanthomonas citri pv. citir Bacterial canker of kiwifruit
Pseudomonas syringae pv. actinidiae
biosecurity built on science
What are we doing about it and how will it be delivered?
Key outputs – knowledge, strategy, tools and capacity
Knowledge: A more fundamental understanding of key plant pathogenic bacteria and the closely associated species that can confuse phytosanitary procedures.Strategy: A generalised genomics-based strategy to develop diagnostic tools for plant pathogenic bacteria.
Delivery Reports and scientific publications
biosecurity built on science
What are we doing about it and how will it be delivered?
Key outputs– knowledge, strategy, tools and capacityTools: Detection and diagnosis tools to support national diagnostic networks and regulatory phytosanitary programs such as Post Entry Quarantine (PEQ) facilities.
Delivery National diagnostic protocols (NDPs) validated in Australia for the Subcommittee on
Plant Health Diagnostics (SPHDs) Field-deployable molecular tools for smart surveillance Scientific publications
Fire BlightErwinia amylovora
Zebra ChipCandidatus Liberibactersolanacearum
Citrus CankerXanthomonas citri pv. citir
Bacterial canker of kiwifruitPseudomonas syringae pv. actinidiae
- PCR diagnostics designed and validated
- LAMP test validated- NDP protocol submitted to
SPHDS
- PCR diagnostics designed & validated
- Field diagnostics developed & validated
- PCR diagnostics designed - PCR diagnostics designed and validated
- Field diagnostics developed & validated
biosecurity built on science
What are we doing about it and how will it be delivered?
Key outputs – knowledge, strategy, tools and capacityCapacity: Training in the disciplines and technologies that underpin plant biosecurity. Delivery Training of people across disease surveillance and diagnostic
networks both domestically and internationally (e.g. training/ workshops with biosecurity officers & plant diagnosticians)
biosecurity built on science
Field-deployable diagnostic tools for “Smart Surveillance”
What are the field-deployable tools?- LAMP (Loop-mediated isothermal amplification)- RPA (Recombinase Polymerase Amplification)
Both isothermal (stable temperature) DNA amplification
Varying ways to visualise result
biosecurity built on science
How will this research be delivered?
In-field validation
biosecurity built on science
How will this research be delivered?
Biosecurity Staff – “Training the Trainer”
biosecurity built on science
How will this research be delivered?Biosecurity Staff –
“Hands-on”
biosecurity built on science
Who will benefit from the research?
PHC/SPHD/NPBDN USDA-APHIS-PPQ; USA NPDN Federal and State biosecurity agencies State and federal diagnostic laboratories Diagnostic laboratories of trade partners NAQS PEQ Biosecurity field officers /Surveillance teams Researchers
INDUSTRY
biosecurity built on science
Benefit for our horticultural industries
Short Term Accurate detection tools with multiple stable targets Fast results with the ability to detect pathogens in-field Rapid and accurate diagnostics facilitate early pathogen
detection and rapid response times. This minimises:- economic loss- environmental impact- social impact on farming communities
Longer Term Building a bank of reliable diagnostics for use in Horticulture Establishing capability which will accelerate delivery of
diagnostics for newly evolved pathogens
biosecurity built on science
End-User Advocate’s Perspective
“Currently many early detection surveillance activities are conducted through visual inspection, with suspect samples sent to the diagnostic laboratory. A test that could be run in field would reduce the number of suspect samples and this would in turn reduce the surveillance turnaround time.”
- Dr. Louise Rossiter, Biosecurity NSW Leader of Plant Pest Surveillance
biosecurity built on science
Future
Complete NDPs for key pathogens Finalise field-deployable “smart surveillance” tools and
protocols for key bacteria Continue to improve diagnostics for other important
plant pathogenic bacteria The Ralstonia solanacearum species complex Rathayibacter toxicus
biosecurity built on science
Thank you
For more information, please email rachel.mann@ecodev.vic.gov.au
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PBCRC is established and supported under the Australian Government Cooperative Research Centres Programme
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