Thyroid Physiology_Dr.E. Muralinath_ Associate Professor
Early and accurate detection of bacterial pathogens
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Early and accurate detection of
bacterial pathogens
Rachel Mann
Research Scientist DEDJTR
Plant Biosecurity Cooperative Research Centre
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Project Team
PBCRC 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
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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
Marker
H20control
E.amylovora(Ea322)
Endemicsp.1
Endemicsp.2
Endemicsp.3
During the 1997 fire blight
incursion a false positive result
from samples in the Adelaide
Botanical Gardens caused the
shut down of trade
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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
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What are we doing about it?
Using genome-informed diagnostic design to
improve detection of exotic phytopathogenic
bacteria that pose a significant threat to Australian
Agriculture.
Relevant pathogens:
Fireblight
Erwinia amylovora
Zebra Chip
Candidatus Liberibacter
solanacearum
Citrus Canker
Xanthomonas citri pv. citir Bacterial canker of kiwifruit
Pseudomonas syringae pv.
actinidiae
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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
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What are we doing about it and how will it be delivered?
Key outputs– knowledge, strategy, tools and capacity
Tools: 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 Blight
Erwinia amylovora
Zebra Chip
Candidatus Liberibacter
solanacearum
Citrus Canker
Xanthomonas citri pv. citir
Bacterial canker of kiwifruit
Pseudomonas 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
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What are we doing about it and how will it be delivered?
Key outputs – knowledge, strategy, tools and capacity
Capacity: 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)
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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
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How will this research be delivered?
In-field validation
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How will this research be delivered?
Biosecurity Staff – “Training the Trainer”
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How will this research be delivered?
Biosecurity Staff –
“Hands-on”
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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
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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
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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
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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
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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