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Novel diagnostic techniques for the detection of pests and diseases of statutory concern - PH0305

Description

Defra currently spends approximately £1.6M p.a. on provision of diagnostic services in Plant Health. There is continuing pressure on the DEFRA Plant Health service to increase the level of monitoring for statutory organisms in compliance with both National and EU Plant Health legislation. Thus either the total budget will need to be increased or the cost per sample reduced to achieve this aim. There exists considerable opportunity to both reduce the cost of testing, as well as improving the quality of response, through the development and adoption of appropriate novel diagnostic methodology. In addition giving ‘first responders’ the ability to carry out diagnostic tests has already proven its worth in plant health with the successful adoption of lateral flow devices (Pocket Diagnostics) by inspectors. With development of equipment and techniques this should become increasingly possible with molecular methods, a major hurdle being nucleic extraction. A number of novel diagnostic methods will be evaluated for the detection and diagnosis of a range of plant pests and pathogens of Plant Health concern, using pests of current statutory concern as model systems. These methods will allow for future improvement of the provision and performance of diagnostic services carried out on behalf of Plant Health Division, applicable to a wide range of pests and pathogens.

The methods fall broadly into two main areas, those methods involved in the laboratory identification of pathogens/pests and on-site molecular testing. The work seeks to exploit and further develop opportunities identified in the recent review of PHD funded projects PH0154 and PH0178. There is also considerable synergy between this and other PHD funded projects, for example PH0304 (in which specific molecular markers will be developed for Noctuidae, using a SCAR approach) and also PH0302 (in which COI sequencing will be investigated for fungal pathogen discrimination, and which will be continued in this project.). The on-site testing aspects are to be matched by complementary funding from the EU FP6 program under the project PORT CHECK (contract number: 502348).

The areas of research to be covered by this proposal fall under the two main themes of laboratory based identification and on site molecular detection and include the following.

• Multi locus sequencing for bacterial identification
• Cytochrome oxidase subunit sequencing for invertebrate and fungal pests/pathogens
• Exploitation of sequence information
• Development of extraction techniques for on-site detection
• Evaluation of on-site real-time PCR equipment


Objective
1. To investigate which gene or genes can be used to discriminate species for bacterial pathogens (Multi Locus Sequence Typing), fungal pathogens and invertebrate pests.
2. To investigate methods of exploiting sequence data for identification purposes (direct sequencing or microarrays).
3. To develop extraction methods and evaluate portable real-time PCR equipment for on-site molecular testing.
Project Documents
• Final Report : Novel diagnostic techniques for the detection of pests and diseases of statutory concern   (2068k)
Time-Scale and Cost
From: 2004

To: 2007

Cost: £380,528
Contractor / Funded Organisations
Central Science Laboratory
Keywords
Alien Species              
Diagnosis              
FP7              
Molecular Biology              
Plant health              
Plant Pests and Diseases              
Plants and Animals              
Fields of Study
Plant Health