New approaches for the early detection of tree health pests and pathogens

Lead Research Organisation: University of Hertfordshire
Department Name: School of Engineering and Technology

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

This project has 6 work packages (WP), each based around a different combination of skills and expertise. For WP2-6 there will be a focus on a particular detection technology, while WP1 will provide the technical oversight needed for effective deployment of these different technologies, as summarised:
WP1:a participatory interdisciplinary approach will be used to evaluate the needs of stakeholders and to ensure that the technologies meet these. It will also focus on the requirements of effective technology deployment, using mathematical modeling to develop sampling strategies, to create network-based risk maps and economic assessments of cost-effectiveness. Further aspects of deployment will be analysed using social science approaches including end-user acceptability and the potential for using citizen science.
WP2:analytical chemistry approaches will be used to identify diagnostic volatile organic compounds produced by pests, pathogens and diseased hosts and to translate these onto commercial-available portable platforms for use by inspectors in the field.
WP3:multispectral imaging will be used to identify markers for the early detection of biotic/abiotic stress in plants. A prototype bioimaging camera will be constructed that can be used to validate this approach in the field.
WP4:will develop mathematical models of spore movement and investigate metagenomics for broad-spectrum surveillance utilizing existing monitoring networks e.g. pollen traps. In addition, a novel integrated cyclone-based trapping and molecular detection system will be developed and evaluated.
WP5:novel semiochemical attractants will be identified for a range of wood-boring beetle pests, incorporated into traps designed for efficient detection and then deployed in a risk-based network.
WP6:methods for sampling and rapid screening water for Phytopthora spp., including 'unknowns' will be developed and validated. This will combine high-throughput sequencing with a rapid bioinformatic.

Planned Impact

The interdisciplinary design of this proposal will ensure maximum ongoing impact. Central to this is stakeholder engagement and our proposal has adopted a novel approach to facilliate this. Traditional approaches to developing new detection or diagnostic technologies have assumed the 'build it and they will come' approach; where the focus is on the technical aspects of the novel methodology, rather than the needs of end-users and the specifics of how it will be effectively deployed. This proposal reverses that by taking an inclusive view of what is required to achieve a successful outcome i.e. the deployment of a new technology that improves our biosecurity, and then co-designs technologies which fit that purpose. It achieves this by embracing an interdisciplinary approach and through establishing early engagement with stakeholders and end-users. Critical to this is the creation of a Learning Platform (Work package 1) which sits at the core of the project and cuts across the other technology-driven work packages (WPs 2-6). This platform will create communication channels, facilitate collaboration and knowledge sharing across work packages and stakeholder groups, actively disseminating project outcomes and enabling the pathways to impact. This will be delivered as a series of workshops; both cross-cutting (looking at the broader issues associated with detection and its successful deployment) and more focused (looking at specific issues associated with a particular technology and the contexts for its use). In addition to interacting with stakeholders (e.g. policy-makers, inspectors, NGOs, industry), this approach will use the breadth of expertise established within the consortium and assembled from across a wide-range of disciplines. This brings together 'technology-owners' (natural and physical scientists) with 'technology-evaluators' (mathematical and social sciences) to ensure that the best technological approaches are married with suitable sampling and risk-based deployment strategies, that they have stakeholder acceptability and offer genuine cost-efficiency benefits to public and private stakeholders alike.

In addition to the novel approach built into the project design, the effective delivery of impact will also benefit from a consortium which has an extremely strong track record of delivering translation science, to policy and industry alike. As government science agencies, the major remit for both Fera and Forest Research is to take science and technology and to translate it into policy-focused tools and evidence. This is a role they provide routinely for Defra and Forestry Commission, and their associated inspectors on the frontline in the field (e.g. Fera PHSI and FC Inspectors). In terms of delivery of technologies to end-users including industry, there is also a strong track record across the consortium in a whole range of contexts e.g. Worcester (horticulture industry diagnostics), JHI (potato industry diagnostics), Greenwich (pest trap deployment) and Fera (field diagnostics deployment). The integration of a number of SMEs within the consortium is another pathway to impact; providing a route for new technologies to be made freely available beyond the end of the project. Finally as plant and tree health sits within a European regulatory framework, the ability to engage with international partners and stakeholders is important. The consortium has a wealth of experience and contacts in this area, in particular through its central role in a range of related EU-funded projects e.g. Q-Detect (Fera-led), ISEFOR (Aberdeen-led) and PERMIT (FR-led). It will also build upon existing systems for knowledge exchange within our region, especially through the use of the European Plant Protection Organization (EPPO). By working with EPPO, using activities such as its workshops and conferences, we will be able to reach out to tree health practitioners across Europe; in many cases the real frontline for UK biosecurity.

Publications

10 25 50
 
Description Our Research work has led to the development of an instrument that can, for the first time, autonomously sample, process, analyse and report the presence of specific airborne tree and plant pathogens in field environment. The implementation of specific advances in aerosol collection capability, and the subsequent processing of the sample to laboratory standards are a major achievement in this award. Maintaining sample integrity while being able to repeat consecutive sampling to enable autonomous deployment of the instrument allows for specific, targeted application of the instrument across a number of biosecurity threat scenarios.

The award objectives were fully met with the research focussing on each core component in the systems and the subsequent integration of these functions into a self-contained device capable of monitoring airborne pathogen transport with specific, tailored, downstream DNA primers adaptable to emerging pathogen threats.

The ability to seamlessly develop and implement individual sub-systems for future new and emerging threats is a particular benefit of this research, allowing for the key findings to be leveraged rapidly. Furthermore future flexibility of this stable biodetection platform instrument has been incorporated at the research and development stage to enables future adaptations across any of the multidisciplinary functions (aerodynamic characteristics of the target biology, sample processing requirements for account for biological type/variation such as spore/virus/protein etc., and system protocol and operational requirements through the onboard embedded operation and system performance programming).
Exploitation Route The findings from this research showcase an integrated biodetection instrument incorporating collection of aerosols, sample processing and onboard molecular diagnostic analysis and reporting capability. These findings have informed ongoing research at the University of Hertfordshire and can be further developed and taken forward by any research or development organisation focussed on monitoring and warning against airborne diseases. The scientific community can also adopt the technology toward longer term research monitoring and modelling specific airborne biological transport vectors for both innocuous and harmful target material, with a specific capability towards quantification and monitoring of changes to airborne biome biodiversity

To date the research has been of particular interest to scientists in three primary sectors, Infection control and prevention, environmental disease monitoring and biowarfare defence. The research is leading to collaborations between the University of Hertfordshire and leading specialists within each sector with a view to applying the findings towards impactful outcomes as follows:

Infection control and prevention. Real-time monitoring of airborne pathogen load in hospital surgical environments where patients with complex medical needs and/or compromised immune systems may require monitoring approaches beyond the current state of the art e.g. Great Ormond Street Hospital.

Environmental disease monitoring - Real-time monitoring of the spread of endemic disease can inform specific, targeted control measures in environmental e.g. control of Viral Foot and Mouth disease research at The Pirbright Institute.

Biowarfare Defence - broad spectrum, multi target airborne threat monitoring for personal and wide area sentinel applications are a primary concern for protection against maliciously released biowarfare agents (BWA) e.g. the Defence Science and Technology Laboratories at Porton Down.

Each of these future relationships are building upon the successful outcomes and findings of this research grant.

Aspects of the findings from this research programme have contributed to the Centre for Doctoral Training in Aerosol Science, both in terms of the PhD projects on offer as well as the teaching material that all CDT students study in the first year of thier PhD programme.

The work has also contributed to a National Core Study: Covid Transmission programme to develop technologies for future monitoring of airborne pathogens.
Sectors Aerospace, Defence and Marine,Agriculture, Food and Drink,Environment,Healthcare,Other

 
Description Findings associated with the development of a demonstrator prototype have been disseminated to commercial partners to support the subsequent development and deployment of fieldable detection platforms. The instrument capability has been presented to other THAPBI researchers with a view to developing cross-cutting capabilities and further understand the capabilities and limitations of existing early warning detection systems for new and emerging airborne threats. Likewise, the capability and approach taken in developing the integrated, automated biodetection platform has been of interest to the Defence Science and Technology Laboratory to inform their research and technology development programme. Individual elements of the research findings have been of interest to several sectors including the Centre for Environment, Fisheries and Aquaculture Science (CEFAS), UH were invited to demonstrate the research findings and opportunity to adapt the resultant instrument capability to target waterborne disease for protection of aquaculture and water environments. UH have also met with specialists in infection control and prevention from Great Ormond Street to ascertain what adaptation can be implemented to enable the use of the research findings to hospital settings. The UH research team have also won internal funding to support the development of this research towards impact in healthcare setting and this activity is continuing with collaborations being setup with 2 leading UK hospitals looking at airborne biodetection in surgery and general healthcare settings. The project has also lead to findings that have been incorporated into the EPSRC Centre for Doctoral Training in Aerosol Science and the associated teaching material as part of the formal academic study year for all CDT PhD students. The outcomes from this research have fed into three new avenues of research within the group - an evaluation of the underlying merits in the approach have been applied to emerging impact funding from the Defence and Security Accelerator via DSTL Porton Down to ascertain whether the research outcomes can advance state of the art biowarfare detection, we have also undertaken Phase 1 of a National core Study on Covid Transmission and are responding to WP4 on instrumentation design for a future technology to monitor and detect airborne disease. Finally, the outcomes of this project have led to an established collaboration with University College London and Great Ormond Street with a response to the EPSRC Transformative Healthcare Technologies call (Real-Time Digital Diagnostics of Environmental and Patient Originating Aerosols: Personalised Patient Environment Monitoring) submitted in March 2021. This application was unsuccessful but we have now established a good network who continue to pursue other opportunities.
First Year Of Impact 2019
Sector Aerospace, Defence and Marine,Agriculture, Food and Drink,Environment,Healthcare,Government, Democracy and Justice,Security and Diplomacy
Impact Types Cultural,Societal,Economic,Policy & public services

 
Description All-in-one Biosampling Cyclone with DNA amplification (abc-DNA)
Amount £97,660 (GBP)
Funding ID ACC2016891 
Organisation Defence Science & Technology Laboratory (DSTL) 
Sector Public
Country United Kingdom
Start 10/2020 
End 12/2021
 
Description National Core Study: Covid Transmission - Phase 1 of 2
Amount £83,647 (GBP)
Organisation Public Health England 
Sector Public
Country United Kingdom
Start 01/2021 
End 04/2021
 
Title High efficiency integrated cyclonic collection test platform for collect/detect system - 1st stage working prototype 
Description Our system incorporates a purpose-designed high efficiency cyclone directly integrated with a custom airmover incorporating a UH design, system matched, impeller to maximise volumetric air sampling while minimising the power requirement. Novel manufacture techniques incorporating 3D printing of metal and plastic was used extensively to validate theoretical models and the particle collection and retention capability of this series of prototypes was evaluated experimentally within our Aerosol test chamber. 
Type Of Technology Detection Devices 
Year Produced 2016 
Impact We found that we could collect greater than 90% of particulate in our target size range for 1/5th the power required for previous prototype systems, thus providing longer term sampling capability for our detection platform front-end . Our system is capable of operating autonomously and at low power, with a high sensitivity to ambient particles. We are now reviewing protection and IP issues for this system. 
 
Title Integrated automated cyclonic pathogen collection and LAMP based DNA detection system - final prototype 
Description This system integrates both the cyclonic pathogen collection module alongside the LAMP based DNA detection system into a single, field deployable unit. Sampling air at between 70-120 l/min the airborne pathogen collection system can be automated to run collection sequences as required by the end user. These collection profiles can be defined temporally or based on atmospheric conditions with inbuilt rain sensing. Setup of the instrument can be achieved via direct connection or through a secure wireless protocol. The platform has been developed with both Ash dieback and potential emerging threats in mind. DNA amplification is primer dependent and the experimental test protocol can be adapted to suit the system application from multiday, single target sampling to single sample broad spectrum multi-target analysis. 
Type Of Technology Detection Devices 
Year Produced 2018 
Impact This system has been developed by the Microfluidics & Microengineering Research Group (MMRG) at the University of Hertfordshire. The completion of the instrument came at the end of the research and development project and as such has not yet been used more widely, however the system has been developed as a modular system to enable rapid modification, as required, to target new and emerging airborne pathogen threats and is the subject of ongoing discussions with Fera Science Ltd. and collaborators on the THAPBI project. 
 
Title Optimised automated cyclonic pathogen collection module - final prototype 
Description This module can be operated as a standalone or integrated system as part of the final Tree Health and Plant Biosecurity Initiative (THAPBI) autonomous collection system. This automated cyclonic collection system incorporates a purpose-designed high efficiency custom air moving system, optimally matched to a cyclone manifold. An electronically actuated carousel provides integration with one of 7 cyclone bodies for sequential testing with an additional sample tube providing a reservoir for chemical lysis/resuspension buffers. The complete system, including cyclone manifold, impeller and sub structure includes novel manufacture techniques incorporating 3D printing of metal and plastic and mini-scale 5 axis machining was used to extensively validate theoretical models of particle collection and retention capability evaluated experimentally within our Aerosol test chamber. 
Type Of Technology Detection Devices 
Year Produced 2017 
Impact This system has been used extensively by the research team at UH in the development of the integrated tree health pathogen detection platform. The completion of the instrtument came at the end of the research and development phase of the project and as such has not yet been used more widely, however the system has been developed in a modular manane to enable rapid modification to target new and emerging airborne pathogen threats, as required. 
 
Title Optimised automated multiplex LAMP DNA amplification pathogen detection module - final prototype 
Description This module can be operated as a standalone or integrated system as part of the final Tree Health and Plant Biosecurity Initiative (THAPBI) autonomous collection system. This automated carousel sample system incorporates an array of 7 LAMP sample strips in an electronically actuated carousel mated to a microfluidic sample delivery system. The complete system is capable of delivering aqueous sample from source to between 1 and 56 reaction sites. In standard configuration the 8 tube LAMP system would delivery 6 aliquots of sample with the remaining 2 reaction tubes providing positive and negative controls. Electromechanical control is integrated with the LAMP detection electronics. The automated carousel unit also enable hot swapping of used reaction tubes by the end user to enable continuous, sequential sampling and detection to be conducted on the unit. 
Type Of Technology Detection Devices 
Year Produced 2017 
Impact This system has been used extensively by the research team at UH in the development of the integrated tree health pathogen detection platform. The completion of the instrument came at the end of the research and development phase of the project and as such has not yet been used more widely, however the system has been developed as a modular system to enable rapid modification, as required, to target new and emerging airborne pathogen threats. 
 
Description Applied Biosecurity Innovations arising from inter-disciplinary Science & Engineering 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact The University of Hertfordshire School of Engineering & Computer Science hosted an exhibition of innovation in biosecurity technology as part of the joint Institute of Engineering & Technology (IET) Turing EngTalk and British Computer Society (BCS) Lecture Series. This was an opportunity to showcase the advances in disciplinary Science & Engineering research at the University of Hertfordshire. Key technology demonstrated included biodetection technology for protection of people and the environment associated with airborne contaminants.

The event has lead to opportunities to discuss collaboration and the potential to develop technolgy for a number of new industries as well as discussions associated with international trade and sales of the production instrument.
Year(s) Of Engagement Activity 2019
 
Description Automated biodetection of airborne pathogens 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This was an invited presentation at the Aerosol Society Annual Meeting, a scientific, non-profit organization aimed at extending knowledge and supporting the study of airborne particles.

The presentation focused on new developments in automated biodetection of airborne pathogens and was presented to an audience of Aerosol Society members as well and being made available to its membership of more than 500 scientists is drawn from academia, government bodies and industry.

The presentation lead to discussions focussed on future collaboration including cross institution PhD research projects that will run under the recently awarded Centre for Doctoral Training in Aerosol Science. This research will focus on capture, analysis and subsequent transport modelling of environmental pathogens in situ. Furthermore this has led to an invitation to join the Aerosol Society organising committee for the 2019 Annual Conference.
Year(s) Of Engagement Activity 2018
URL https://aerosol-soc.com/events/annual-aerosol-science-conference-2018/programme/
 
Description Bioprocessing Microfluidics & System Integration 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The University of Hertfordshire were invited to host a workshop at the 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences (µTAS 2018) held in Kaohsiung, Taiwan. The event saw over 1100 worldwide scientists and professionals engaged in research on and the use of integrated microsystems and nanotechnology for chemistry and life sciences alongside an industry cohort of over 50 companies.
Year(s) Of Engagement Activity 2018
URL https://cbmsociety.org/conferences/microtas2018/
 
Description Development of a fieldable autonomous bio detection platform for collection of low concentration airborne tree and plant pathogens 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This was an invited presentation to Scientists and policy makers at the Defence Science & Technology Laboratory, Porton Down. This was a one-off presentation specifically to provide a technical presenation on the development of a fieldable autonomous bio detection platform for collection of low concentration airborne tree and plant pathogens to a highly relevant community, assessihng cross cutting capability of the instrument.
Year(s) Of Engagement Activity 2017
 
Description Development of biodetection technology for defence of aquatic organisms 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This was an invited presentation to Scientists and policy makers at the Centre for Environment, Fisheries & Aquaculture Science, Weymouth. This was a one-off presentation specifically to provide a technical presentation on the development of fieldable autonomous bio detection platforms and the associated challenges that need to be overcome in order to provide meaningful monitioring capability in real-world settings. This presentation highlighted the research findings of teh THAPBI instrument development process to a highly relevant community, emphaisising the cross-cutting capability of the core elements of the fluidic analysis system within the instrument.
Year(s) Of Engagement Activity 2018
 
Description EXPO - AGROFUTURO 2018: Advances in automated, integrated biodetection systems for future agritech applications towards intelligence led farming. 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Expo Agrofuturo is the leading Business and Knowledge Platform for the Agro industry in Latin America. Our research findings were presented alongside our prototype automated pathogen biodetection systems at the British Embassy in Columbia. The exposure to this research was broad with over 12800 visitors across 12 countries visiting the exposition. The Agrofuturo Expo has become the most relevant hub or all farming and agri-tech agencies to converge, with a specific focus on strategic development towards the future of agriculture and the technology that supports this industry.
Year(s) Of Engagement Activity 2018
URL https://expoagrofuturo.com/en/about-expo-agrofuturo/
 
Description Innovation in Plant Biosecurity Conference Oral Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This activity will happen within teh reporting period but has yet to occur. This is a major conference bringing together plant health professionals and invasive species experts from across Great Britain & beyond, to discuss novel strategies for improving plant biosecurity and establish a sustainable knowledge exchange. The conference is organised against the backdrop of the Plant Biosecurity Strategy for Great Britain, as released in 2014, and revisions to the EU Plant Health Regime, which are soon to be realised. There are a number of ways in which biosecurity innovations can be imagined and realised and these are reflected in the four main themes of the conference with our submission primarily focusing on thematic area 1: 1. technology 2. emerging risks 3. movement and borders 4. behaviours
Year(s) Of Engagement Activity 2017
URL http://researchprofiles.herts.ac.uk/portal/en/publications/design-of-a-high-efficiency-cyclone-for-c...
 
Description Intelligent Sensing Systems for Early Detection of Animal and Plant Health Threats Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact 70+ individuals from across the Animal and Plant Health protection arena met at a joint workshop organised and delivered by the BBSRC, ESPRC and DSTL to identify any existing gaps, potential opportunities and available knowledge &skills to adress emerging animal and plant health threats. The event was an opportunity for significant cross dicsiplinary discussion and potential multidisciplinary solutions to be discussed with a view to informing future BBSRC activities in future.
Year(s) Of Engagement Activity 2017
 
Description Invited to Rothamsted Open Innovation Forum 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact The Innovtaion Forum was an aopportunity to meet and work with international delegates from across the agri-food supply chain and beyond. Experts in crop protection, plant breeding, seeds, animal and crop traits, crop nutrition, animal breeding, animal feed, animal health, agronomy, primary production, food manufacturing and food retailing were in attendance and there were a variety of active break out sessions designed to engage and highlight existing barriers to the plant and agri-food sectors. During the event UH were able to present their existing to work and highlight capability in resolving technological challenges in particular with refernce to existing intelligent mechanical and electronic devices, sensors and equipment.
Year(s) Of Engagement Activity 2016
URL http://roif.co.uk/
 
Description Presentation to open Agri-Tech East Agritech week 2018 at the University of Hertfordshire 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact This was one of 3 main keynote presentations to showcase the breadth of agri-tech research at the University of Hertfordshire to launch the start of the 2018 Agri-Tech East Agri-tech week.

The event celebrates innovation across the east of England with a week of agri-tech events. Agri-Tech Week is a partnership initiative to showcase excellence in innovation across the agri-tech value chain, brokering links and fostering new relationships between businesses, researchers and government. This was also an opportunity to welcome new collaborators on research in the agri-tech arena.
Year(s) Of Engagement Activity 2018
URL https://www.agritech-east.co.uk/agritech-week-2018/
 
Description Tree Health and Plant Biosecurity Initiative (THAPBI) final project dissemination conference poster presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact A Poster presentation and multi-user 'speed dating' technology talk was presented to the audience of the Tree Health and Plant Biosecurity Initiative dissemination event organised by the BBSRC. The poster presented detailed the 'Development of an automated smart trap for detection of Chalara Fraxinea [Hymenoscyphus fraxineus]'.
Year(s) Of Engagement Activity 2018
 
Description Tree Health and Plant Biosecurity Initiative (THAPBI) final project dissemination event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This event was the final dissemination workshop of the Tree Health and Plant Biosecurity Initiative organised by the BBSRC. With keynote speakers including Lord Gardiner or Kimble, Parliamentary Under Secretary of State for Rural Affairs and Biosecurity and closing remarks by Dr Nicola Spence, Defra Chief Plant Health Officer, this event was an opportunity for researchers and practitioners to engage with the wider community, stakeholders and policy makers to showcase the achievements of the THAPBI programme. The University of Hertfordshire Microfluidics & Microengineering Research Group, under the "New Approaches for the early detection of tree health pests and pathogens" research programme, demonstrated the prototype Integrated automated pathogen collection and detection instrument.
Year(s) Of Engagement Activity 2018