Optisense Limited Public Funding

Increased international trade is moving plant material and their pests globally, whilst climate change is extending their new and natural ranges. Non-native pests are regulated by Defra and the diversity of pests, materials and pathways through which they can arrive make early detection problematic. The biosecurity front line, the Animal and Plant Health Agency (APHA), inspect traded plants for planting and plant commodities, including wood and wood products, and perform in-land inspections in nurseries, recently planted sites and the wider environment. This is mostly achieved by visual examination for signs of pests and symptoms of disease. In recent years APHA have deployed field tests (e.g. Loop mediated AMPlification -- LAMP - technology) at borders to confirm identifications, which benefits trade as goods do not have to be held whilst inspectors await results of laboratory analysis. However, the relatively complex methodology used consumes time, taking inspectors away from inspection activity to perform diagnostic analysis. In addition, their unfamiliarity with diagnostic techniques can lead to poor reproducibility. Phase 1 of the project, developed and tested a prototype. The work proposed here seeks to develop a completely automated, microfluidic cartridge-based LAMP detection system to enable APHA inspectors to perform tests at point of entry (PoE) without hands-on intervention. In addition, a lysis buffer was selected and tested in a prototype sample disruptor. Finally, work with phytosanitary inspectors identified the priority pests for Phase 2 of the project. Phase 2 will first concentrate on preparing the microfluidic cartridge system for commercial production. The prototype sample disruptor developed in Phase 1 will be redesigned to be fit for purpose. Assembly jigs and automation equipment will be developed to support preparation of thousands of cartridges for delivery to customers. The injection moulded cartridges will be validated to international standards (EPPO PM 7/98) for the priority pests identified (_Bemisia tabaci__, Liriomyza huidobrensis, L. sativae and L. trifiolii_). Phytosanitary inspectors will be trained to use the new equipment to facilitate deployment and broader dissemination activities will introduce the technology to a wider stakeholder group. The new approach will use the same validated LAMP tests that are currently available but will provide end-to-end automation of the process of sample disruption, reaction set up and interpretation of results. The outcome of phase 2 will be improved time and resource efficiency of inspectors, improved detection rates of regulated pests and faster movement of traded goods through border control posts.

Whilst the need to produce more food from a smaller area of land has never been greater, we still lose 1/3 of all crops to pests (invertebrates, bacteria, fungi and viruses). Increased global trade is moving plant material and their pests globally, whilst climate change is extending their new and natural ranges. Non-native pests are regulated by Defra and the diversity of pests, materials and pathways through which they can arrive make early detection problematic. The biosecurity front line, the Animal and Plant Health Agency (APHA), inspect traded plants for planting and plant commodities, including wood and wood products moving in trade and perform in-land inspections of plants in nurseries, recently planted sites and the wider environment. This is achieved primarily through visual examination for signs of pests and symptoms of disease. In recent years APHA have deployed field tests (e.g. Loop mediated AMPlification -- LAMP - technology) at Points of Entry (PoE) to confirm identifications, this benefits trade as goods don't have to be held whilst inspectors await results of laboratory analysis. However, the relatively complex methodology used consumes time, taking inspectors away from inspection activity to perform diagnostic analysis. In addition, their unfamiliarity with diagnostic techniques can lead to poor reproducibility resulting in false positive and false negative results. The proposed work seeks to develop a completely automated, microfluidic cartridge-based LAMP detection system, to enable APHA inspectors to perform tests at the point of entry (PoE) without any hands-on intervention. The new approach will use the same validated LAMP tests that are currently available but will provide end-to-end automation of the process of sample disruption, cell lysis, reaction set up and interpretation of the results. The outcome of this is expected to be improved time and resource efficiency of inspectors along with improved detection rates of regulated pests and faster movement of traded goods through border control posts.

Apple scab and downy mildew are devastating diseases of apple orchards and vineyards, respectively. They are spread by airborne spores and, if left untreated, cause significant losses to growers. Currently, growers control these diseases by frequent applications of fungicides (up to 15 treatments annually in apples and 10 in vineyards), which are costly to the grower, can adversely impact the environment and are increasingly unacceptable to many consumers. Growers and agronomists use weather-based disease risk forecasting tools to identify when the crop is at risk of infection, though these tools give frequent false positive and negative signals, resulting in both under and over use of synthetic pesticides. The outcome of which are unnecessary costs for the grower when sprays are unneeded (false positives) and disease emergence/increase when they are not used (false negatives). The risk forecasting tools do not currently take into account the presence of spores which spread disease. This project will demonstrate the feasibility of using spore measurements to indicate to growers when the disease is moving into their crops. The SporeSentry (Optisense) instrument is a prototype battery-powered, automated spore sampling and testing device that comprises a multi-functional microfluidic cartridge that separates spores from the air, breaks up the spores to release the DNA and performs DNA based tests for the specific disease targeted. The instrument is connected to the mobile network to transfer data in real-time. The project will test the feasibility of using real-time measurement of spores moving in a crop to predict disease. In addition we will value engineer the consumable cartridge to make it as affordable as possible for uptake in the agri-tech sector. Linking information on spores to risk forecasting tools that predict when conditions are conducive for infection and indicating this to the growers/agronomists in real-time is a significant innovation which could massively change our use of pesticides. This will lead to both a decrease in unnecessary spraying when risks are low and improvement in precision application and fungicide choice when the risk of disease is high.

Clinical mastitis is one of the major causes for antimicrobial use on dairy cattle farms. There is evidence to demonstrate that on-farm tests help motivate and engage farm staff with the control of mastitis, but continuous monitoring of farm protocols and procedures is required by the herd's vet. There are now many options for on-farm mastitis diagnostics available, helping to decide which antimicrobial to use. However, the mastitis treatment protocols integrating on-farm diagnostics are rapidly changing with some data now available to demonstrate that gram-negative infections are likely to result in self-cure. Therefore, appropriate quality assurance should be considered for a successful on-farm diagnostic test. The use of diagnostics is widely recognised as a powerful tool for improving animal health, with a wide variety of diagnostic tests available using a variety of biochemical and physical techniques. However, a common challenge to most diagnostics tools used in agriculture/veterinary medicine is a lack system integration and a slow pace of diagnosis. As a result, massive inefficiencies in logistics, increased wastage, and a lack of evidence for key policy making, especially for the dairy industry exist. In this project, the consortium will build upon work completed in IUK project 105144 for the rapid target identification of mastitis pathogens capable of identifying 16 different pathogens, facilitating specific diagnosis. Delivering fast (~1hr), low-cost testing whilst maintaining excellent sensitivity/specificity. A specific innovation focuses on the combination species panel of target microorganisms included in the diagnostic, enabling the discrimination of contaminated samples and identifies the pathogens present in each sample, informing treatment decisions. By developing a novel hardware and software solution to collate and share diagnostic results, it is hoped that animal health and welfare will be improved and protected, farm productivity maximised through disease reduction and logistical barriers relating to expression of expected milk yield can be overcome.

The use of diagnostics is widely recognised as a powerful tool for improving animal health as well as food hygiene and safety, with a wide variety of diagnostic tests available using a variety of biochemical and physical techniques. However, a common challenge to most diagnostics tools used in agriculture/veterinary medicine is a lack of ability to interface with the entire supply chain, without considerable efforts from the veterinary surgeon or farmer. As a result, massive inefficiencies in logistics, increased wastage and a lack of evidence for key policy making, especially for the dairy industry exist. In this project, the consortium will attempt to a) expand the impact of _currently available_ diagnostic tests, developed by the consortium and designed to help vets choose a suitable treatment outcome, and targetted antibiotic therapy where appropriate and b) create new targeted modules relevant for the dairy industry. By developing a novel hardware and software solution to collate and share diagnostic results, it is hoped that animal health and welfare will be improved and protected, farm productivity maximised through disease reduction and logistical barriers relating to expression of expected milk yield can be overcome.

Red Apple is looking to develop and implement technological innovation in the China and UK apple production systems to increase yield and quality as well as reduce supply chain losses. The project is testing two technologies: 1) spectral cameras that can identify plant stresses due to, for example, water or nutrient imbalances or pest and disease; 2) traceability systems that can transfer appropriate information to stakeholders along the supply chain to maintain higher quality levels and reduce losses. The findings from the first technology are expected to help growers to achieve a better orchard management around pruning, blossom management and harvest dates, which will eventually increase yields and quality in a sustainable manner, reducing inefficient inputs of fertiliser and pesticides. The second will ensure not only the reduced losses but also that quality attributes can be linked to particular producers as well as production techniques, management of the crop, and harvest dates. Thus the two parts of the project are interlinked

Controlling disease relies on early and accurate diagnosis informing timely and targeted intervention strategies. Good resistance management is based on minimising the levels of exposure of the target pathogen to the fungicide, only spraying where the risk warrants treatment. Knowledge of the resistance status of a field population will allow specific targeting of products avoiding use of ineffective treatments, maximising efficacy and longevity of active compounds. This multi-disciplinary project brings together agronomy services providers (Agrii) diagnostic providers (Optisense/GeneSys) and underpinning science (Fera) stakeholders to deliver a rapid, hand-held, in-field test for real-time monitoring of fungicide resistance strains of Mycosphaerella graminicola (Septoria tritici) within crops. The results of testing will directly inform the user on interventions using the correct fungicide to control the specific genotype of the pathogen present in the crop. This method will save money on ineffective spraying, improve yield, decrease losses, prevent build up of resistance and prolong the life of active chemicals and promote their responsible use improving environmental stewardship.

National survey data show fungicide use on wheat continues to increase despite fluctuations in disease pressure, reaching a 30 year high in 2012 (Defra). Septoria tritici is the most significant foliar disease in UK wheat causing between £43 to 53M in yield losses annually; control is by fungicide application costing £82M annually (GFK Kynetec 2013). Yellow and brown rust are more sporadic but cause significant losses in bad years; control relies on preventative spraying. This cross-disciplinary project proposes a precision agriculture solution, developing a field-based instrument for detecting pathogen ingress into crops and reporting results of pathogen presence into a decision support tool such asCropMonitor in real-time. The proposed instrument will provide growers/agronomists with real-time information on inoculum moving into a crop (rather than symptoms), enabling more effective timing and selection of fungicide application, resulting in better control, increasing yield, and improved environmental stewardship.

This project will develop a system for rapid detection of hazardous bacteria in foodstuffs. The system is highly innovative, and will be easy to use by food handlers, and farm workers, without needing to send samples to third parties for analysis. This system will help to improve food safety and reduce infections in humans, which will increase consumer confidence in the UK food supply.

Background The research work is being undertaken by a consortium of research and industry based technologists, scientists and poultry producers. The aim is to develop a rapid test system that can be used with great accuracy to evaluate on the farm whether the flock is carrying in its visceral tract the campylobacter’s of C Jejuni or C Coli. The bacterium does not harm the birds but is a major human pathogen causing outbreaks at the level of between 70.000 and 300.000 cases per year in the United Kingdom. We believe that via greater knowledge and a targeted response in the slaughter plant with increased carcass washing and the development of other factory interventions, we can reduce the human infection rate by up to 70%, saving the Health service considerable sums and reducing the human cost of many lost days off work. Progress to date. Selective studies have been undertaken to prove that the lamp assay process can show when either C Coli or C Jejuni are present. Further tests have then been undertaken to show that the response on the analyser to C Coli is dramatically different to that for S Aureus, L Monocytogenes, and S Epidermis. All of these tests have been successful. We have then moved to assess at what levels of capture of the Campylobacter cells can we still get a distinctive and positive test result, having collected the organisms on beads encrusted with the antigen for the target bacteria. Results at annealing temperatures. Further work has been undertaken to show the effects of the tests on samples that have been selected using coated beads, and then the samples are heated to kill and break down the DNA of the target organism. This test group was also effective with a distinct and clear plot for the target organism and with no effect being seen from other bacteria tested alongside the campylobacter’s. Progress We are pleased with the progress and success of the work in the first quarter, and have progressed better than we had expected. Samples of faecal samples have been collected direct from turkey farms and further tests are being undertaken. Second Quarter targets. Additional verification work will be undertaken to verify the selectivity and to determine the detection limit of the assay. An internal amplification control will also be constructed and incorporated into the assay. We hope to complete the instrument design specification, and continue with the electronics development. The concept is starting to look like a farm friendly process that can deliver accurate results even from lightly infected flocks, with very good accuracy, and with tests completed in well under an hour. JEREMY HALL - Lead Co-ordinator and Industrial lead. 13 July 2012

Awaiting Public Summary