Early Disease Detection and Monitoring in Farm and Field

Lead Research Organisation: Harper Adams University
Department Name: Food Science & Agrifood Supply Chain Mgt

Abstract

This research proposal specifically targets Campylobacter infection of broiler chickens to demonstrate the utility of this
sensor-based detection system in addressing a significant global meat production problem that impacts on animal health
and welfare, and human health. Campylobacter jejuni, the most frequently reported food-borne pathogen associated with
human illness in the UK, causes over 460,000 reported cases of campylobacteriosis annually, leading to over 22,000
hospitalisations and 100 deaths, at a cost to the UK government of over £900 million. While substantial research funding
has been invested by the UK Food Standards Agency (FSA) and other organisations across the farm to fork continuum, the
industry is currently focussed on Campylobacter reduction using carcass processing interventions such as rapid surface
chilling rather than on farm-level interventions which would serve to prevent/reduce the substantial impact C. jejuni infection
has recently been estimated to have on animal health and welfare in intensively farmed poultry.
The aim of this research is to develop a commercially viable on-farm real time portable sampling and detection tool to
determine the Campylobacter status of flocks during production and prior to slaughter. The preliminary research to be
carried out by this team will use an appropriate extraction system in synergy with GC-MS technology to capture and identify
unique volatiles released through the metabolic activities of Campylobacter. Determination of detectable levels of known
Campylobacter-associated volatiles will be investigated using several species and strains of Campylobacter in pure culture
and in the presence of a range of different background materials (e.g. chicken faeces; litter) at different stages of growth.
Screening for Campylobacter-associated volatiles in chicken (and possibly other poultry) faecal material using confirmed
Campylobacter-positive and -negative samples will also be conducted, including PCR identification of isolates as required.
The unique volatiles identified by GC-MS will then be used to optimise the sensor, and on-farm detection will be re-evaluated
using adsorbents containing trapped volatiles. The Harper Adams team will utilise a competent, post-doctoral
analytical chemist who will be supported by Dr Lynn McIntyre with her wealth of knowledge on Campylobacter biology and
by Dr Frank Vriesekoop who brings expertise in pathogen physiology and the application of analytical chemistry and
method development.
A number of potential applications and benefits are associated with the development of this testing platform which could
extend beyond the single issue of Campylobacter detection in poultry to multiple target pathogens/analytes of relevance to
crops and animals such as E. coli O157, Salmonella, mycotoxins and botrytis, and detection of specific diseases such as tuberculosis and mastitis. In relation to this specific application, the development of a hand held air sampling device
capable of instantaneously detecting the presence of Campylobacter would offer a real time detection method not currently
available to the poultry industry which could be applied at various points in the poultry production chain, from hatchery
through farm production and processing, to the retail level. The ability to make simple frequent measurements to
accurately pinpoint disease onset would enable farm/area mangers to identify potential links to farm activities and biosecurity practices, which is not currently possible using pathogen culture or PCR protocols. Likewise, such a detection system could be used during processing to assess the impact of carcass reduction strategies. Empowering poultry industry staff to make changes that can reduce the incidence of Campylobacter in poultry destined for the retail market would ultimately result in the greatest benefit; that of a reduction in public health burden associated with this zoonotic pathogen.

Technical Summary

This research proposal specifically targets Campylobacter infection of broiler chickens to demonstrate the utility of this sensor-based detection system in addressing a significant global meat production problem that impacts on animal health and welfare, and human health. Campylobacter jejuni causes >460,000 reported campylobacteriosis cases annually, at a cost to the UK government of >£900 million. While substantial research funding has been invested, industry is currently focussed on Campylobacter reduction using carcass processing interventions rather than farm-level interventions. The aim of this research is to develop a commercially viable on-farm real time portable sampling and detection tool to determine Campylobacter status of flocks during production prior to slaughter. Preliminary research will use an extraction system in synergy with GC-MS technology to capture and identify unique volatiles released through the metabolic activities of Campylobacter. Determining detectable levels of known Campylobacter-associated volatiles will be investigated using several species and strains in pure culture and in different background materials (e.g. chicken faeces; litter) at different stages of growth. Screening for Campylobacter-associated volatiles in poultry faecal material using confirmed Campylobacter-positive and -negative samples will also be conducted. The unique volatiles identified by GC-MS will then be used to optimise the sensor, and on-farm detection will be re-evaluated using adsorbents containing trapped volatiles. Instantaneously detecting the presence of Campylobacter would offer the poultry industry a method which could be applied at various points in the poultry production chain, from hatchery through farm production and processing, to the retail level. This will enable farm/area mangers to identify potential links to farm activities and biosecurity practices while it could also be used during processing to assess carcass intervention strategies.

Planned Impact

There are a number of clearly identifiable and wide-ranging beneficiaries of this research, including:
* The project research team;
* UK and international academic and research organisations working in the area of Campylobacter infection/contamination
of poultry (see academic beneficiaries section);
* Commercial private sector poultry companies and retailers;
* Policy-makers, within international, national, local and government agencies;
* The wider public as food consumers.
The project team will benefit directly from involvement in the proposed consortium comprised of professionals with a
diverse set of skills ranging from project management through microbiology and chemistry analytical techniques to
advanced technology, data handling and industry application experience. Participation in this project will also put the
Harper Adams team in a strong position to promote and develop this technology for other animal and crop diseases,
potentially in collaboration with colleagues in the Animals and Crops Departments, and with other UK and international
academic and research collaborators.
The work being proposed here will be progressed in collaboration with Banham Poultry Ltd., an independent family
business with a turnover of approximately £100m per year and sales of 650,000 chickens per week. There are a number of
practical benefits associated with adoption of this technology by this company including identifying potential links to day-today
farm activities and biosecurity practices, and knowing the disease status of flocks prior to slaughter which will allow
them to schedule positive flocks to the end of the slaughter window to eliminate cross-contamination. Where certain
processing interventions (such as rapid surface chilling) may be implemented in the future, knowing the Campylobacter
status of flocks would allow interventions to be "turned on/turned off" as required, rather than keeping them "turned on",
potentially resulting in cost savings. Proactive use of the technology being proposed in this application could also give
companies such as Banham a competitive advantage in the retail market, and allow retailers to promote the sale of "clean"
poultry meat from such suppliers.
There are of course many other UK (and international) poultry companies that would benefit from the implementation of an
on-farm detection system for Campylobacter (and other pathogens). The potential to monitor chemicals such as ammonia
emissions from poultry houses could also be appealing to poultry companies looking to expand production at existing sites
rather than trying to get permission for new farms.
Ultimately, expected improvements in Public Health would benefit all stakeholders in the poultry production chain including,
importantly, the wider public end user. The FSA's target to reduce cases of campylobacteriosis by 50% would, for example,
result in a reduced cost to the UK government of £450 million. In many countries, including the UK, New Zealand and
Australia, significant funding has also being invested by regulators and the poultry industry to reduce Campylobacter
contamination of poultry. There are therefore significant international opportunities to be gleaned from this research which will potentially contribute to cost savings, and the potential to refocus Campylobacter reduction at the farm level rather than
further along the food chain. It is anticipated that a commercial detection system will be produced as a direct output of this
multidisciplinary research project within a 3 - 4 year period which could conceivably develop a new approach to routine
Campylobacter detection techniques, positively change current on-farm attitudes and (biosecurity) practices of poultry
industry staff, enhance the health and well-being of consumers, and contribute a significant quantity of valuable on-farm
research data to organisations such as the FSA and Defra to inform future policy decision-making.
 
Description INCREASED RESEARCH CAPABILITY GENERATED FROM TRAINING DELIVERED IN SPECIALIST SKILLS: Involvement in this project has enabled us to increase our research capability beyond our original remit of microbiological and GC-MS analyses, into Enose sensor development and detection. Through the purchase of the Bloodhound 307B system developed in this project and training provided by Roboscientific in the use and analysis of data, we are now in a position to employ this tool for other applications of relevance both on-farm and across the food supply chain. SIGNIFICANT NEGATIVE RESULTS AND/OR RESEARCH PATHS CLOSED OFF: Our original goal (as specified by Roboscientific) was to identify a set of unique Volatile Organic Compounds (VOCs) associated with Campylobacter species to develop more specific Enose sensors for the early detection of Campylobacter in chicken sheds. We ran a year-long project to detect and identify the unique VOCs associated with Campylobacter which would enable us to differentiate Campylobacter from other bacterial cultures and to detect any possible Campylobacter-unique VOCs against the background VOCs from a chicken house. However, Campylobacter is a difficult organism to culture and the growth conditions used in a laboratory are somewhat different to a poultry shed environment. This presented a real challenge in getting meaningful results. Following set-up and calibration of the GC-MS and using the expertise of two experienced PDRAs, we were unable to identify any unique VOCs that could be associated with Campylobacter grown under microaerophilic or aerobic laboratory conditions. With Campylobacter-positive litter samples, it was possible to see some VOCs that changed in detection level when compared to Campylobacter-negative litter samples. While they were not unique for Campylobacter, they changed significantly giving a route to the detection of Campylobacter in the environment where it needed to be measured.
NEW IMPROVED RESEARCH METHOD: The inability to identify unique VOCs through GC-MS analysis was overcome by adopting a "iterative learning" process. Through this practical process Roboscientific was able to build a highly sensitive sensor head to Campylobacter. This process was both simple and did not require expensive computing and analytical equipment. It also presented Roboscientific with a generic process that can be used in the future development of sensor heads to other targets.
IMPORTANT NEW RESEARCH QUESTIONS OPENED UP: During the course of this project, it has become apparent through interactions with industry that there are a number of diseases of greater concern to the poultry farmer than just the detection of Campylobacter (although at the time of funding this was being identified as a priority). These include dysbacteriosis and coccidiosis - economically impactful diseases where early diagnosis would enable the farmer to more efficiently manage the flock, potentially reducing the need for medical intervention and improving the overall health of the birds, leading to higher yield. Successful future on-farm detection systems will therefore need to be multi-facetted in nature, and move beyond the detection of traditional bacterial targets into more challenging avenues of research including protozoan and viral diseases. The key question for us to answer is whether the Enose approach can achieve this.
Exploitation Route AGRICULTURE, FOOD AND DRINK: The Enose detects the activities of viable microorganisms, which is a key advantage over DNA-based techniques where environmental DNA derived from dead cells can give positive results. The Enose is one means whereby detection can be monitored in situ and in parallel with other detection methods to determine whether a positive detection event is truly indicating the presence of flock infection/disease. Detection capability also needs to expand to a wider range of organisms/diseases in order to enhance the utility of the Enose in poultry production environments, and to broaden application to a wider range of farming environments. Beyond the farm gate, there is also great scope for application but detection of lower levels of contamination typically found in foods and processing environments will remain a key challenge.
HEALTHCARE: Evaluating microbial metabolism via an Enose approach may also have application in the healthcare sector, where presumptive pathogen detection using traditional microbiological culture techniques can take several days to confirm. An understanding of the VOC profiles produced during culture of different pathogens may provide a means to enhance and/or speed up the diagnostic process, producing more accurate and/or faster results.
Sectors Agriculture, Food and Drink,Healthcare

 
Description Our findings have been crucial in developing a functional on-farm Campylobacter detection system, which has enabled our poultry industry partner to study Campylobacter levels on one of their biggest Company-owned farms, allowing them in turn to consider biosecurity and disease control, and to increase general awareness and understanding of Campylobacter within their business. Through our many dissemination activities, we have been active in promoting the concept of on-farm detection of Campylobacter, and Dr Lynn McIntyre was invited to present research findings at a Poultry Industry Association of New Zealand (PIANZ) Livestock Managers meeting where the emphasis on Campylobacter control is shifting from the poultry processing plant back to the practicalities of on-farm production. Our involvement in the project has also been instrumental in developing a new "process" to develop new sensors for new applications, replacing a previously expensive and scientifically valid process using GC-MS and computer modelling in favour of "iterative learning". This has the potential to greatly increase the speed at which sensors can be selected and developed for new applications in a very cost effective manner. Through subsequent and more recent post-graduate research funding we have also been able to review the data analysis approach related to sensor data collection, and to apply the detection system to the red meat sector.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Education
Impact Types Cultural

 
Description Agilent research visit 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Industry/Business
Results and Impact Research meeting with Agilent to investigate opportunities for collaboration. We have used an Agilent GC-MS system for this research project.
Year(s) Of Engagement Activity 2017
 
Description Conference presentation at International Association for Food Protection European Symposium on Food Safety, Brussels, Belgium. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Gibson, T., Curtis, S., Curtis, B., McIntyre, L., Vriesekoop, F., Hardy, S., Lock-Pender, S. and Stacey, A. 2017. Early Detection of Campylobacter Using Air Sampling and VOC Analysers. International Association for Food Protection European Symposium on Food Safety, Brussels, Belgium (talk). 29-31 March.
Year(s) Of Engagement Activity 2017
URL https://www.foodprotection.org/upl/downloads/library/programme-book-brussels.pdf
 
Description Conference presentation at International Association for Food Protection annual meeting, Tampa Convention Center, Tampa, Florida, USA. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation made in Meat, Poultry and Eggs, and Epidemiology technical session to raise awareness in North America of UK research. McIntyre, L. and Gibson, T. 2017. Tuning the Bloodhound® VOC Analyser to Detect Campylobacter spp. During Broiler Poultry Production. International Association for Food Protection annual meeting, Tampa Convention Center, Tampa, Florida, USA. 12 July 2017.
Year(s) Of Engagement Activity 2017
URL https://iafp.confex.com/iafp/2017/webprogram/Paper15388.html
 
Description Conference presentation at XXth World Veterinary Poultry Association Congress, Edinburgh International Conference Centre, Edinburgh, Scotland. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Conference presentaton in Public Health/E.coli/Salmonella/Campylobacter parallel session. Gibson, T., Curtis, S., Curtis, B., Hardy, S., Lock-Pender, S., Strydom, Q., Ethridge, T., McIntyre, L., Vriesekoop, F., Stacey, A. and Hammond, P. 2017. Early Detection of Diseases in the Field by Monitoring Volatile Organic Compounds. XXth World Veterinary Poultry Association Congress, Edinburgh International Conference Centre, Edinburgh, Scotland. 6 September 2017.
Year(s) Of Engagement Activity 2017
URL http://www.wvpac2017.com/docs/default-source/default-document-library/pdfs/wvpa-2017-full-version-pr...
 
Description FOOD MICRO 2016 conference (Dublin, Ireland) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact McIntyre, L., Gibson, T., Kardar, M., Elgina, F. & Vriesekoop, F. 2016. Developing an electronic nose for on-farm detection of Campylobacter spp. with a view to improving poultry meat food safety. FOOD MICRO 2016 conference, Dublin, Ireland (poster presentation).
Year(s) Of Engagement Activity 2016
 
Description Food Safety Conference (Indonesia) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Dr Lynn McIntyre presented a talk entitled "Improving Poultry Meat Safety by On-farm Detection of Human Pathogens" at the UK-Indonesia Symposium on Engineering, Energy, Environmental Sustainability and Food Security 2015, Universitas Diponegoro, Semarang, Indonesia. The intended outcome is to apply for a UK-Indonesia Newton grant in the area of Campylobacter.
Year(s) Of Engagement Activity 2015
 
Description Innovate UK KTN meeting at Harper Adams University 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Dr Lynn McIntyre presented a review of departmental research including the Campylobacter Enose research (Early Disease Detection and Monitoring in Farm and Field) to visiting Innovate UK staff. A discussion was held regarding complementary research activities in other departments and the potential to apply for KTN funding. 29th November 2017.
Year(s) Of Engagement Activity 2017
 
Description Innovate UK visit to Harper Adams University 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Dr Lynn McIntyre presented a summary of findings of the Campylobacter Enose research (Early Disease Detection and Monitoring in Farm and Field) to visiting Innovate UK staff. A discussion was held regarding outcomes and future research directions. 9th February 2018.
Year(s) Of Engagement Activity 2018
 
Description LEAF Integrated Farm Management Bulletin 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Article on "Fighting Campylobacter in the UK Chicken Industry" written for LEAF Integrated Farm Management Bulletin.
Year(s) Of Engagement Activity 2016
 
Description MSc teaching (Forces Influencing Poultry Production) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Dr Lynn McIntyre gave a lecture entitled "Poultry Flock Health and Food Safety", during which she presented research findings from the Campylobacter Enose project (Early Disease Detection and Monitoring in Farm and Field) to post-graduate students. Questions and discussions were held on the topic with students working in the poultry sector. 17th November 2017.
Year(s) Of Engagement Activity 2017
 
Description MSc teaching (Meat Science and Public Health) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Dr Lynn McIntyre gave a lecture to industry-based post-graduate students entitled "Microbiological detection and enumeration methods", during which she presented research findings from the Campylobacter Enose project (Early Disease Detection and Monitoring in Farm and Field). Questions and discussions were held on the topic with students working in the red meat sector. 12th February 2018.
Year(s) Of Engagement Activity 2018
 
Description Meat Industry Short Course delivery 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Four meat industry graduate trainees and two MRes post-graudate students attended a four day short course entitled 'Animal Production and Meat Processing'. During this event, I gave a presentation on Meat Microbiology and presented the results of the Enose work. This sparked some conversation regarding how the Enose could be applied in other meat applications. One of the MRes students will be undertaking an Enose research project funded by the Worshipful Company of Butchers.
Year(s) Of Engagement Activity 2020
 
Description NFU Poultry Board Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Dr Lynn McIntyre gave a research presentation entitled "What's that fowl smell? Sniffing for Campylobacter in poultry sheds" at a NFU Poultry Board Meeting held at Harper Adams University. The session was set up to showcase poultry-related research happening at Harper Adams. Following this session, I was invited to present my Enose research at a poultry research seminar held at the NFU headquarters.
Year(s) Of Engagement Activity 2018
 
Description NFU Poultry Research Seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Dr Lynn McIntyre gave a research presentation entitled "Sensor-based methods to assess the Campylobacter status of broiler chicken flocks" at the NFU Poultry Research Seminar, NFU Conference Centre, Stoneleigh Park. The intended purpose was to communicate current and topical research activities to the poultry industry. The talk prompted some interesting discussions about Campylobacter, farm biosecurity, UK processing practices and legislation (versus other countries such as the USA) and the challenges of understanding how Campylobacter gets into poultry sheds. One company was particularly interested in looking at further research opportunities.
Year(s) Of Engagement Activity 2019
 
Description New Zealand Institute of Food Science and Technology (NZIFST) Annual Conference (Rotorua, New Zealand) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Dr Lynn McIntyre gave an invited presentation entitled "Campylobacter in the UK" at the New Zealand Institute of Food Science and Technology (NZIFST) annual conference Food Safety Workshop, Rotorua, New Zealand.
Year(s) Of Engagement Activity 2016
 
Description New artificial intelligence sensor 'smells' disease on farm (Farming UK article) 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact "New artificial intelligence sensor 'smells' disease on farm"
This press release highlights the advances made by RoboScientific since the end of this project to commercialise the VOC analyser Campylobacter sensors developed in this project for poultry disease detection.
Year(s) Of Engagement Activity 2021
URL https://www.farminguk.com/news/new-artificial-intelligence-sensor-smells-disease-on-farm_57588.html
 
Description Pirbright Institute Biosensors meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact I was asked to give a talk on my use of biosensors for on-farm detection of Campylobacter at an interest meeting coordinated by Claire Colenutt and Chris Sanders at the Pirbright Institute. The intended purpose was to showcase the use of biosensors in (primarily) animal health research. My talk was well received and has resulted in further discussions with one of my fellow presenters regarding further research opportunities.
Year(s) Of Engagement Activity 2018
 
Description Poultry Industry Association of New Zealand (PIANZ) Livestock Managers meeting (Auckland, New Zealand) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Dr Lynn McIntyre gave an invited presentation entitled "On-farm Campylobacter Control and Detection" at the Poultry Industry Association of New Zealand (PIANZ) Livestock Managers meeting, Auckland, New Zealand.
Year(s) Of Engagement Activity 2016
 
Description Sensors in Food and Agriculture Conference (Cambridge, UK) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Dr Lynn McIntyre and Fittonia Elgina attended the Sensors in Food and Agriculture conference, Moller Centre, Cambridge. Dr Lynn McIntyre also presented an invited talk entitled "Developing a Biosensor Method for On-farm Detection of Campylobacter in Broiler Chickens" which raised awareness of the specific food safety issue of Campylobacter, and participated in a panel question and answer session on the applications and future of sensors in food and agriculture.
Year(s) Of Engagement Activity 2015
 
Description Southern Illinois University Research Seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact On-line seminar entitled "An electronic nose to detect Campylobacter in poultry" delivered by Dr Frank Vriesekoop to PG students in the Molecular Biology, Microbiology and Biochemistry Graduate Program at Southern Illinois University, USA.
Year(s) Of Engagement Activity 2021
 
Description Talk on Electronic detectors (electronic nose) on farms to detect quality related issues. Beijing Polytechnic, China. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Vriesekoop, F. 2017. Electronic detectors (electronic nose) on farms to detect quality related issues. Beijing Polytechnic, China. 23 November.
Year(s) Of Engagement Activity 2017
 
Description Technical discussion regarding Campylobacter testing in the poultry industry 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Invited to attend a meeting with 3 people representing industry and business to discuss Campylobacter testing strategies. Two student research projects (at Undergrad and MSc level) have been initiated following this interaction.
Year(s) Of Engagement Activity 2015