Examining the potential of environmental DNA analysis and enhanced biosecurity for the management of Zoonotic Iceberg Diseases on Sheep Farms

Iceberg diseases are a group of five untreatable wasting diseases which cause significant losses to the sheep industry. In recent years, substantial increases in the prevalence of these diseases have been observed in UK sheep flocks, which has been compounded by poor farmer awareness/understanding and by limitations of diagnosis methods. Urgent action is required to limit the spread of these diseases and to minimise their impact. Of particular concern are Ovine Johne’s Disease (OJD), caused by M. avium subsp. paratuberculosis (MAP) and Caseous Lymphadenitis (CLA), caused by C. pseudotuberculosis, which are zoonotic. In humans, C. pseudotuberculosis infections can cause painful skin lesions and abscesses, whilst MAP infections can lead to Crohn’s disease.

Although CLA cases in humans in the UK is currently rare, the increasing prevalence of CLA within UK flocks will enhance opportunities for this emerging zoonotic disease to transmit to humans. High CLA prevalence in Australian sheep in the 90s was associated with a significant rise in human CLA. MAP is also a public health concern as a zoonotic pathogen, which can cause Crohn’s disease in humans, with OJD regarded as an emerging zoonotic disease risk. Both CLA and OJD can also transmit to cattle, companion animals (dogs/cats), and wildlife species (deer/rabbit).

Both diseases are highly contagious and can be transmitted through direct contact with animals/bodily fluids, aerosols, contaminated surfaces, and environmental sources, and thus environmental screening has potential to determine disease presence whilst effective farm biosecurity is regarded as a key control strategy to limit transmission. Recently, substantial progress has been made in the field of eDNA analysis, where large volumes of water/air can be screened for the presence of pathogen genetic material which can indicate the presence/prevalence of pathogens in the environment and potentially in host animals. Despite the successful application of eDNA analysis in ecology, the application in health has been limited despite its great potential. Regarding biosecurity, on-farm practices that are associated with disease transmission, as well as other factors such as sheep purchasing policies can be optimised to limit disease risk. However, enactment of these practises are influenced by cultural factors such as trust in other farmers, or institutional factors such as forms of certification. Trust may also affect the use of and interpretation of diagnostic tests.

This proposed project has two aims. Firstly, it will develop and utilise an eDNA assay to screen environmental matrices to identify the presence of C. pseudotuberculosis and MAP. The second aim will be to evaluate current sheep farmer biosecurity policies and seek to develop guidance for behavioural interventions to reduce disease risks associated with sheep trading and between farm movements.

Objectives:

1. Investigate optimal eDNA capture and extraction methods for various farm environmental matrices including drinking water from troughs, water pools on pasture and the air
2. eDNA analysis of the farm environment to identify presence of CLA and OJD in sheep flocks: farms with known iceberg disease statuses will be identified and eDNA analysis will aim to identify if these iceberg disease pathogens can be detected using a metabarcoding methodology.
3. Identify the main behavioural factors affecting farmers’ approaches to managing Iceberg diseases via semi-structured interviews with farmers who have and have not experienced these diseases.
4. Develop an interactive game with which to explore farmers responses to different behavioural influences designed to managed Iceberg diseases, including the provision of environmental sampling data, disease risk status and other forms of flock health information.

The successful candidate will develop multi-disciplinary expertise in molecular biology, livestock science and social science. Specifically, the student will receive extensive training in eDNA analysis, nanopore sequencing and the use of social science methods (surveys, interviewing) and theories (such as socio-cultural approaches including ‘good farming’) to analyse farmers’ behaviour. Furthermore, the successful candidate will engage with industry including project partners Hybu Cig Cymru/Meat Promotion Wales (HCC), an industry-led organisation responsible for the development, promotion and marketing of Welsh red meat and the National Sheep Association (NSA) who represents the views and interests of UK sheep producers. HCC and NSA will provide industry expertise to aid project development and will also facilitate industry engagement via farmer events and their respective networks to recruit participants and to share research findings.  

Studentship Information

The studentship will commence in October 2023 and will cover tuition fees (for both UK and international applicants) as well as providing a maintenance grant. In 2023 the maintenance grant for full-time students was a minimum stipend of £17,668 per annum. As well as tuition fees and a maintenance grant, all students receive access to OneZoo training and additional courses offered by Aberystwyth University’s Graduate School.

A very high standard of applications is typically received, the successful applicant is likely to have a very good first degree (a First or Upper Second class BSc Honours or equivalent) and/or be distinguished by having relevant research experience.

How to apply:

You can apply online - consideration is automatic on applying for a PhD with an October 2024 start date.

Please use our online application service at:

How to apply : Study With Us , Aberystwyth University and choose Aberystwyth University - Biological Sciences C1250 PhD

Please specify in the funding section that you wish to be considered for UKRI OneZoo funding.

Please specify that you are applying for this particular project and name the supervisor.

Information on the application process can be found here How to apply : Study With Us , Aberystwyth University

If not successful in being shortlisted for this particular studentship you could be considered for other studentships within the OneZoo program, please see the full list here: OneZoo

Application deadline:

1^st May 2023 with interviews (either in person or online) being held on or around end of May and decisions being made by June 2023 for a 1^st Oct 2023 start.

General Information

Our transdisciplinary OneZoo CDT will equip the next generation of world-leading scientists with the skills and insight necessary to tackle current and future zoonotic threats.