Project Description

A full project description can be found on Find A PhD. Please see below for additional information about this project:

In a changing world, the transmission of pathogens between wildlife, livestock and humans can result in significant livestock productivity loss and increased zoonotic disease risk. Therefore, understanding and predicting how changes in land use and bioclimatic conditions are likely to affect pathogen transmission across the human-wildlife-livestock interface is a key societal challenge that is at the core of NERC’s remit.
The applied nature of this project and the focus on the challenge of managing potentially zoonotic and economically important pathogens within wildlife species falls squarely within the QUADRAT Environmental Management research theme. By addressing a key environmental management challenge, namely how increasing deer numbers and land use and bioclimatic change may impact livestock and human health, this project is relevant to UN sustainable development goals (SDGs), such as reducing food waste and supporting local farmers to eliminate hunger (SDG2), improving health and well-being (SDG3) and mitigating the effects of climate change (SDG13).

Wildlife play an important role in the epidemiology of some of the most important pathogens of livestock and humans, either as reservoirs or vectors of infection. The presence of wildlife hosts can complicate disease management as traditional control measures, such as vaccination, are challenging in wildlife species. Despite the abundance and widespread distribution of both red (Cervus elaphus) and roe (Capreolus capreolus) deer in the UK and increasing awareness that deer may play a role in the epidemiology of numerous zoonotic and livestock pathogens (1, 2), less is known about how these roles may differ between deer species, whose ecology can differ significantly (3), and to what extent land use and bioclimatic conditions drive infection risk in wild deer.
Globally, two environmentally transmitted bacterial pathogens, Leptospira spp. and Mycobacterium avium subsp. paratuberculosis (Map), have been shown to infect livestock and wild deer species (2). Both pathogens are economically important, causing significant disease and productivity losses in livestock and Leptospira spp. are also one of the most common and widespread causes of zoonotic disease. Bioclimatic conditions that favour the survival of these pathogens in the environment, and/or land use changes that facilitate contact between wildlife and livestock are likely to play an important role in driving infection risk. To advance our understanding of the role of wildlife in the maintenance and transmission of these environmentally transmitted pathogens, this project aims to: i) quantify exposure and carriage in wild deer, ii) explore how the epidemiology of these pathogens differs between deer species, and iii) identify and quantify the effects of land use and bioclimatic conditions on infection probability.
Royal Deeside in Aberdeenshire will form the core sampling landscape for this project, providing access to samples collected across an altitudinal and land use gradient (low altitude farmland to high altitude uplands). In addition, samples of tissue, serum and faeces are being collected from deer in Ireland at partner institution Queen’s University Belfast (Morgan lab). A combination of serological and molecular approaches will be used to identify evidence for previous exposure and current infection, respectively. A Geographic Information System (GIS) of the study area will be compiled from remote sensing databases and spatial (landscape, livestock and climatic) associations with positive test results evaluated using a variety of statistical approaches (random forest models and generalised additive mixed models).
This project will suit a student interested in the effects of environmental change on disease ecology and epidemiology. The student will receive multidisciplinary training and will interact with experts in disease ecology, veterinary science, and statistics. This PhD will involve a combination of field work, including liaison with local gamekeepers and deer stalkers to co-ordinate sample collection, laboratory testing and data analysis. There will also be opportunities for the student’s interests to drive the evolution of the project.
Essential skills
  • Strong communication skills
  • Ability to work independently

Desired skills

 

  • Familiarity with statistical software e.g. R and Geographic Information Systems

Supervisors

Primary Supervisor:

Mark Mosely,

mark.moseley@abdn.ac.uk

Eric Morgan

Secondary Supervisor:

Profile: Eric Morgan
Email: eric.morgan@qub.ac.uk
Institution: Queen's University, Belfast
Department/School: School of Biological Sciences

Sandra Telfer

Additional Supervisor:

Profile: Sandra Telfer
Email: s.telfer@abdn.ac.uk
Institution: University of Aberdeen
Department/School: School of Biological Sciences

Additional Supervisor:

Dr Kathryn Allan
University of Glasgow
Veterinary Pathology, Public Health and Disease Investigation
Email

References

  1. Chintoan-Uta C, et al (2014) Wild deer as potential vectors of anthelmintic-resistant abomasal nematodes between cattle and sheep farms. Proc R Soc B Biol Sci 281(1780). doi:10.1098/rspb.2013.2985.
  2. Böhm M, et al (2007) Wild deer as a source of infection for livestock and humans in the UK. Vet J 174(2):260–276.
  3. Latham J, et al (1999) Comparative feeding ecology of red (Cervus elaphus) and roe deer (Capreolus capreolus) in Scottish plantation forests. J Zool 247(3):409–418.
  4. Rahelinirina S, et al. (2019) Leptospira in livestock in Madagascar: Uncultured strains, mixed infections and small mammal-livestock transmission highlight challenges in controlling and diagnosing leptospirosis in the developing world. Parasitology 146(14). doi:10.1017/S0031182019001252.

Research Methods

Sampling and metadata collection will be performed in collaboration with local gamekeepers and Forestry Commission stalkers. Roe deer will be sampled across their range from coastal habitats around Aberdeen to Highland estates (up to 1000m elevation) around Ballater and Braemar. Red deer will be sampled from the lower edge of their range (~100m elevation) around Banchory to some of the highest uplands in the UK in the Cairngorms (up to 1300m elevation). High resolution land use and land cover data will be drawn from free-to-access remote sensing (land.copernicus.eu/ and https://www.space-intelligence.com/scotland-landcover/ ) and used to compile a Geographical Information System (GIS) of the study area, adding data layers comprising interpolated temperature and rainfall records (www.ecad.eu/) and livestock density (apha.defra.gov.uk/), with sampling locations as point data. Following laboratory analysis this will permit testing of associations between disease status and landscape and bioclimatic factors.

Samples will be analysed using a combination of serology and molecular approaches. Serological assays, such as Microscopic Agglutination Testing (MAT) for leptospirosis and ELISA for Map, performed on serum samples, will be used to evaluate levels of exposure. However, because fresh serum is difficult to obtain from wild-shot deer, tissue exudate (‘meat juice’) samples, which pilot data has suggested may be useful for serological surveillance, will also undergo serological testing and evaluated for their suitability to underpin future wider-scale disease surveillance in deer. Quantitative polymerase chain reactions (qPCRs) will be used to identify current infections and quantify infection loads. As both Leptospira spp. and Map are slow growing and challenging organisms to culture, further genetic typing will be undertaken using approaches developed for livestock that allow direct PCR and DNA sequencing from field samples (1).

Expected Training Provision

We are committed to fostering an inclusive and dynamic working environment. We will equip you with highly demanded transferable skills including coding, theoretical and statistical modelling. We anticipate the PhD project leading to publications in international journals. Moreover, you will develop skills in science communication through a variety of traditional and emerging media.

Impact

By addressing the effects of land use and bioclimatic conditions on the transmission of economically important and potentially zoonotic pathogens between wildlife hosts and livestock, this project directly addresses key research areas identified by stakeholders, such as the British Deer Society (BDS), namely:
  • Deer impact on the environment and human interests
  • Impact of humans on deer especially upon their health and welfare
  • Human disturbance and its effects on behaviour, ecology and welfare of deer
  • The role of deer in spread and transfer of livestock and human diseases
  • Responses of deer and their habitat to climate change
Both Leptospira spp. and Map are economically important livestock pathogens that are included in Cattle Health Certification Standards (CHeCS) licensed schemes that aim to promote improved herd health in the UK. Exploring the role that deer might play in the transmission of these pathogens will allow the design of the improved herd health plans, reducing the economic impact of these important pathogens on livestock. These pathogens have been shown to cause disease in deer species around the world. Therefore, identifying the landscapes where transmission between livestock and humans takes place and developing potential strategies for limiting this transmission is likely to improve deer health and welfare. Environmentally transmitted pathogens are particularly sensitive to bioclimatic conditions and by sampling deer across a wide altitude gradient these results may be used to explore how pathogens of deer are likely to respond to climate change.

Proposed Timetable

October 2022-December 2022:
Literature review and study design
October 2022-March 2023:
Red hind and roe doe sample collection in collaboration with local deer managers
January 2023-April 2023:
Laboratory training, molecular and serological analysis of initial samples and further sampling design
April-October 2023:
Red stag and roe buck sample collection
April 2023-March 2024:
Student field work and laboratory analysis
– Engagement with local deer managers and landowners
– Deer and environmental sample collection
– Bioclimatic and land use data collection
– Sample analysis
– Compilation of GIS data
April 2024-October 2024:
Continued field work, statistical analysis, and manuscript preparation
October 2024:
Manuscript submission
October 2024-March 2025:
Final hind and doe sampling refined to address outstanding questions raised by initial analyses
April 2025-October 2025:
Final stag and buck sampling refined to address outstanding questions raised by initial analyses
October 2025-April 2026:
Final analyses and thesis write up

QUADRAT Themes

  • biodiversity

Partners

British Deer Society

BDS believes that if wild deer management is based upon sound scientific principles, it will encourage the co-existence of wild deer populations in balance with farming, forestry, public access and other land uses and also safeguard the health and welfare of the deer themselves. We undertake and fund pure and applied research projects aiming to scientifically explore and understand deer, and the issues they bring for people. Particular topics may be favoured from time to time. These will be listed on the research pages of the BDS website. By addressing the effects of land use and bioclimatic conditions on the transmission of economically important and potentially zoonotic pathogens between wildlife hosts and livestock, this project directly addresses five of the nine BDS research priorities, namely:
  • Deer impact on the environment and human interests
  • Impact of humans on deer especially upon their health and welfare
  • Human disturbance and its effects on behaviour, ecology and welfare of deer
  • The role of deer in spread and transfer of livestock and human diseases
  • Responses of deer and their habitat to climate change

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