A Non-invasive Method to Monitor Status of Johne’s Disease in Dairy Cattle

Secondary Supervisor(s): Dr Karim Farag, Dr Gemma Charlton

University of Registration: Harper Adams University

BBSRC Research Themes: Sustainable Agriculture and Food (Animal Health and Welfare, Microbial Food Safety)

Project Outline

Johne’s Disease (JD), caused by Mycobacterium avium subspecies paratuberculosis (MAP), is a chronic and economically significant gastrointestinal infection affecting dairy cattle worldwide. The disease causes progressive damage to the intestine resulting in persistent diarrhoea, malabsorption and weight loss. Within the dairy industry, reduced milk yields and infertility resulting from JD cause significant financial and welfare concerns. In the UK, JD was ranked as the top cattle disease affecting national production efficiency in a survey conducted in 2021 ¹. Moreover, dairy cows with JD are found to emit up to 25% more greenhouse gases than healthy cows highlighting the substantial environmental and sustainability challenges it poses for the dairy industry.

There is no permanent cure or designated treatment for the disease. Currently, JD is managed by regularly screening and removing chronically infected animals. Timely and accurate detection of JD, especially in during the early sub-clinical infection is therefore crucial for disease management and prevention of the spread. Although various diagnostic methods such as ELISA, culture, PCR, and histopathology are available, the accuracy and sensitivity of those methods are limited, especially in the early stages of infection, due to the transient nature of the disease and pathogen shedding. Hence, this PhD proposal aims to explore an early detection method by integrating Volatile Organic Compounds (VOC) analysis ² with behavioural indicators (BI) from affected cows. We utilise existing diagnostic techniques to validate this innovative approach, aiming to enhance diagnostic accuracy as a non-invasive method for identifying JD using focus studies.

To develop and validate a novel VOC and BI-based tool for monitoring Johne's disease (JD) on farms, we will undertake several key objective;

1. We will collect diagnostic samples, including faeces and blood, along with VOC samples from both JD-affected and healthy animals on a dairy affected with JD. Additionally, we will collect tissue samples (e.g., ileum and mesenteric lymph nodes) from animals culled due to JD for histopathological analysis.

2. We will characterise the VOCs present in these samples using gas chromatography-mass spectrometry (GC-MS) while performing routine diagnostic assays including enzyme-linked immunosorbent assays (ELISA), polymerase chain reaction (PCR), and histopathology to assess the animals' infection status.

3. We will integrate the diagnostic data, VOC profiles, and histopathological findings to design a monitoring tool specifically for JD detection, exploring appropriate statistics to observe the differences in the data to identify key predictive factors associated with the disease.

4. Finally, we will conduct a focus assessment to evaluate the tool's feasibility for use on affected farms, ensuring that it meets practical needs for effective JD monitoring in real-world agricultural settings.

This project aims to develop a non-invasive monitoring tool for JD in dairy cattle, offering a novel diagnostic approach that complements existing methods. By enhancing early disease detection, this tool will help mitigate economic losses associated with JD and support sustainable, carbon-neutral management strategies. Dairy farmers will benefit from a more accurate and efficient method of disease detection and control, ultimately improving herd health and farm profitability while fostering responsible farming practices.

In addition, the project will provide valuable training for an early career researcher (ECR) in veterinary disease monitoring and diagnostics enhancing their skills and employability and scientific knowledge. The multidisciplinary supervisory team consisted of animal health, diagnostics and welfare will facilitate collaboration with industry stakeholders and promote engagement with the scholarly community, aiming to publish peer-reviewed articles and press release. Promoting innovative research skills and strengthening partnerships between academia and industry, this project will contribute to sustainable farming practices.

References

1. Morrison, R. & Rose, D. C. Factors that influence dairy farmers’ decision to implement Johne’s Disease control practices: A systematic review. Preventive Veterinary Medicine vol. 220, https://doi.org/10.1016/j.prevetmed.2023.106053 (2023);

2. Rodríguez-Hernández, P., Rodríguez-Estévez, V., Arce, L. & Gómez-Laguna, J. Application of Volatilome Analysis to the Diagnosis of Mycobacteria Infection in Livestock. Frontiers in Veterinary Science vol. 8, https://doi.org/10.3389/fvets.2021.635155 (2021).

Improving the Welfare of Farmed Fish by Personality and Physiological Profiling in Aquaculture Settings

Secondary Supervisor(s): Dr Ellen Williams

University of Registration: Harper Adams University

BBSRC Research Themes: Sustainable Agriculture and Food (Animal Health and Welfare)

Project Outline

Millions of fish are reared in aquaculture settings as part of farming food for human consumption. While stocking fish at high densities can increase their commercial potential, it can also expose fish to environmental stressors that may negatively impact their health and welfare, in addition to exposing fish to poor water quality, pathogens or injury. These stressors can detrimentally affect fish, influencing their health, welfare and behaviour, decreasing their production performances and market value and causing negative welfare experiences. There is paucity of significant gap in knowledge regarding farmed fish, because most research has been carried out in controlled laboratory conditions¹. The aim of this project is to develop a reliable toolset to measure and monitor welfare indicators in farmed fish at the production level. We will utilise personality profiles, immune and stress biomarkers and the microbiome to identify non-invasive parameters that can be used in welfare assessment.

Measuring fish health and welfare can be challenging because of their small size and the invasive nature of many current procedures. Individual fish may also respond differently to environmental stressors because of their personality or coping style.This project aims to collect data on rainbow trout (Oncorhynchus mykiss), a commercially important farmed fish species, to develop robust welfare indicators across production levels, due to their year-round availability and easy accessibility as a model species. We will record environmental changes (seasonal changes, water quality, handling methods, production parameters and disease prevalence) as well as pre-defined non-invasive welfare measures, including behaviour, stress (e.g. cortisol), immune readouts (e.g. immunoglobulins) and the composition of the gut-microbiome as biomarkers^2,3. We will then assess whether we can correlate a fish’s personality and physiological profile with its response to the environmental stressors providing a holistic overview of the welfare of the fish in commercial settings.

In the first year of this project, we will define the non-invasive welfare indicators using a systematic scoping study (months 13 – 17 of the PhD) and tank experiments (months 18 – 24 of the PhD) that measure personality indicators, immunological and stress markers and16s sequencing data to investigate the microbiome. These data will be correlated to standard environmental parameters (i.e. water quality, disease status, overall health) at the rearing environment. We aim to correlate changes in the environment with heightened release of cortisol, expression of immune markers and change to the gut microbiome. The reliability of the tool set will be assessed at different commercial settings, including hatchery and production. Our aim is to assess the applicability and feasibility of these tools across various life stages and environments. We will measure the health and welfare status of trout that are reared on a commercial fishery (Month 24 to 30 – grow out study) and fish farm (Month 31 to 41 – hatchery). The candidate will complete thesis writing in months 42 - 48)

The information gathered in the project allow us to examine whether fish that display certain behavioural profiles grow quicker in the aquaculture setting and are more resistant to stress. It will also determine how seasonal changes affect fish from different families. In addition, by integrating physiology and behavioural indicators, this work will provide the aquaculture industry with reliable metrics to evaluate fish health and welfare non-invasively ultimately enhancing production efficiency and market value. Assessing the microbiome will provides critical insights into fish health and welfare by serving as a non-invasive indicator of gut health, immune function, and stress response, ultimately contributing to the development of robust welfare metrics that enhance production efficiency and promote sustainable aquaculture practices. This project thus supports the broader goal of promoting sustainable food production and aquatic animal welfare.

The PhD student will have the opportunity to work with a multidisciplinary supervisory team comprised of Fish Health and welfare as well as collecting data in situ at commercial fishery and fish farms. Identifying whether some personality types are more favourable in fish farms and drawing information about how changes in the farm environment can interact with stress allow this project to improve growth and market value of the business.

References

1. Wiese TR, Rey Planellas S, Betancor M, Haskell M, Jarvis S, Davie A, Wemelsfelder F and Turnbull JF (2023). Qualitative Behavioural Assessment as a welfare indicator for farmed Atlantic salmon (Salmo salar) in response to a stressful challenge. Front. Vet. Sci. 10:1260090. https://doi:10.3389/fvets.2023.1260090.

2. Canosa LF and Bertucci JI (2023) The effect of environmental stressors on growth in fish and its endocrine control. Front. Endocrinol. 14:1109461. https://doi:10.3389/fendo.2023.1109461.

3. Tamsyn M. Uren Webster, Sofia Consuegra, Carlos Garcia de Leaniz (2021). Early life stress causes persistent impacts on the microbiome of Atlantic salmon. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. https://doi.org/10.1016/j.cbd.2021.100888.

Improving Welfare of Salmonids: Impact of Stress on Behaviour and Host-Pathogen Dynamics During Early Life Stages

Secondary Supervisor(s): Dr Robert Mukiibi, Dr Ellen Williams

University of Registration: Harper Adams University

BBSRC Research Themes:

• Sustainable Agriculture and Food (Animal Health and Welfare, Microbial Food Safety)
• Understanding the Rules of Life (Immunology)

Project Outline

Early life stages (ELs) of salmonids are critical to the success of commercial production, as they significantly influence the overall health and development of the fish. In salmonids, this period comprised of several key developmental phases, including fertilisation, embryonic development, and larval stages, each of which is essential for proper growth and survival. During these stages, farmed fish are often subjected to overcrowding, exhaustive handling, and social stressors. In addition, environmental factors, such as poor water quality and temperature fluctuations, exacerbate stress levels. The stress in young fish not only weakens their immunity but also increases their susceptibility to diseases, leading to significant mortality rates. Reports indicate that around 38% of fish mortalities occur during the hatchery phase, with approximately 70% attributed to infectious diseases¹ (e.g. Yersinia ruckeri and Flavobacterium psychrophilum). Addressing early life stressors is essential for improving the health, welfare, and productivity of salmonids in aquaculture settings; however, current research on this topic is limited².

Stress in farmed salmonids can occur at both group and individual levels, with significant implications for fish welfare and performance³. It’s known that immune system plays a crucial role in how fish cope with stress. Group-level stressors, such as overcrowding, handling during farming practices, and poor water quality, can impact all fish in a tank. However, individual-level factors, including personality traits, coping styles and genetics could influence how specific fish perceive and respond to these environmental conditions. For example, acute stress responses can vary among individuals; some may exhibit quicker physiological changes, such as elevated cortisol levels, while others may take longer to respond. These differences can lead to varied health outcomes, including the severity of disease manifestations​. This suggests the importance of implementing effective practices that consider both group dynamics and individual variability in fish husbandry to maintain optimum welfare.

Our study aims to enhance the welfare of salmonids by investigating the effects of stress on behaviour and host-pathogen dynamics ELs. In order to achieve, this we will conduct personality assessments to understand how individual traits influence group behavioural differences, particularly during first feeding and fry stages. In conjunction with personality testing, we will develop a set of welfare metrics (WM), which will include physiological stress indicators such as cortisol levels, haematological and immune parameters. We will incorporate behavioural observations such as feeding patterns, activity levels and social interactions recorded using underwater cameras, in the WM. In addition, environmental quality parameters like water temperature, pH, and ammonia levels will be included in the WM.

Our research program will first systematically monitor behavioural changes in salmonids during vulnerable ELs stages to identify baseline personality traits (months 12 – 21). Next, we will investigate stress parameters and immune status in salmonids during the vulnerable period to establish host-pathogen dynamics and assess the impact stress and pathogens on ELs (Months 24 - 36). Finally, we will evaluate the monitoring tool we develop through a feasibility study (months 36-42) to determine its effectiveness in assessing salmonid welfare.

This project will enhance the welfare of salmonids during early life stages by exploring the interplay between stress, behaviour and host-pathogen dynamics. By identifying baseline personality traits and assessing the genetic mechanisms underlying on response to stress at ELs, we aim to establish reliable welfare assessment tools. The development of a practical monitoring tool will assist hatchery operators to improve management practices and in doing so decrease disease incidence, mortality and therapeutic use of antibiotics, leading to healthier and higher welfare fish increased productivity in aquaculture settings. This project will be supported by a multidisciplinary team specialising in fish health, behaviour and welfare, and genetics, with opportunities for collaboration with industry partners.

References

1. Gåsnes, S. K., Oliveira, V. H. S.,Gismervik, K., Ahimbisibwe, A., Tørud, B., & Jensen, B. B.(2021). Mortality patterns during the freshwater productionphase of salmonids in Norway. Journal of Fish Diseases, 44,2083–2096. https://doi.org/10.1111/jfd.13522.

2. Wiese, T.R., Haskell, M, Jarvis, S., Rey-Planellas S., Turnbull J. (2023). Concerns and research priorities for Scottish farmed salmon welfare – An industry perspective, Aquaculture, V 566. https://doi.org/10.1016/j.aquaculture.2023.739235.

3. Castanheira, M.F., Conceição, L.E.C., Millot, S., Rey, S., Bégout, M.-L., Damsgård, B., Kristiansen, T., Höglund, E., Øverli, Ø. and Martins, C.I.M. (2017), Coping styles in farmed fish: consequences for aquaculture. Rev Aquacult, 9: 23-41. https://doi.org/10.1111/raq.12100.