Rhythms of Infection: Understanding the Circadian Control of Schistosome Development in Snails

Circadian clocks are an essential feature of life that synchronise physiological and behavioural processes with daily environmental cycles. Perturbation of an organism’s clock, or misalignment between the clock and environment, can exacerbate disease states and can be fatal. The relationships between parasites and their hosts raises questions about the clock-driven biology of each; only now are chronobiologists and parasitologists recognising this. While a recent study demonstrated that canonical clock genes (i.e. genes that regulate circadian clocks) were absent from Schistosoma mansoni, no similar study has yet to ask whether they are present in the genomes of sister schistosome species (e.g. S. rodhaini) or intermediate hosts (e.g. Biomphalaria glabrata). Taken together, the study of schistosome/host chronobiology requires further investigations as insights into this area could reveal new aspects of schistosome evolution, epidemiology, zoonoses and transmission in a One Health context. Our student and supervisory team will co-create a research programme focused on studies of behaviours impacted by biotic (clock genes) and abiotic (light/dark) factors. Our student will also gain at least six months experience working within the Schistosome Snail Repository team across LSHTM and NHM sites.

Supervised by Professor Karl Hoffman at Aberystwyth University. Co-supervised by Dr Bonnie Webster (NHM), Dr David Wilcockson (Aberystwyth University) and Professor Amaya Bustinduy (LSHTM). External partner is Dr Bonnie Webster at the Natural History Museum.

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Exploring Canine-Human Interfaces and Geographies of Zoonotic Disease: The Case of Hydatid Disease in Mid-Wales

This project will explore the interfaces between human and farm dogs in relation to the transmission and prevention of Hydatid Disease in mid-Wales, a known hot-spot where the causative parasite, Echinococcus granulosus, is endemic. Dogs are the end host of E. granulosus, with the parasite requiring an intermediate host that ingest oocytes from infected canine faeces. n the UK, sheep are primarily the intermediate host, developing “hydatid” cysts filled with immature E. granulosus, with dogs becoming infected by being fed or scavenging on sheep carcasses thus completing the transmission cycle. Humans can become accidental intermediate hosts, and therefore the presence of disease in the canine population presents a risk to in-contact humans. Despite several high-profile public health campaigns, Hydatid Disease is re-emerging in this region (Collins, 2019) and poses an ongoing threat to human health along with negative impacts on livestock health and welfare and farm productivity. This transdisciplinary project will combine research methodologies from human geography, clinical parasitology, epidemiology and human behavioural science.

Supervised by Dr Gwenllian Rees at Aberystwyth University. Co-supervised by Professor Gareth Enticott (Cardiff University). External Partner is Dr Andrew Nelson at Public Health Wales.

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Improved Detection of Bovine Tuberculosis Infected Cattle using Artificial Intelligence

Bovine Tuberculosis is caused by M. bovis which can also infect humans and many other mammals. Thus, M.  bovis is a One Health threat as zoonotic infection and by its effect on cattle productivity and consequent threat of food security. The current statutory test, the single intradermal cervical comparative tuberculin test, has a 99.98% specificity and 80% sensitivity. Animals co-infected with M. avium subspecies paratuberculosis (MAP) and M. bovis are at greatest risk of being diagnosed as false negatives. Thus, co-infection requires the development of more specific tests that are not affected by the presence of other environmental mycobacteria. The main goal of the project is to develop an AI system for early identification of MAP and M.  bovis co-infected animals.

Supervised by Dr Otar Akanyeti at Aberystwyth University. Co-supervised by Professor Bernardo Villareal-Ramos (Aberystwyth University), Dr Amanda Gibson (Aberystwyth University), Professor Ilias Kyriazakis (Queens University Belfast) and Dr Wayne Aubrey (Aberystwyth University). External Partner is Dr Rachelle Avigad at the Animal and Plant Health Agency.

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Investigating the zoonotic infection risk from feral cats in rural landscapes

The project will survey feral cats (Felis catus) and their associated zoonotic agents across rural areas in Wales and explore the links with environmental factors (e.g. landcover) and anthropogenic activities such as farming practices. Feral cat population dynamics will be assessed using complementary approaches for abundance estimation including mark recapture, random encounter models and camera trapping alongside population genetic methods of dispersal estimation. Interspecific behaviours such as predation patterns, recognised as important in zoonotic transmission, will be analysed by faecal dietary analyses. The student will work closely with the Vincent Wildlife Trust (VWT) in field sampling of feral cats. Field samples will be interrogated for a range of zoonoses (endoparasites, ectoparasites, diseases and viruses) with the student supported by an assembled team with expertise in aspects of wildlife and human epidemiology, parasitology, immunology, and access to the cutting-edge facilities at Aberystwyth VetHub.

Supervised by Dr Niall McKeown (Aberystwyth University), Dr Sarah Helyar (Queen's University Belfast), Dr Amanda Gibson (Aberystwyth University), Dr Bibi Linden (Aberystwyth University) and Professor Luis Mur (Aberystwyth University). External partner is Dr Jenny MacPherson at the Vincent Wildlife Trust (VWT).

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Assessing and predicting liver fluke risk on farms via satellite image analysis

The liver fluke (Fasciola hepatica) is a highly pathogenic zoonotic trematode parasite, highly prevalent in livestock globally and in humans in certain endemic regions of the world. It is estimated that the parasite and its disease (fasciolosis) cost the European livestock sector €635 million annually due to decreased production levels and increases in mortality rates and veterinary treatment costs. Climate change and anthelmintic resistance are predicted to further increase costs associated with F. hepatica in future decades and to allow for increased opportunities for zoonotic transmission. Considering that fasciolosis risk fluctuates widely between years, there has been substantial efforts to develop accurate fasciolosis risk models over the past century that can inform farmers of current infection risk in livestock and guide appropriate and sustainable treatment strategies. This PhD project aims to develop and validate a remote sensing imagery analysis algorithm to detect and monitor moisture levels on pastures, with the ultimate goal of identifying and mapping liver fluke risk hotspots on farms over time.

Supervised by Dr Rhys Jones (Aberystwyth University), Dr Oktay Karakus (Cardiff University) and Dr Hefin Williams (Aberystwyth University). External partner is Ms Leisia Tudor at Dunbia.

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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 5 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. Of particular concern are Ovine Johne’s Disease (OJD), caused by Mycobacterium avium subsp. paratuberculosis (MAP) and Caseous Lymphadenitis (CLA), caused by Corynebacterium pseudotuberculosis, which are zoonotic. 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. This proposed project has two aims. 1) develop and utilise an eDNA assay to screen environmental matrices to identify the presence of C. pseudotuberculosis and MAP and 2) 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. 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.

Supervised by Dr Hefin Williams at Aberystwyth University. Co-supervised by Professor Gareth Enticott (Cardiff University), Dr Rhys Jones Aberystwyth University) and Dr Cennydd Jones (Aberystwyth University). External Partner is Dr Heather at McCalman Hybu Cig Cymru - Meat promotion Wales.

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Assessing the potential for aerosol transmission of zoonoses within critical environments

Zoonoses with the potential to cause pandemics face two fundamental obstacles. The first is transfer between species boundaries, from reservoirs to immunologically naïve new hosts, and the second is efficient transmission between members of the new host population. Airborne transmission provides unique opportunities for rapid transmission of a zoonosis from one-to-many susceptible people. Humans spend ~90% of our time indoors, mostly in environments with poor or variable air quality, accelerating the airborne transmission of novel zoonoses. Expert syntheses conclude that improving air quality would make airborne diseases preventable in the way that waterborne or foodborne diseases are routinely controlled. Nonetheless, this requires a paradigm shift in our capacity to investigate and understand zoonoses entrained within air. Given the trifecta of the unfathomable diversity of putative zoonoses in wildlife, the vast interface between humans and wildlife, and our destabilizing climate, another pandemic is highly likely. The project will enhance our understanding of bioaerosols within critical interface environments: where animals meet people, and where people meet people to provide fundamental knowledge of bioaerosols within these environments.  The PhD student will work with experts in the airborne ecology of critical interfaces within natural, agricultural, and built environments.

Supervised by Dr Arwyn Edwards at Aberystwyth University. Co-supervised by Mr John Griffith (Coleg Sir Gâr), Dr Cennydd Jones (Aberystwyth University), Professor Gareth Griffith (Aberystwyth University), Dr Peter Dennis (Aberystwyth University) and Dr Rachel Wheatley (Queen’s University Belfast). External partner is Coleg Sir Gâr Gelli Aur Campus.

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Reducing the carriage of pathogens in the food chain using myxobacterial biological control

Myxobacteria are non-pathogenic environmental bacteria, able to kill a wide variety of microbes, including most bacteria, fungi and oomycetes. We will investigate their use as biocontrol agents to increase the welfare and safety of farmed crickets, which are a source of protein for human consumption, and also a model of agriculture-relevant animals more widely (e.g. pollinators, disease vectors and other farmed animals). The project addresses the key challenge of disease control, focusing on managing and mitigating zoonoses by providing a therapeutic barrier to transmission. Insect farming is a sustainable source of nutritional protein, but farmed insect microbiomes can be reservoirs/vectors of important human/animal pathogens. Our novel project gathers expertise in insect husbandry/behaviour, molecular microbiology and commercial insect farming, to explore the use of predatory myxobacteria to target insect pathogens for safer alternative protein production.

Supervised by Professor Dave Whitworth at Aberystwyth University. Co-supervised by Dr Geoffrey Knott (Edibl – the UK Insect Company), Dr Katerina Theodoridou (Queen's University Belfast) and Dr Roger Santer (Aberystwyth University). External partner is Dr Geoffrey Knott at Edibl – the UK Insect Company.

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Towards a biosecurity system to manage the threat of Avian Influenza in Nigeria

Avian influenza (AI) is a highly contagious and devastating zoonotic disease so that World Health Organization (WHO) emphasize the importance of surveillance in both animal and human populations to detect and respond to outbreaks promptly. The threat to African nations such as Nigeria is particularly acute as poultry is a major source of dietary protein. Nigeria was the first African country to report highly pathogenic avian influenza (HPAI) H5N1 in 2006, its re-emergence is a pressing threat to food security. Smallholder farmers, who constitute 80% of the industry, often lack knowledge and are particularly threatened. This research project aims to bridge the knowledge gap among smallholder farmers in Nigeria regarding AI and One Health implications. This PhD project will work with NVRI, Nigeria to lay the foundations of an evidence based-biosecurity strategy. The gathered data will serve as a foundation for developing an effective mapping information platform and app to raise awareness and disseminate relevant information on AI One Health implications, and preventive measures.

Supervised by Dr Edore Akpokodje at Aberystwyth University. Co-supervised by Professor Luis Mur (Aberystwyth University), Professor Punam Mangtani (LSHTM) and Dr Reuben Ocholi (National Veterinary Research Institute, NVRI). External partner is Dr David Brooke at Valley Diagnostics Ltd and Ms Maria Luisa de la Puerta Fernández at Omeva Solutions UK.

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Small but mighty - Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions

Fascioliasis and bovine tuberculosis (bTB) are zoonotic diseases caused by Fasciola hepatica and Mycobacterium bovis, respectively, leading to significant livestock production losses exceeding £450 million annually in the UK. Research has primarily focused on coding sequences, overlooking short ORFs (sORFs) within long non-coding RNAs (lncRNAs) due to their presumed lack of protein-coding capacity . Recent studies have shown that sORFs are translated and can modulate the host-parasite immune response . This project aims to investigate the role of sORFs within lncRNAs in F. hepatica and M. bovis, and their impact on the host immune system. The student will use bioinformatics skills to identify new genes that are potentially novel drug and vaccine targets. The supervisory team includes bioinformaticians from Belfast Health and Social Care Trust and academics specialising in data science and parasitology.

Supervised by Dr Wayne Aubrey at Aberystwyth University. Co-supervised Dr Martin Swain (Aberystwyth University), Dr Russ Morphew (Aberystwyth University), Dr Amanda Gibson (Aberystwyth University) and Dr Paul McVeigh (Queen's University Belfast). External partner is by Dr Derek Fairley at the Belfast Health and Social Care Trust.

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The role of the rural veterinarian in optimizing animal health, enhancing human wellbeing and ensuring environmental sustainability

There is a dearth of evidence on the value and role of rural veterinarians in supporting livestock farmers in Wales or as champions of government initiatives that seek to reduce disease or promote sustainability. There is significant, possibly untapped potential in perceiving veterinarians as One Health practitioners, able to enhance not only livestock health, but also enhancing human wellbeing, supporting rural community structures and promoting environmental conservation. The project will be delivered through interviews, focus groups and surveys of practices, vets, educationalists, government advisors and farmers. The student will work closely with the supervisory team in designing surveys, writing and administering questionnaires, and arranging and running small group discussions. The project has received support from multiple veterinary groups - in government, practice and those with a specialist interest in sustainability. The student will have a unique opportunity to spend time with each of these groups and thereby gain insights and experience in issues that go to the heart of food security and environmental sustainability. The novel nature of the project should result in the graduate being an authority, not only in qualitative methods of research, but in a field with direct application to other countries and diverse settings.

Supervised by Professor Darrell Abernathy at Aberystwyth University. Co-supervised by  Professor Gareth Enticott (Cardiff University), Professor Mike Woods (Aberystwyth University) and Dr Simon Payne (Aberystwyth University). External partner is Mr Peter Howard from Welsh government - Office of the Chief Veterinary Officer (OCVO).

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Environmental monitoring of agricultural run-off as potential sources of animal and zoonotic diseases

Faecal waste from livestock can be stored as slurry for use as fertilizer applied to pasture and crops to support production. This can be beneficial to minimise the use of chemical fertiliser, reduce farm costs, increase production and minimise waste. Slurry contains both nitrates and phosphates amongst other nutrients, which can be beneficial for soil and plant growth and health. However, a wide variety of pathogens may also be present in the waste and water contamination is a global concern, ranging from bacteria to viruses, parasites and fungi. This project aims to assess and monitor the effects of farm-related pollutants on Welsh water bodies with the aim of creating an application and dashboard that can help evidence-based decisions at both policy making and farm level. To achieve this, large dataset mining and machine learning will create models by leveraging existing data. To gain accuracy and further insight, data will be validated by ground-truthing through placement of biosensors in strategic sites and regular monitoring. The presence of pollutants will be determined during both data mining and data validation based on the presence of parameters such as pH, ammonia, nitrates, phosphates, and microbial eDNA markers in water systems.

Supervised by Dr Elizabet Hart at Aberystwyth University. Co-supervised Dr Edore Akpokodje (Aberystwyth University), Dr Justin Pachebat (Aberystwyth University) and Dr Linda Oyama (Queen's University Belfast). External partner is Dr Theopoline Omagano Amushendje at University of Namibia (UNAM).

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Gut Reactions and Ground Rules: The Microbial and Environmental Drivers of Zoonotic Hookworm Hatching

Of the soil-transmitted helminths, hookworm infections impose the highest disease burden on humans and animals. The central hypothesis is that changes in host diet and soil nutrient composition alter the products made by the gut microbiota, which in turn regulate hookworm egg hatching and transmission. How dietary changes to the microbiome or soil composition affect these products is unknown. The study will focus on identifying specific bacterial products and soil nutrients that impact the parasite's lifecycle. This project will draw on our parasitology, microbiology, and environmental science expertise to address this knowledge gap.

Supervised by Dr Katherine Smith at Cardiff University. Co-supervised by Professor Hany Elsheikha (ESCCAP UK & Ireland), Dr Sarah Perkins (Cardiff University), Dr Russ Morphew (Aberystwyth University) and Dr William Stiles (Aberystwyth University).

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Enhancing Food Safety: Volatile Organic Compound-Based Early Detection of zoonotic pathogens in Leafy Greens

The project focuses on addressing the rise of foodborne illnesses linked to ready-to-eat salads, particularly caused by zoonotic pathogens like Shiga toxin-producing Escherichia coli (STEC). These pathogens are responsible for approximately 500,000 cases annually in the UK, costing £1.8 billion. A recent outbreak of STEC tied to contaminated lettuce highlighted the need for faster and more efficient contamination detection methods. Current detection methods in the UK rely on ISO standards, taking 2-3 days to confirm contamination. This delay often allows contaminated produce to reach consumers, increasing health risks and economic losses due to product recalls. Furthermore, testing facilities are limited, especially during outbreaks, reinforcing the urgent need for quicker detection tools to protect public health and the economy. This cutting-edge project tackles food safety by developing a rapid bacterial contamination detection system using VOC profiling and dual transcriptome analysis. With world-class experts in microbiology, plant science, and food safety, plus strong industry ties and advanced facilities, you'll gain hands-on experience in solving global food safety challenges.

Supervised by Dr Cedric Berger at Cardiff University. Co-supervised by Professor Séamus Fanning (Queen's University Belfast), Professor Hillary Rogers (Cardiff University) and Dr Carsten Muller (Cardiff University). External partner is Mr Anthony Wilson at the Food Standards Agency (FSA) and Ms Kelly Shields the Fresh Produce Consortium (FPC).

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Pathogen Analysis and source Tracking for Health (PATH): A One Health Approach to Tracking Waterborne Pathogens in Pakistan and Wales

Environmental degradation has severely impacted agriculture, causing losses in food security and the economy, which in turn worsens socioeconomic issues. In Pakistan, about 80% of the population is currently drinking contaminated water, risking exposure to pathogens such as E. coli, Cryptosporidium, Campylobacter, Salmonella and Shigella, and facing diseases such as dengue, malaria, salmonellosis, hepatitis, cholera, typhoid, schistosomiasis, and giardiasis. As such water security is a major issue, with water-borne diseases negatively impacting human, animal and environmental health worldwide. Currently, 75% of UK rivers fail to meet established ecological standards, with human waste contributing to 49% of these failures. Only through a One Health approach can we fill this knowledge gap and better direct funding and resources to address the issues in hand. The student will have the opportunity to contribute to real-world change, applying an interdisciplinary, mixed methods approach to compare and contrast perceptions, drivers and risk related to water quality issues within the UK and Pakistan, while establishing a knowledge and information sharing partnership between the two countries.

Supervised by Professor Jo Cable at Cardiff University. Co-supervised by Mr Luis Priegue Molinos (Dŵr Cymru Welsh Water, DCWW), Dr Sophie Watson (Cardiff University), Dr Haroon Ahmed (COMSATS University Islamabad), Mr Oliver Cumming (LSHTM). External partner is Dŵr Cymru Welsh Water (DCWW).

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Rodent Routes: Mapping the Hidden Highways of Zoonotic Transmission on Farms

Over 75% of emerging epidemic diseases are zoonotic, with around 40 known zoonotic diseases infecting 300,000 people annually in the UK. Rodents, which harbour more zoonoses than any other taxa, pose a high spillover risk due to their close association with humans. To prepare, we must understand the conditions under which pathogens spillover. Agricultural land covers >70% of the UK and farmers represent the highest occupational exposure to zoonoses. On and around farms, rodents have high contact rates with wildlife, domestic animals and humans, acting as a potential conduit of pathogens between multiple species. Rapid change in natural environments (e.g. flooding, drought) and in anthropogenic impacts (e.g. farming policy change) may change the human-rodent interface and therefore affect pathogen spillover. This PhD seeks to determine the on-farm risk from rodent-borne zoonoses including both direct rodent to human transmission, and indirect mechanisms, where rodents may act as ‘bridging hosts’ transmitting wildlife derived zoonotic pathogens to domestic animals from which they may transmit to people.

Supervised by Professor Gareth Enticott at Cardiff University. Co-supervised by Catherine Moore (Public Health Wales), Dr Sarah Perkins (Cardiff University), Dr Joanne Lello (Cardiff University), Dr Cedric Berger (Cardiff University) and Professor Kris Murray (LSHTM). External partner is Public Health Wales (PHW).

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Understanding host-parasite-microbiota interactions in African biomes to prevent zoonotic disease transmission (BIOZOON)

Small mammals play an integral role in ecosystems and provide important ecosystem services (for example, acting as pollinators and seed dispersers). These small mammals are also important hosts of ectoparasites and endoparasites, many of which are vectors of disease of veterinary and medical importance. These parasites will in turn interact with the host and its microbiota and will be influenced by the physical environment. This multidisciplinary and innovative project will investigate host-parasite-microbiota-environment interactions in a widely distributed small mammal across southern African savanna and grassland biomes. Ectoparasites and microbiota will be characterised using microscopy, amplicon and shotgun sequencing. In addition, a landscape genomics approach will be utilised to test for correlations between the environment, microbiota and disease status. Simulation modelling of these variables and the genetic profiles of individuals small mammals will determine movement and connectivity between populations. Finally, predictive risk models for spread of zoonotic and potentially zoonotic organisms will be generated under different climate change scenarios.

Supervised by Dr Oktay Karakus at Cardiff University. Co-supervised by Dr Isa-Rita Russo (Cardiff University), Dr Michael Scantlebury (Queen’s University Belfast). External partner is Dr Heidi Hauffe at Fondazione Edmund Mach, Italy and Dr Danny Govender at SANParks, South Africa.

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The Hidden Risks: Identifying and Addressing High-Risk Behaviours for Zoonotic Disease Transmission

Zoonotic exposure risk is not equal across people, locations and/or behaviours. To design effective mitigation to reduce zoonotic exposure we need to identify i) who is most exposed, ii) where and why that exposure happens iii) how people respond to interventions designed to reduced exposure. Zoonotic risk can be driven by environmental factors but ultimately human behaviour is a major driver of exposure. Occupation, types of recreation and food consumption behaviours are all important in translating exposure into infection, but the relative role these factors play for given zoonoses are not well quantified or understood. Public Health Wales’s (PHW) response to confirmed zoonotic infection in humans includes carrying out ‘enhanced surveillance’ which collates information on the individual exposure behaviours, for example, ‘animal contact’ or ‘water exposure’. In this project, we will analyse PHW’s ‘enhanced zoonotic surveillance data’ to identify exposure factors associated with infection. Secondly, ethnographic surveys developed with a multidisciplinary team (sociology, psychology, ecology) will identify exposure behaviours NOT captured via enhanced surveillance. Finally, we will assess high-risk groups’ response to disease mitigation via a simulation game.

Supervised by Dr Sarah Perkins at Cardiff University. Co-supervised by Dr Lewis Bott (Cardiff University), Dr Joanne Lello (Cardiff University), Professor Darrell Abernethy (Aberystwyth University) and Professor Julian Drewe (Royal Veterinary School). External partner is Dr Chris Williams at Public Health Wales (PHW).

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Implications of mixed infection on the evolution of Cryptosporidium spp.

In this interdisciplinary project, the student will investigate infection complexity within clinical Cryptosporidium datasets and its implication on the evolution of zoonotic Cryptosporidium. This project will utilise a diverse skillset from biology, computer science, and statistics to analyse NGS data and test evolutionary hypotheses. The supervisory team includes Clinical Scientists from Public Health Wales, bioinformaticians specialising in genomics, data science and software development for use in public health laboratories, and statisticians with expertise in modelling biological systems. The research will be primarily computational, but with the opportunity for a placement in a UKAS-accredited public health laboratory.

Supervised by Professor Thomas Connor at Cardiff University. Co-supervised by Dr Guy Robinson (Public Health Wales), Dr Arthur Morris (Cardiff University),  Professor Jo Cable (Cardiff University), Dr Martin Swain (Aberystwyth University) and Professor Owen Jones (Cardiff University). External partner is Public Health Wales (PHW).

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Vector-Borne Disease Surveillance Using Metagenomic Sequencing

Vector-borne diseases pose a significant global health threat, responsible for millions of infections and deaths each year. Climate change and increase urbanization affect vectors habitats and increase the risk of emerging and re-emerging vector-borne diseases. Traditional surveillance methods often fall short in rapidly identifying both known and new pathogens and new methods are needed for rapid and pathogen identification. Our team’s background in metagenomics, bioinformatics, entomology and vector-borne diseases will ensure the student is supported in both the technical and applied aspects of this project. This PhD project aims to develop and implement a metagenomic sequencing framework for the surveillance of vector-borne diseases, focusing on the detection of pathogens and the identification of vector species, including invasive species. In addition, the student will explore the use of environmental DNA (eDNA) in combination with metagenomics to detect the presence of invasive species and pathogens in various environments without the need for capturing live specimens.

Supervised by Professor Susana Campino at London School of Hygiene and Tropical Medicine (LSHTM). Co-supervised by Professor Taane Clark (LSHTM), Dr Mojca Kristan (LSHTM), Dr Ross Cuthbert (Queen's University Belfast). External partner is Dr Louisa Messenger at the University of Nevada.

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Genomic insights into the transmission pathways of foodborne pathogens in fish from aquaculture to consumer in Thailand

The rapid globalisation of food systems has intensified the threat of foodborne illnesses, posing significant challenges to public health, food safety, and economies worldwide. In Thailand, fish is a primary food source, supported by extensive aquaculture regions. However, there is evidence of foodborne pathogen transmission across farms, polluted environments, markets, and to humans, contributing to diarrheal infections and increased mortality in children under five. Our project aims to leverage genomics to understand pathogen transmission mechanisms within Thailand’s aquaculture food supply chain. Early childhood diarrhoea caused by Escherichia coli pathovars is a One Health challenge, with Thailand experiencing a high burden from fish-related sources. This multidisciplinary project will utilise advanced sequencing and pathogen genomics to trace and understand the transmission dynamics and virulence of E. coli pathovars across fish farms, related environmental settings, and marketplaces.

Supervised by Professor Taane Clark at London School of Hygiene and Tropical Medicine (LSHTM). Co-supervised by Professor Susana Campino (LSHTM) and Professor John McGrath (Queen's University Belfast). External partner is Professor Saharuetai Jeamsripong at Chulalongkorn University in Thailand.

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Landscapes, mosquitoes and arboviruses: using xenosurveillance to characterise arboviral risk in Thailand

Exploitation of the natural environment and resources by humans drives landscape change, increases the geographical overlap of animal reservoirs of disease and human populations, and increases the risk of disease spillover. Arboviruses are transmitted between mammalian hosts in tropical forests and to humans living in close proximity to forest by Aedes mosquitoes. These mosquitoes are now also well-adapted to breed in urban environments, where high human population densities result in periodic outbreaks. Understanding fundamental aspects of mosquito ecology is a prerequisite for discerning spatiotemporal patterns of arbovirus transmission and conceiving disease control strategies. This project aims to characterise the distribution of Aedes mosquitoes, patterns of host-feeding and diversity and stability of their core virome, and how this differs across forest, rural and urban landscapes in Thailand.

Supervised by Professor Sian Clarke. Co-supervised by Patchara Sriwichai (Mahidol University, Thailand), Professor Mary Cameron (LSHTM), Professor Susana Campino (LSHTM), Dr Pablo Orozco-terWengel (Cardiff University) and Dr Pornsawan Leaungwutiwong (Mahidol University, Thailand). External University is Mahidol University in Bangkok, Thailand.

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Implications of wetland creation for mosquito-borne disease risk

Wetlands are crucial habitats for biodiversity conservation and ecosystem integrity. However, newly constructed wetlands could have implications for mosquito communities and disease risk by increasing habitat availability. This project brings together an interdisciplinary group of scientists and stakeholders comprising ecologists, virologists, parasitologists, and social scientists to understand the risks and opportunities around mosquito-borne disease following wetland creation under a One Health framework. We will focus sampling in Northern Ireland because there is a paucity of understanding around mosquito-borne disease risk compared to other parts of the UK/Ireland in the context of wetland creation. However, the results will be relevant globally owing to the broad relevance of vector-borne disease and international wetland creation initiatives.

Supervised by Dr Ross Cuthbert at Queen's University Belfast. Co-supervised by Dr Archie Murchie (Agri-Food and Biosciences Institute, AFBI), Dr Jolyon Medlock (UKHSA), Professor Susana Campino (LSHTM), Dr Connor Bamford (Queen’s University Belfast), Professor Ruth Hunter (Queen’s University Belfast) and Professor Eric Morgan (Queen’s University Belfast). External partner is Agri-Food and Biosciences Institute (AFBI).

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Using comparative genomics of schistosome species to better understand the molecular basis of zoonoses

Schistosome species are a group of helminths that are a substantial burden to human health across many economically developing regions. Clinical schistosomiasis occurs in the tropics and subtropics and is caused by four main species, of which Schistosoma japonicum and S. mekongi are traditionally considered zoonotic. Occurring in Africa between S. haematobium and other species, particularly Schistosoma bovis and Schistosoma curassoni, hybridisation may give rise to a further zoonotic schistosome. Species hybridisation have the potential to increase both the zoonotic potential of the disease and the number of animal reservoirs available to maintain transmission rates to humans. To response effectively to new zoonotic sources of schistosomiasis the basis of speciation and hybridisation are important for schistosome pathogens. This project will include both substantial bioinformatic training and laboratory-based skills. Expertise gained will include the comparison of genomic resources to identify species specific and species common features. The supervisory team will support the development of the contrasting but complementary skills in both molecular and in silico areas as needed for this project.

Supervised by Professor Geoffrey Gobert (Queen's University Belfast). Co-supervised by Dr Aidan Emery (NHM), Dr Martin Swain (Aberystwyth University) and Dr Karen Siu Ting (Queen's University Belfast). External partner is the Natural History Museum (NHM).

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Mapping the spread of zoonotic bacterial pathogens and their mobile genetic elements as drivers of infection

Two commonly reported zoonoses of livestock origin are the gastrointestinal diseases salmonellosis and campylobacteriosis, with their causative agents being the bacterial pathogens, Salmonella spp. and Campylobacter spp., respectively. Mapping the distribution of zoonotic bacterial pathogens in the environment can help us identify their reservoirs and learn more about the barriers to their transmission. This project will work with a unique and exciting dataset from the Agri-Food and Biosciences Institute (AFBI) where soil samples have been collected from farms across Northern Ireland. The goal of this project is to use this collection to address two major aims:
Aim One: To characterise how varied biological and geographical factors relate to the prevalence and identity of zoonotic bacterial pathogens within farm-associated soil samples.
Aim Two: To define the frequency and characteristics of cross-niche mobile genetic elements (e.g. plasmids) that spread between the environment and healthcare-associated settings.

Supervised by Dr Rachel Wheatly (Queen's University Belfast). Co-supervised by Selvakumar Dhandapani (Agri-Food and Biosciences Institute, AFBI), Dr Andrew Mitchell (Aberystwyth University), Dr Linda Oyama (Queen's University Belfast) and Dr Arwyn Edwards (Aberystwyth University). External partner is Agri-Food and Biosciences Institute (AFBI).

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Buzz Off! Understanding public perceptions of vector borne disease and control in the UK to inform public health interventions

Vector-borne diseases (VBDs) are of increasing public health concern globally. Several compounding environmental, ecological and social factors are driving the changing epidemiology of VBDs. These changes in global epidemiology of VBDs are reflected across Europe and the UK.  In the past five years, human cases of dengue fever, chikungunya, Zika, West Nile Virus (WNV), Usutu Virus, Crimean-Congo Haemorrhagic Fever (CCHF), tularaemia, and Tick-borne Encephalitis (TBE) virus infections have been reported in Europe, at increasing rates and in some countries, for the first time. The most common tick-borne disease reported in England is Lyme disease; over 1600 cases were reported in 2023. This interdisciplinary project will explore public knowledge of and attitudes towards vector borne diseases (VBD) and control methods in the United Kingdom. Outcomes from this project will contribute to the development of UKHSA’s VBD contingency planning, as well as informing development of VBD-related public health advice and guidance, to improve adherence to and uptake of vector control measures by the public.

Supervised by Professor Ruth Hunter at Queen's University Belfast. Co-supervised by Dr Ross Cuthbert (Queen's University Belfast), and Professor Jo Cable (Cardiff University Belfast).

External partner is the UK Health Security Agency (UKHSA), including Jolyon Medlock, Dr Charlotte Robin, Dr Aimee Harragan and Dr Katie Russell. Partners also include Dr Archie Murchie from Agri-Food and Biosciences Institute (AFBI) and Dr Christopher Williams from Public Health Wales (PHW).

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Advancing zoonotic disease ecology through eDNA monitoring of infectious agents

Increased international travel, trade in and transport of animals and increasing global temperatures provides a perfect storm for the introduction of non-indigenous zoonotic parasites and pathogens to non-endemic areas, The successful detection of such emerging threats comprises time-intensive collection methods targeting a diverse range of hosts and biological samples such as faeces, blood or indeed necropsies across several time points throughout the year. By employing molecular methods to survey parasites and pathogens from a diversity of environmental samples such as water processing plants, agricultural sites and public areas conventional detection methods can be complemented and time-consuming or invasive screening methods replaced. Additionally, Environmental DNA sequencing across a diversity of geographically widespread areas enhances our understanding of the spatiotemporal dynamics of pathogens and parasites in the test region. The high frequency of surveillance afforded with eDNA facilitates the rapid update of genetic databases and increased effectiveness of management plans and an early warning mechanism for future disease outbreaks. This project comprises interdisciplinary research encompassing the fields of parasitology, microbiology/ virology, public/veterinary/environmental health, ecology, social science and epidemiology offering the student a diverse training package and unique transferrable skill set and expertise and knowledge offered by the supervisory team and partners.

Supervised by Professor Aaron Maule at Queen's University Belfast. Co-supervised by Professor Nikki Marks (Queen's University Belfast), Professor John McGrath (Queen's University Belfast) and Dr Russ Morphew (Aberystwyth University). External partner is Dr Derek Fairley at Belfast Health and Social Care Trust.

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Interrogating the importance of zoonotic transmission routes

Human, animal and environmental health is inextricably interconnected as evidenced by the increase in the number of emerging infectious disease events (EIDs) in recent decades. Indeed, 75% of EIDs are zoonotic “spilling over” from wild animal species to human populations. Therefore, wildlife species such as birds are important to public health as they can harbour multiple pathogenic microorganisms transmissible to humans. Additionally, birds migrate across national and intercontinental borders becoming long-range vectors for zoonotic pathogens or drug-resistant organisms establishing new endemic disease foci along migratory routes. Wild birds are known reservoirs for multiple agents, including arboviruses such as West Nile virus, Borrelia burgdorferi, influenza A virus, enteropathogens and drug-resistant bacteria. Birds infested by arthropod vectors such as Ixodes tick species may also inadvertently serve to expand their geographic distribution as ticks become detached along migratory routes introducing pathogens into new areas. Of course, disease transfer through contact also occurs at the wildlife-domestic animal, wildlife-agricultural and domestic animal- human interphases highlighting additional zoonotic disease transmission routes. The importance of each of these transmission routes will be investigated involving the screening of animals for ectoparasites which when recovered will be screened for a range of pathogens including bacteria, viruses and protozoa, Additional screens of faecal samples will facilitate the identification of zoonotic endoparasite species. An added complexity in terms of determining the impact of zoonotic infections on the host is the occurrence of co-infections which will also be interrogated at both the vector and host level.

Supervised by Professor Nikki Marks at Queen's University Belfast. Co-supervised by Mr Edward Adamson (National Sheep Association, NSA), Dr Michael Scantlebury (Queen's University Belfast), Dr Connor Bamford (Queen's University Belfast) and Dr Joanne Lello (Cardiff University). External partner is the National Sheep Association (NSA).

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African mole-rats as potential reservoirs for zoonotic disease : variation with species, habitat and effects of climate change

This project will explore zoonotic disease transmission within the understudied subterranean rodent family of African mole-rats. Pathways of disease spread will be explored to wild, agricultural, and domestic animals, in the context of changing climatic conditions. Physiological capabilities could influence the mole-rats’ role as potential reservoirs for zoonotic diseases, which may be further impacted by climate change. By studying disease and parasite load, the student will gain a comprehensive understanding of how environmental challenges might alter disease dynamics within mole-rat populations, which occur across diverse habitats. They will apply their findings to evaluate zoonotic risks to agricultural, domestic, and wild animals, as well as humans, identifying biosecurity measures to mitigate spill-over threats. This holistic approach will prepare the student to address complex challenges at the interface of wildlife health, ecosystem integrity, and human well-being.

Supervised by Dr Michael Scantlebury at Queen's University Belfast. Co-supervised by Professor Nikki Marks (Queen's University Belfast) and Professor Darrell Abernethy (Aberystwyth University). External partners are Professor Nigel Bennett and Dr Daniel Hart at the University of Pretoria.

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One Health and climate determinants of zoonotic enteropathogen transmission in Senegal

Globally, over one million deaths are caused each year by diarrhoeal diseases resulting from exposure to enteropathogens. Many of these enteropathogens, such as Campylobacter, non-typhoidal Salmonella, and Giardia, are potentially zoonotic. Whilst the fraction of the diarrhoeal disease burden attributable to zoonotic – versus human-to-human – transmission is difficult to estimate it is undoubtedly important, especially in settings that combine a high burden of disease and high risk of exposure to animal waste.  This project will focus on one such setting – in northern Senegal – where there is a high burden of diarrhoeal disease combined with a range of potential animal and environmental risk factors for zoonotic transmission of  enteropathogens. Using a One Health approach, the project will investigate the environmental and animal risk factors for zoonotic enteropathogen exposure and related disease outcomes, like diarrhoea and assess the sensitivity of these variables to climate variables. This project provides a unique opportunity to examine these important issues in a climate vulnerable, high-burden setting by combining data on stool-based molecular detection of enteropathogens, trial data, satellite-based remote-sensing techniques and climate modelling approaches.

Supervised by Dr Jacqueline Knee at LSHTM. Co-supervised by Mr Oliver Cumming (LSHTM) and Professor James Lewis (Cardiff University). External partner is Dr Dieynaba N’Diaye at Action Against Hunger, France.

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