London School of Hygiene & Tropical Medicine

The London School of Hygiene and Tropical Medicine (LSHTM) has been awarded funding as part of the OneZoo CDT to support studentships over the next three years, with planned cohort intakes in the 2024-25 and 2025-26 academic years, with up to six studentships.

The OneZoo CDT offers an unprecedented level of diversity and transdisciplinarity, with award-winning educators and experts in zoonotic diseases and environmental sciences, from Cardiff University, Aberystwyth University, Queen’s University Belfast, and the London School of Hygiene and Tropical Medicine, working collectively, fostering creation of the OneZoo research community, and empowering students to develop their own training to acquire strong employability skills.

More than 60% of current and emerging human infections have a zoonotic origin (i.e. they are transferred between animals and people) and zoonotic pandemics cost the global economy over $60 billion each year. Being able to predict, detect and control zoonoses represents one of the greatest challenges faced by humanity.

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. To design successful, innovative environmental prevention and control strategies, zoonotic drivers need to be understood through an integrated systems approach. As part of the OneZoo programme you will build an in-depth understanding of the connectivity between key drivers of pathogen host shifts, spillover and onward transmission; exploring pathogen, environmental and human societal processes that can promote zoonotic disease and form the basis of integrated environmental solutions.

The London School of Hygiene & Tropical Medicine is pleased to invite applications for six projects, based at the London School of Hygiene & Tropical Medicine.

As a OneZoo student you will undertake a 3.5 year systematic programme of training in core transferable and specialist skills, alongside your specific PhD project, that will build an in depth understanding of the key drivers of zoonotic diseases and form the basis for devising holistic solutions.

Award details

The studentship will provide:

• Tuition fees (at the LSHTM Home fee rate), and
• A student stipend (at the UKRI studentship rate, which was GBP 20,622.00 per annum in 2023-24), and
• A Research Training and Support Grant to go towards consumables and training for the duration of the award.

Eligibility for funding

Applicants must meet minimum LSHTM entry requirements. Please see the specific project details above for any further requirements.

Some projects may be suitable for part-time study; anyone wishing to undertake part-time study is encouraged to contact the supervisor for more details.

This studentship is open to applicants assessed as both ‘Home’ and ‘Overseas’ fee status.  For further information about Fee Status Assessments please see the School’s Admissions policies.

Successful applicants who are nationals of low income countries and lower middle income countries (LLMICs) may be eligible for an LSHTM bursary to cover the fee top up costs. LLMIC applicants who are short-listed for interview, will be contacted by the LSHTM Scholarships Team at that time to provide further details of the LSHTM bursary scheme as per our UKRI international recruitment statement.  

Successful international applicants who are not from an LLMIC will be required to cover the tuition fee top up costs from other sources (e.g. other scholarship or bursary awards). Awardees may not use their studentship stipend to top up fees.

Project details

The OneZoo Centre for Doctoral Training invites applications from eligible candidates for interdisciplinary PhD studentships. Applicants may express interest in up to 3 projects from amongst 20 potential projects are available for enrolment in 2023/24 (see OneZoo website for the full project list), of which the following 6 projects are based at LSHTM:

Project 1: Thermal biology of midges as vectors of leishmaniasis

Supervisory team

• Principal Supervisor: Dr Matthew Rogers (LSHTM)
• Co-Supervisor: Dr Laith Yakob (LSHTM)
• Co-Supervisor: Dr Tom Bishop(Cardiff University)
• Partner Supervisor: Dr Marion England (Pirbright Institute)

Project description

Background

Leishmania are parasitic protozoa responsible for a spectrum of zoonotic diseases ranging from cutaneous leishmaniasis (CL) to the life-threatening organ failure of visceral leishmaniasis (VL). The recently established subgenus Mundinia has been found to have a wide geographical distribution and has the potential to infect and cause disease in humans. While the other Leishmania subgenera are transmitted exclusively by phlebotomine sand flies, natural vectors of Mundinia remain uncertain; however, the North American midge, Culicoides sonorensis, has been shown to support infection and transmission in laboratory studies. Our preliminary data has demonstrated that UK midges can also be infected with Leishmania (Mundinia) chancei. The influence of temperature on the life history of Culicoides midges and their vectorial competency for Leishmania transmission needs to be investigated fully to understand the risk of Leishmania spreading in Europe and the UK.   

Research questions

What is the vectorial competency of European midges for Leishmania (Mundinia) species transmission, what are the thermal boundaries for these interactions and the risk of spill-over infection in Europe and the UK?

Aim and objectives

This project aims to address this potential threat by taking a multidisciplinary approach to test, model, and predict Europe and UK risk based on climate variables identified to be favourable for transmission and land use changes that could influence vector distribution and vector-host contact. Temperature is likely to be a key driver for transmission of Culicoides-borne diseases as it directly influences the physiology and life histories of both pathogen and vector. In turn, these temperature-dependent traits drive the biological processes required for transmission but have yet to be considered for leishmaniasis.     

The successful student will start by measuring these traits (such as life span, activity, biting rate, developmental period of the parasite and the probability of midges becoming infectious) over a range of temperatures to start to build a robust mathematical model of L. chancei transmission.. This model will be parameterized using colonized midges kept at the Pirbright Institute and wild-caught midges collected from sites across the UK. Using cutting-edge techniques in the thermal biology of insects developed in Cardiff University and from bionomic, epidemiological and vector competence studies a temperature-dependent models of relative vectorial capacity and relative force of infection will be generated. 

Student experience

The student will work closely with Dr Matt Rogers and Dr Laith Yakob from The London School of Hygiene & Tropical Medicine | LSHTM, Dr Tom Bishop from the School of Biosciences - Cardiff University and Dr Marion England from the Pirbright Institute to explore the transmission potential of Leishmania (Mundinia) from native midge species. The student will be taught to:

• Culture parasites, maintain lab-reared midgess
• Sample and identify wild midges
• Infect midges and measure parasite growth and development
• Asses the influence of temperature on vectorial capacity through life history traits, including midge activity using infra-red monitoring technology
• Assess the influence of temperature on vector competence through infection studies and transmission of parasites
• Construct mathematical models and perform risk factor analyses to bring together infection, ecological and climate data

Where will the project be based?

Primarily at LSHTM, however, the student will also spend time at Cardiff University and the Pirbright Institute.

Further details

For further information contact Dr Matthew Rogers – matthew.rogers@lshtm.ac.uk.

Project 2: Assessing the impact of land use on Schistosomiasis transmission sites 

Supervisory team

• Principal Supervisor: Dr Laura Braun (LSHTM)
• Co-Supervisor: Dr Andy Hardy (Aberystwyth University), Dr Aidan Emery (Natural History Museum)

Project description

Schistosomiasis is a water-based disease that can lead to organ damage, infertility, and numerous under-recognised morbidities, including stunting. Infection occurs through contact with contaminated freshwater bodies that contain aquatic snails infected with hatched schistosome eggs. These are released through human faeces or urine and hatch when in contact with freshwater. Despite being a treatable and preventable disease, schistosomiasis affects around 250 million people worldwide. It can also infect livestock, leading to economic losses for farmers and the risk of zoonoses and animal reservoirs of infection.  Transmission zones require suitable habitats for intermediate host snails. This includes freshwater bodies such as ponds or rivers, and rice paddy fields. Changes in land use can create new freshwater ecosystems or alter the conditions of existing water bodies, thereby influencing the abundance and distribution of snail populations. This project will focus on the impact of deforestation and agricultural expansion on schistosome snail habitats.  There is evidence that deforestation increases biological water contamination, especially in areas with low sanitation coverage. This can increase the release of schistosome eggs into waterbodies, thereby increasing infectivity. This is especially the case following extreme weather events such as heavy rainfall. The project will focus on south Madagascar where deforestation rates are continuing to increase, in particular for the expansion of rice paddy fields.   

The student will start with a systematic review on the link between land use change and schistosomiasis. Next, satellite data will be analysed to map deforestation sites. The student will conduct snail surveys to determine snail presence and infection rates. High resolution satellite imagery sources such as Planet (3 m) will provide fine-scale data of the study site and help identify and map water bodies. There is also scope for classifying types of vegetation, with some associated with snail habitats. Multi-variate statistical analysis will explore associations between deforestation and snail habitats, to understand areas that are high risk for snail vectors. Further analysis of readily available satellite data will allow for the examination of climatic factors within the study site, and whether any of them are risk factors for snail habitats.

This multi-disciplinary project touches on all three CDT themes, with a focus on a) disease preparedness by using remote sensing for environmental monitoring of snail habitats and b) diseases transmission by studying the effects of environmental change. The research will inform theme c) disease control, by highlighting the effects of changing land use such as deforestation.   Engagement in this project promises a rich and varied experience. In London, the student will gain hands on laboratory experience at Natural History Museum. This will involve handling all aspects of the schistosome lifecycle (e.g., infections) and testing the impact of environmental conditions on snails. Fieldwork will be conducted in Madagascar, developing skills in field sampling and an understanding of the local setting. The student will be integrated in a multidisciplinary and multicultural team driven by fairer partnerships. The research journey also encompasses data management, analysis, and dissemination to both scientific and public audiences, ensuring the student acquires a versatile skill set essential for navigating scientific research.

The student will develop expertise in remote sensing, epidemiology of Schistosoma, vector ecology, and land use assessment. Fieldwork will provide practical insights into snail surveying, water quality testing and land use assessment. Proficiency in R and data management, spatial analysis, and risk factor analysis will be developed, equipping the student for a future research career.

Where will the project be based?

The student will be based in London, with travel to Madagascar (approximately one visit/year).

Further details

For more information, contact Dr Laura Braun email: Laura.Braun@lshtm.ac.uk.

Project 3: Identifying exposure pathways for environmentally transmitted zoonoses (Leptospira spp. and T. gondii) in climate-vulnerable peri-urban informal settlements in Brazil

Supervisory team

• Principal Supervisor: Dr Max Eyre (LSHTM)
• Co-Supervisor: Dr Robert Dreibelbis (LSHTM)
• Co-Supervisor: Dr Sara Macbride-Stewart (Cardiff University)

Project description

Over 2 billion people live in urban informal settlements that are characterised by environmental degradation and unsanitary conditions and vulnerable to extreme weather events driven by climate change. These socio-ecological and climatic conditions favour environmental transmission of zoonotic diseases, such as Leptospira and Toxoplasma gondii, which can persist in water and wet soil for long periods, making them sensitive to rainfall events and flooding.

This project will examine how socio-demographic and environmental processes that drive zoonotic spillover of Leptospira and T. gondii interact with flooding events in marginalised urban communities in the city of Salvador, Brazil. It will take an intersectional eco-epidemiological approach to jointly analyse existing data collected at the human-environment-animal interface during a longitudinal community cohort study, linking data on human seroincidence, animal reservoirs, and pathogen load in soil and water samples. The student will also be responsible for collecting data to explore how exposures and social actions vary with socio-demographic status and following flooding events, and how this determines spillover risk. This project will generate evidence on how climate change will drive transmission of environmentally-transmitted zoonoses and inform the development of interventions that target high-risk population groups.   

Specific objectives

1. Conduct a systematic and/or scoping  review on the impact of flooding events on transmission of environmentally persistent zoonoses across socio-demographic status.
2. Use qualitative participatory methods to establish a theoretical framework that will guide quantitative, direct measurement of i) exposure to animal excreta and the environment and ii) household hygiene and sanitation activities relevant to the two target diseases. Analyse these data to examine how they vary by socio-demographic status and before/following flooding events.
3. For each disease, determine how individual infection risk and household risk vary by sociodemographic status and can be explained by exposures and hygiene activities measured during flooding events.

The student will work within established interdisciplinary research teams in this UK-Brazil research partnership. They will be hosted at LSHTM’s Environmental Health Group, a world leading, multidisciplinary team of 40+ professional researchers, PhD students, and project support staff working on environmental health issues in high burden settings. During the placement in Salvador (minimum of four months), they will be embedded in research groups at ISC-UFBA and IGM-Fiocruz with decades of experience conducting community-centred research on zoonoses in informal settlements.  They will have the opportunity to disseminate their research outputs in meetings with local researchers, community members and public health agencies, and at national and international academic conferences. The proposed multidisciplinary supervisory team and placement will allow them to develop the interdisciplinary skills and experience that are essential for studying zoonotic disease transmission at the human-animal-environment interface. This development will be supported with quantitative and qualitative methods training at LSHTM, Cardiff School of Social Sciences and UFBA/Fiocruz.

The student will gain expertise in quantitative methods (hierarchical regression models, geospatial methods), R coding, causal inference, and participatory/qualitative methods. They will also develop skills in systematic reviews, data synthesis, and interdisciplinary communication through collaborating with, and disseminating research outputs to, local and international stakeholders.

Where will the project be based?

The student will be primarily based in London, with travel to Brazil.

Further details

For more information, contact Dr Max Eyre - max.eyre@lshtm.ac.uk.

Project 4: Using genomics to understand animal, human and environmental transmission of diarrheagenic Escherichia coli pathovars in Bangladesh 

Supervisory team

Principal Supervisor: Professor Taane Clark (LSHTM)

Co-Supervisor: Professor Susana Campino (LSHTM)

Co-Supervisor: Professor John McGrath (Queen’s University Belfast)

Co-Supervisor: Dr. Dinesh Mondal (International Centre for Diarrhoeal Disease Res.; icddr,b)

Project description

Diarrhoea is the second leading cause of mortality among children <5 years age globally. In developing countries like Bangladesh, diarrheagenic pathovars of Escherichia coli are highly prevalent. These pathovars can be passed in the faeces of humans and other animals. Transmission occurs through the faecal–oral route, via consumption of contaminated food or water, and through person-to-person contact, contact with animals or their environment, and swimming in untreated water. The sequencing of E. coli genomes from samples collected across these potential sources and chains of transmission can inform on circulating pathovar variants. Advances in genome sequencing techniques, notably Oxford Nanopore Technology (ONT), provides a rapid, portable, and cost-effective approach to generating E. coli genomic data. The subsequent application of big data methods (e.g. bioinformatics, phylogenetics) can provide insights into virulence genes and transmission patterns.

Our project aims to understand the genetic variability of diarrheagenic E. coli pathovars across patients from a growing cohort of 200 children in Dhaka, along with potential transmission sources. The objectives are to: (1) collect, process, and assess samples from diverse sources (e.g., stool); (2) characterize the genetic variation of the isolates through ONT sequencing; (3) construct transmission networks within a spatial-temporal-genomic analysis using phylogenetic methods; (4) infer genes and mutations linked to virulence, transmissibility, and antimicrobial resistance. Our project links with the icddr,b, who routinely collect samples from the cohort of children, along with associated epidemiological data. Publicly available sequence data will also be analysed.

Upon successful execution of the project, we will have generated evidence on the transmission in E. coli in Bangladeshi and other settings. The results will be disseminated through scientific publications in peer reviewed journal and seminar presentations, as well as with key stakeholders (e.g., policy makers) through existing icddr,b links. The knowledge gained will inform on decisions in diarrhoeal disease treatment, management, and control.

Where will the project be based?

The student will be primarily based in London, with travel to Bangladesh.

Further details

For further information contact Prof Taane Clark - taane.clark@lshtm.ac.uk.

Project 5: Understanding the distribution and spread of Anopheles stephensi, a new and invasive malaria vector in Africa

Supervisory team

• Principal Supervisor: Professor Sian Clarke (LSHTM)
• Co-Supervisor: Professor Jonathan Lines (LSHTM)
• Co-Supervisor: Dr Mojca Kristan (LSHTM)

Project description

The main objective of this project is to understand the environmental factors that influence the spread of Anopheles stephensi, and potential to increase the local risk of malaria transmission. The project examines the role of humans and animals in malaria transmission, and adopts an interdisciplinary approach, encompassing entomology, epidemiology, transmission modelling, vector control and policy development.     The project will be undertaken in close collaboration with the World Health Organization (WHO) Initiative to stop the spread of Anopheles stephensi in Africa, and WHO/Roll Back Malaria Vector Control Working Group Taskforce on An stephensi to ensure research findings feed into policy recommendations.   

The project involves three stages, modifiable according to student interest and expertise, including:   

1. The project will start by reviewing the known biology and bionomics of An stephensi, in comparison with existing key vectors in Africa such as An arabiensis and An gambiae – to understand the parameters affecting the distribution of each vector and their role in malaria transmission. Given the ready proclivity of An stephensi to feed on animals, particular attention will be given to differences between vectors in degree of anthropophily (tendency to feed on humans vs other animals), infection rates, and contribution to overall disease transmission risk.     
2. The second stage will include fieldwork to characterise the larval ecology and investigate host feeding preferences of An stephensi in one country, potentially Cameroon, Ghana, or Tanzania (country to be confirmed). The location will be dependent on the results of ongoing vector surveillance to detect the presence of An stephensi in these countries. This phase of the work also includes the opportunity to utilise a new e-DNA based sampling method (developed by one of the supervisors, MK) to investigate the distribution, breeding habitat and ecology of this new disease vector; and to help adapt this sampling approach for use in routine vector surveillance.   
3. Data collected in phases 1 and 2 will be used to parameterise a disease transmission model  (third phase of the project) to assess how variation in the relative density of humans and alternative hosts, such as cattle and other animals, across Africa could modify disease risk according to different degrees of anthropophily. This phase could include an attachment to ILRI, to gather data and understand trends in livestock farming and animal husbandry practices, with a view to modelling how these might affect future vector distribution and transmission risk. Given the paucity of published data on An stephensi bionomics in Africa, as well as to assess risk in countries where An stephensi has not yet been detected, this analysis will also be performed for An arabiensis (another malaria vector without a strong preference for human blood meals, and for which there is more existing data from Africa).

The aim of these models is to estimate the impact of the introduction and establishment of An stephensi on malaria burden across a range of geographies – illustrative of variations in disease risk at a local-scale scale within countries, as well as larger-scale variation between countries, taking account of human density, livestock density, human-blood-index (HBI of the vector), and probability of human-vector contact.   

Overall, this project has the potential to make a significant contribution to our understanding of the consequences of the recent invasion of Africa by An stephensi and help us prepare by anticipating where and how to apply appropriate control measures.

The student will acquire knowledge and skills in vector biology and develop an in-depth understanding of the control of vector-borne diseases. Understanding the ecological context of vector-borne disease is essential for effective management strategies. The student will also gain knowledge and understanding of the principles and practices of public health, including epidemiology and surveillance.

Where will the project be based?

The student will be based in the UK, with opportunity to travel to one or more countries in Africa.

Further details

For more information, contact Prof Sian Clarke - sian.clarke@lshtm.ac.uk.

Project 6: Investigating the relationship between market hygiene and human immunity, and the risk of spill over of avian influenza viruses from poultry to humans in live poultry markets in Bangladesh

Supervisory team

• Principal Supervisor:  Dr Patrick Nguipdop Djomo (LSHTM)
• Co-Supervisor: Professor Punam Mangtani (LSHTM)
• Co-Supervisor: Professor Zhiwen Luo (Cardiff University)

Project description

Background

Avian Influenza Viruses (AIV) are endemic in poultry in Bangladesh. Marketing practices, for example mixing of chicken with other bird species in markets, and sale and slaughter of birds in live poultry markets with various degree of biosecurity, increase human exposure and the spill-over potential, therefore the pandemic risk.   Aims: Through this PhD, the student will investigate determinants of AIV spill-over risk at the human-poultry interface in live poultry markets in Bangladesh, focusing on the role of market hygiene and human immune resistance to infection given exposure.  Specific objectives:  - Explore the relationship between overall market hygiene and marketing practices in poultry stalls, and risk of exposure in humans, notably through aerosolization of virus particles.  - Investigate the association between immune response in market workers and the risk of infection, including the potential role of mucosal immunity and existing immunity to human influenza viruses.  - Use mathematical modelling approaches to integrate the information on exposure in live poultry markets and levels of susceptibility in market workers, and support spill-over risk assessment.   

The student will be supported by a multi-disciplinary team, including epidemiologists, immunologists, mathematical modellers, and social scientists. They will have access to novel data collected from a large multi-disciplinary study (One Health Poultry Hub) investigating zoonotic threats along the poultry production and distribution networks in Bangladesh. They will have the opportunity to plan and collect supplementary data to complement their PhD research.

Technical skills including quantitative epidemiology (design and analysis of observational designs), applied statistical analysis skills, immuno-epidemiology and mathematical modelling. The student will also have real-life experience of working in a multidisciplinary one health team, with collaboration with veterinary epidemiologists, immunologists and social scientists

Where will the project be based?

The student will be primarily based in London, with travel to Bangladesh.

Further details

For more information, contact Dr Patrick Nguipdop Djomo - patrick.nguipdop-djomo@lshtm.ac.uk

For details of other projects available at the OneZoo CDT from other institutions, please see the OneZoo website.

How to apply

Apply to OneZoo CDT

Studentship Applications must be submitted via the online application survey. Applications received in any other format will not be considered.

Read more information and further guidance about applying.

For further details of other projects currently available with the other three universities also participating the OneZoo Centre for Doctoral Training please see the website: www.onezoo.uk

Deadline

Closing date: 25 March 2024 at midnight.