NIHRDataInsights/HRCSData huggingface dataset:
Title: The proteomic architectures of apicomplexan cells: the molecular complexity of pathogens revealed
Funder: Wellcome Trust

Abstract: Apicomplexan parasites represent highly adapted eukaryotic pathogens that have evolved to exploit multiple human and animal niches causing widespread disease and food deprivation. Key to their success as parasites are novel organelles and structures adapted for invasion and mediation of interactions with their hosts. They have also reprogrammed canonical cell compartments with modified metabolic capacities and regulatory control. An overwhelming obstacle to understanding the biology of these parasites and their mechanisms of pathogenesis is that much of the parasite proteome is unique in Apicomplexa, with most proteins of unknown location or function. My group uses a novel method for whole-cell spatial proteomics in apicomplexan parasite-host systems that simultaneously captures the locations and associations of thousands of parasites proteins. This provides intimate and thorough illumination of the architecture and adaptations of these devastating pathogens at an organelle-, sub-compartment- and protein complex-level. We will define the commonalities and differences between major pathogen groups Plasmodium and Toxoplasma, the destinations of proteins they export into their hosts, and the spatial dynamics of their proteomes during infection developmental cycles. This comprehensive knowledge will enable molecular mechanistic understanding of these pathogens that is essential for effective design and implementation of disease management and prevention strategies.

Lay abstract: Apicomplexan parasites are a related family of pathogens that cause several devastating diseases including malaria that threatens 30% of the world’s population. Key to their success are highly adapted cell compartments evolved for efficient invasion of their hosts, defence against the immune system, and disease transmission. Most of the molecular organisation and composition of these compartments, however, is unknown and approximately half of the parasite’s proteins are completely uncharacterised, severely limiting our understanding of these pathogens and strategies for disease prevention. We have pioneered the use of a new technology that enables determination of global spatial distributions of parasite proteins. This allows thorough knowledge of the locations and associations of parasites proteins and the compositions of their novel compartments. We will generate global protein atlases for related parasites Plasmodium and Toxoplasma in various stages of parasite development, providing unprecedented understanding and access to the cellular architecture of these devastating pathogens.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Understanding and predicting the evolution of antibiotic resistance in human infection
Funder: Wellcome Trust

Abstract: The evolution of antibiotic resistance is a threat to modern medicine. Patients with chronic bacterial infections are at particular risk from antibiotic resistant genotypes, which typically arise from within the infection. However, a lack of controlled studies means that we don't understand how antibiotic resistance evolves within the human host environment, and why the emergence of resistance varies among patients. We identify randomised clinical trials (RCTs) of new antibiotic treatments as a powerful way to study resistance evolution in action during a controlled, replicated natural experiment. We will exploit a unique opportunity to perform an evolutionary analysis of two parallel Phase-III RCTs for inhaled ciprofloxacin treatment of chronic lung infections caused by Pseudomonas aeruginosa, which is a WHO Priority-1 pathogen in critical need of improved antibiotic therapies. Ciprofloxacin resistance emerged in ~40% of the treated patient infections but this patient-to-patient variation is unexplained. We aim to explain why resistance evolved in some patients but not in others. To do this, we will (1) discover the evolutionary mechanisms of resistance emergence in patient infections, (2) identify the bacterial and host properties that drove resistance evolution, and then (3) test how well biomarkers of these drivers predict resistance emergence in other patients.

Lay abstract: Antibiotics are our main defence against bacterial infections, but rising levels of resistance risks rendering antibiotics ineffective. We do not yet understand how resistance evolves within human infections, or why resistance emerges in some individuals but not in others. Clinical trials for antibiotics offer a powerful way to answer this question because they are, in effect, large experiments where the evolution of resistance can be observed in real-time in humans. To explore why resistance emergence varies between patients we will study the evolutionary processes leading to resistance in two clinical trials: during the trials, patients with long-term bacterial infections were treated with an antibiotic, and resistance emerged in around half of the patient infections. We will then use this understanding of bacterial evolution to develop tools that help doctors predict which patients are at risk of their infection developing resistance, allowing better treatment choices and more sustainable use of antibiotics.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Controlling emergent Anopheles stephensi in Ethiopia and Sudan (CEASE)
Funder: Wellcome Trust

Abstract: Malaria is predominantly a rural disease in Africa and whilst urbanisation is occurring rapidly it was thought unlikely to lead to substantial increases in malaria transmission because Africa lacks an urban-adapted malaria vector. However, Anopheles stephensi, a common and efficient urban malaria vector in South Asia and the Persian Gulf, has recently been found in the Horn of Africa, including Ethiopia and Sudan and is associated with a rise in malaria in Djibouti. This prompted the WHO to call for urgent action to control the spread of the vector. This proposal brings together biologists, epidemiologists, mathematical and geostatistical modellers and medical anthropologists with the aim of preventing the spread of An. stephensi in Ethiopia and Sudan. The research will: (i) investigate the distribution, routes of introduction/reintroduction and spread of An. stephensi; (ii) quantify the importance of An. stephensi for malaria transmission and iii) evaluate multi-sectoral vector control strategies. This incredibly timely research will quantify the threat posed by An. stephensi in Ethiopia and Sudan and identify control measures to reduce populations and combat further spread in Africa. Historic examples (e.g. An. gambiae in Brazil) demonstrate that without prompt action, invasive species can become established with massive impacts on morbidity/mortality.

Lay abstract: Malaria in Africa is mainly a rural disease because the local malaria mosquito species are not well adapted to urban settings. Unfortunately, current efforts to control malaria are threatened by a new, invasive mosquito species called Anopheles stephensi which has been identified in towns and cities in the Horn of Africa, including Ethiopia and Sudan and is associated with an increase in malaria in Djibouti. This research aims to control the spread of Anopheles stephensi in Sudan and Ethiopia. We will: 1) Discover the current distribution of the mosquito and route of introduction using mosquito sampling, genetic ancestry analysis and spatial modelling. 2) Determine whether Anopheles stephensi is associated with increased malaria using health system data, prospective studies to identify malaria cases, and mathematical models. 3) Identify social and ecological factors which influence the spread/control of Anopheles stephensi and will define the most appropriate mosquito control strategies.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Discovering human host defence mechanisms at the Toxoplasma gondii vacuole
Funder: Wellcome Trust

Abstract: The protozoan parasite Toxoplasma gondii chronically resides in 30% of humans as infections cannot be cleared. Infection is often asymptomatic, with serious complications and death in immunocompromised and congenitally infected humans. It is unclear how normal immunocompetent individuals control Toxoplasma during acute infection. Multiple unknown unique and overlapping mechanisms of Toxoplasma defence must exist in different human cell types. Host defence acts directly at the membrane between the parasite and the cytoplasm. We have developed an artificial intelligence-driven image analysis pipeline to conduct high-throughput single-cell analysis of these defence mechanisms. We will combine this approach with mechanistic cellular studies and unbiased mass spectrometry approaches. Like this, we will systematically define and characterise the human intracellular host defence machinery targeting Toxoplasma gondii in endothelial cells and macrophages. We will address the following aims: I. Elucidate mechanisms driving endo-lysosome-mediated control of Toxoplasma in endothelial cells. II. Define mechanisms of ubiquitin-dependent host defencetargeting Toxoplasma in macrophages. III. Identify novel cellular networks targeting Toxoplasma employing host defence proteins as tools for discovery-based mass spectrometry. By discovering the compendium of host defence machinery that operates at the human Toxoplasma host defence vacuole in two divergent cell lines, this research directly contributes to human health.

Lay abstract: Toxoplasma gondii is the most prevalent human parasitic infection on the planet, causing disease in people with compromised immune systems. Normal individuals control the infection, but we do not understand how. The parasite forms a vacuole inside cells to hide from the immune system. A signalling molecule, gamma interferon, activates various pathways in different cells to control Toxoplasma. We will compare these pathways in two cell types Toxoplasma likes to infect, human endothelial cells and macrophages, to study mechanisms of control. We have developed an artificial intelligence software for detailed classification of anti-Toxoplasma effects in these cells. Human proteins central to anti-Toxoplasma control are ubiquitin-associated proteins. We will study these proteins on vacuoles to define how they control the parasite. To discover new pathways, we will use these proteins as bait to identify novel players in the vicinity. Our discoveries will help clarify human anti-Toxoplasma control and aid drug development.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Exploiting genetics, genomics, and immunological responses to construct novel conjugate vaccines against Salmonella Paratyphi A; an emerging global health threat
Funder: Wellcome Trust

Abstract: Enteric fever is a febrile disease caused by the bacteria Salmonella Typhi and Salmonella Paratyphi A. Typhi is well studied and new conjugate vaccines will likely have a major impact on disease burden. In contrast, Paratyphi A is poorly studied and there are currently no licensed vaccines that protect against this organism. This fellowship aims to provide a better understanding of the population structure and biology of Paratyphi A, leading to the construction of novel conjugate vaccines. Firstly, through a network of collaborators in Asia, I will define the population structure of a contemporary Paratyphi A collection. Pivotal selective events will be identified using phylogenetics and genome mapping; the conservation of potential vaccine candidates will be investigated. O-antigen is a key structure in Paratyphi A and a component of all developmental Paratyphi A vaccines. However, we have observed O-antigen phase variation in Paratyphi A which may limit vaccine efficacy. I aim to identify the mechanism of Paratyphi A O-antigen variation and assess the potential role of antigenic variation in immune escape. Lastly, I have identified a panel of immunogenic Salmonella antigens. I will investigate their function in Paratyphi A and link them to O-antigen to generate novel, bespoke conjugate vaccines.

Lay abstract: Enteric (typhoid) fever is a disease caused by the bacteria Salmonella Typhi and Salmonella Paratyphi, the disease is serious and common in developing countries in Asia. There are new vaccines which will have a dramatic impact on enteric fever. However, these vaccines are not protective against Paratyphi. I aim to provide a better understanding of the biology of Paratyphi and generate candidate vaccines for future disease control efforts. I will collaborate with researchers in developing countries to establish a collection of Paratyphi. The genomes of these organisms will be decoded to generate an understanding of their genetic relationship, their evolutionary history, and validate potential vaccine targets. I will investigate changes in the surface antigen (O) of Paratyphi that may play a role in immunity. Using data from these studies I will additionally develop candidate vaccines using a new approach, linking O-antigen to several novel targets I have identified previously.

Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Unravelling the molecular mechanisms of invasive pneumococcal disease
Funder: Wellcome Trust

Abstract: Invasive pneumococcal disease causes over a million deaths per year worldwide, particularly in sub-Saharan Africa. Streptococcus pneumoniae strains vary considerably in virulence, but the reasons for this are unclear. Capsular serotype 1 strains are particularly invasive and cause a major proportion of severe infections, including meningitis, but are poorly studied, partly because they have been genetically intractable. We want to understand why serotype 1 strains are highly invasive, and to identify mechanisms that distinguish aggressive S. pneumoniae strains from less aggressive variants. Furthermore, a low-cost serotype 1 vaccine is urgently needed, especially in sub-Saharan Africa. In this project, we will combine and exploit (i) recently-developed in vitro and in vivo infection models, (ii) bacterial RNAseq data (including our data obtained from cerebral spinal fluid from Malawian meningitis patients) and (iii) our methodologies for mutating serotype 1 strains, to identify and characterise the roles of multiple novel genetic determinants important for the pathogenesis of invasive S. pneumoniae infections. We will also characterise in detail the zwitterionic capsular polysaccharide that defines serotype 1 strains and assess its role in pathogenesis. Finally, we will exploit Protein Glycan Coupling Technology (pioneered by the applicants) to produce a much-needed and affordable glycoconjugate serotype 1 vaccine.

Lay abstract: The bacterium Streptococcus pneumoniae is a leading cause of pneumonia and meningitis worldwide. The most dangerous “serotype 1” strains, that are often multi-antibiotic resistant, have a cell-surface capsule made of specific sugar-chains. This project is motivated by the urgent need to understand how serotype 1 strains cause severe disease and to develop a low-cost vaccine against them. Recently, we have (i) studied patients in Malawi and The Gambia to provide further clues to why some S. pneumoniae strains can cause severe infections, (ii) overcome technical limitations to create mutant serotype 1 strains to facilitate laboratory studies. We will now undertake several co-ordinated studies to work out precisely how and why serotype 1 strains are so effective at causing severe disease. In addition, we will use our knowledge of bacterial capsules to produce a novel S. pneumoniae vaccine that will be affordable in the geographical regions where it is needed most.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: The fight for success: inter-bacterial competition mediated by the Type VI secretion system and its effectors
Funder: Wellcome Trust

Abstract: The Type VI secretion system (T6SS) is used by many Gram-negative bacteria to deliver toxic ‘effector’ proteins into rival bacterial cells as a means of inter-bacterial competition. The T6SS likely plays a central role in shaping many polymicrobial communities, but important aspects of effector delivery and action in target cells, and the ‘real-life’ relevance of T6SSs in a clinical context remain elusive. We will investigate the journey of individual and co-operating groups of effectors, from their recruitment by the T6SS to their fate and action in targeted cells, and dissect the mechanism of individual anti-bacterial effectors. We will also consider the global availability and mobility of anti-bacterial effectors and how the T6SS and its effectors can influence bacterial success in a clinical context. Using multidisciplinary approaches, we aim to: 1. Determine the mechanism of toxicity of novel anti-bacterial effectors 2. Elucidate the fate of effectors inside target cells 3. Define mechanisms of versatile effector recruitment and delivery in attacker cells 4. Use genomics to reveal the diversity, evolution and real-life relevance of T6SS effectors Our findings, combining mechanistic detail with insight into biological relevance, will provide fundamental advances in our understanding of T6SS-mediated anti-bacterial activity and may inform future strategies to counter bacterial pathogens.

Lay abstract: Infectious diseases caused by bacteria represent a major global health issue, exacerbated by ever-increasing antibiotic resistance. Bacteria normally live in mixed communities and can compete with each other by actively killing their rivals. This ability to compete is important for the success of pathogenic bacteria and may also provide lessons in how to kill bacterial cells. We will study a bacterial weapon called the Type VI secretion system (T6SS), which many bacteria use to fire toxins into competitors. We will use molecular techniques to learn how the T6SS can deliver many different toxins, what happens to toxins inside recipient cells, and how new types of toxin kill bacterial cells. We will use genomics to detect ‘arms races’ between bacteria as they pick up new toxins and to understand the importance of T6SS in disease. Our work will reveal new aspects of bacterial biology and may contribute towards future anti-bacterial therapies.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Mitigating bat viruses: from forecasting spillover to control at the source
Funder: Wellcome Trust

Abstract: Bats are among the most important sources of emerging viral threats, responsible for Ebola, SARS and Nipah. We currently mitigate the impacts of bat viruses reactively, by treating humans or domestic animals after viruses emerge and cause disease. This fellowship proposes that deeper understanding of viral epidemiology, combined with new statistical and biological tools, could empower a strategic shift towards prevention. Using a tractable and important bat virus, vampire bat-transmitted rabies, I will first use routinely-collected surveillance data to develop models that rapidly forecast spatiotemporal emergence risk as epidemiological situations change, enabling use of life-saving human and animal vaccines prior to outbreaks. Next, field studies, experiments and viral genomics will allow individual-to-landscape epidemiological models to identify sensitive points in viral transmission cycles that could be exploited by interventions. Finally, I will explore whether revolutionary new approaches to vaccinology using self-spreading vaccines can reduce human and livestock mortality by controlling bat viruses at their source. This research delivers immediate translational benefits by mitigating health and economic costs from the most important bat virus in the Americas, strengthens international research capacity, and creates a biological and methodological toolbox to manage pathogens in bats, an historically intractable reservoir of zoonotic viruses.

Lay abstract: Bats are a notorious source of new viral threats, responsible for Ebola, SARS and Nipah. Being able to anticipate and prevent the next outbreak would dramatically improve human health and prosperity. However, bats are notoriously difficult to study and blindly-implemented interventions can backfire. This fellowship will use a uniquely tractable and economically important study system, vampire bat rabies in Latin America, to develop a methodological toolbox for managing bat viruses. Routinely collected data from health systems will feed models that forecast risk in real time, enabling live-saving vaccination of humans and livestock before outbreaks begin. Field studies, viral genome sequencing, experiments, and computer simulations will explore whether new immunization paradigms using self-spreading vaccines could protect human health by combating viruses from within wild bat populations. Results will bring a future of vampire bat rabies eradication into sight and establish a model to manage bat viruses of global concern.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Plasmid biology in human adapted pathogens
Funder: Wellcome Trust

Abstract: Plasmids are responsible for virulence and antimicrobial resistance in many bacteria. We will dissect fundamental mechanisms of plasmid maintenance in the obligate human pathogens, Shigella spp. and Neisseria gonorrhoeae, declared as high priority organisms by WHO/CDC. Toxin:antitoxin (TA) systems (addiction systems) are important for plasmid maintenance by eliminating bacteria failing to inherit a plasmid after cell division. For example, the VapBC TA system is essential for maintaining the 210kb Shigella virulence plasmid. Additionally, TA systems (including VapBC) are increasingly recognised for their role in antibiotic tolerance, often a precursor to resistance. Despite this, little is known of how plasmid maintenance is integrated with the bacterial host, and how TA systems are activated after plasmid loss/during tolerance. Combining our understanding of variation in VapBC and the VapC toxin target tRNAfMet with multidisciplinary approaches (mutagenesis/structural:function studies/single cell analysis), we will define mechanisms of TA system activation and the temporal dynamics of events following plasmid loss that culminate in cell death. We will examine the acquisition and maintenance of resistance plasmids in Shigella and N. gonorrhoeae, and the interactions between plasmids and their contribtion to tolerance and horizontal transfer.

Lay abstract: The rise and spread of antimicrobial resistance is a recognised threat to public health, with much attention focused on the 'superbugs'. However, it is less well appreciated how plasmids (small circles of DNA) make bugs super, by acting as important vehicles for the pread of resistance and virulence. We will study plasmids in important human pathogens Shigella, which causes dysentry, and the gonococcus, a leading cause of sexually transmitted disease. Shigella, which kills around 200,000 people every year, has emerged from harmless bacteria after they acquired a single plamsid called pINV. We will study how pINV is kept by Shigella, and the way it affects how the bacterium accumulates resistance plasmids. We will use similar approaches to study gonococcal plasmids. Understanding how plasmids are maintained in bacteria should enable us to design strategies to eliminate them, thereby making bacteria harmless and/or restoring our ability to treat them with avaiable antibiotics.

Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION