NIHRDataInsights/HRCSData huggingface dataset:
Title: Dissecting the molecular basis for gamete recognition in the malaria parasite, and its targeting to block transmission
Funder: Medical Research Council

Abstract: We propose to examine 41 proteomically-identified proteins, bioinformatically predicted to be present on the surface of the male gamete of P. berghei for localisation, and their interacting partners on the female gamete. Briefly, we will produce GFP- or c-myc tagged parasites for each proteins of interest. Transgenic parasites expressing tagged proteins will be cloned following drug selection, and analysed by UV microscopy and IFA. Using these methods (with tubulin co-staining) we will identify which putative fertilisation-related proteins are located on the surface of the male gamete, and are potentially involved in interaction with female gametes. Only proteins located on the gamete surface will be used in co-IP. Proteins will be co-IP'd from P. berghei female gamete preparations, identified by MS/MS, and analysed by the production of further transgenics to characterise function (by gene KO) and localisation (protein tagging). Each KO parasite will be analysed for the ability to; produce gametocytes, exflagellate, form ookinetes/oocysts. We will assess if male and female gametes bind; if male gametes fuse to females, and if nuclear fusion occurs. Tagged parasites will be analysed to assess when they are expressed, and if they co-localise with other fertilisation implicated molecules. We will additionally assess the importance of individual molecules in fertilisation by raising mAbs against proteins confirmed as present on the male gamete surface. We will then use these in exflagellation, ookinete, and SMFA assays to assess their ability to block transmission, identifying molecules that mediate reproduction while informing the development of novel transmission blocking vaccines. The use of these assays allows us to elucidate the point of action in the lifecycle for each protein examined. In this manner, we will identify molecules involved in plasmodial fertilisation, increase our knowledge of the gamete surface, and establish how male and female gametes interact.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Determination of the dynamics of antimicrobial resistance genes in the human and animal gut microbiome.
Funder: Medical Research Council

Abstract: Research on Antimicrobial resistance (AMR) in host people and animals has focused on pathogenic bacterial species which are readily cultured in the laboratory. Recent advances in chromosome conformation methodology such as enable the metagenomic DNA sequencing of complex microbiomes with the assembly of genomic data from individual constituent bacterial species. Using these techniques it is possible to track the fate of AMR genes when they move between species of bacteria, or move between separate lineages of the same species. The aim of the proposed research is to define the nature and frequency of transfer of antimicrobial resistance (AMR) genes between pathogenic and commensal bacteria within their hosts under varying selection pressures. The proposed research consists of 6 work packages (WP) with the following objectives: WP1. To establish the accuracy and reproducibility of two novel metagenome sequencing methodologies that enable the individual genomic backgrounds of bacteria containing AMR genes to be identified from within faecal microbiome samples. WP2 & WP3. To use these novel genomic techniques in experimental conditions (in mice and pigs) to investigate horizontal AMR gene transfer from E. coli expressing Extended Spectrum Beta-Lactamase (ESBL) and Salmonella enterica serovar Typhimurium with plasmid-mediated fluoroquinolone resistance within the gut microbiome both following the therapeutic use of antimicrobials that lead to bacterial cure, and following the use of antimicrobials to which these strains are resistant. WP4 & WP5. To perform longitudinal studies of the gut microbiome in farmed pigs and humans receiving antibiotics for treatment of clinical disease to test the external validity of observations made from experimental animal infections. WP6. To develop mathematical models that capture the flux of AMR genes in bacterial populations to identify key parameters in the build-up or transmission of resistance.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION
Title: MICA: Mechanistic understanding of cell wall biosynthesis to combat antimicrobial resistance
Funder: Medical Research Council

Abstract: Penicillin and the wider family of beta-lactams are the single most important family of antibiotics. They target the final stage of bacterial cell wall biosynthesis, specifically cross-linking the structural polymer peptidoglycan (PG) by a family of enzymes called penicillin-binding-proteins (PBPs). Given this pivotal importance of PBPs we know little about how they interact with their natural substrates, precisely what these substrates are for different PBPs, and, astonishingly, how beta-lactam antibiotics interfere with this process. The SWaN Alliance brings together a multidisciplinary team of the UK's leading experts in PG biology, imaging and PG focussed chemistry to tackle these outstanding questions. Our aim is to build an integrated, multi-centre, multidisciplinary research programme as the UK hub of activity in cell wall biosynthesis. This hub will, in the first instance, develop new insight, and open up new ways to target PBPs, to sidestep the current mechanisms of resistance. We intend to decipher the fundamental mechanisms of PBPs at the structural, functional and cytoplasmic levels, including how PBPs interact with their substrates, and how the two PBP enzymatic (transpeptidase and transglycosylase) activities are co-ordinated. This will include, for the first time, determination of kinetic constants for the TP reaction of PBPs and the development of a dual quantitative continuous TP/TG assay. We will extend this new functional and structural insight, to explore interactions of PBPs with landmark beta-lactams, recently developed novel non-lactam PBP inhibitors, and control proteins. In doing so we will develop a transformative understanding of how PBPs interact with beta-lactams from which we will better understand the role of PBP alterations and substrate alterations in the emergence of target mediated resistance. All of this activity will reinvigorate PBPs as targets for drug discovery and development by industry and academia.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Interrupting transmission of soil-transmitted helminths: cluster randomised trial evaluating alternative treatment strategies in Kenya
Funder: Medical Research Council

Abstract: In recent years, an unprecedented emphasis has been given to the control of neglected tropical diseases, including soil-transmitted helminths (STH). The mainstay of STH control is school-based deworming, but recent modelling has shown that in all but very low transmission settings, the treatment of school-aged children is unlikely to interrupt transmission, and that new treatment strategies are required. This study seeks to answer the question: is it possible to interrupt the transmission of STH, and if so, what is the most cost-effective treatment and delivery strategy to achieve this goal? Two paired cluster randomised trials in are being implemented in distinct settings in western and coastal Kenya. The interventions are annual mass anthelmintic treatment delivered to pre-school and school-aged children, as part of a national school-based deworming programme, or to the entire community delivered by community health workers. In each site, 120 clusters will be randomised to one of three groups: receiving either (i) annual school-based deworming; (ii) annual community-based deworming; (iii) biannual community-based deworming. The primary outcome measure is the prevalence of hookworm infection, assessed by repeat cross-sectional, age-stratified parasitological surveys. Secondary outcomes include intensity of STH species and treatment coverage, and among a randomly selected sub-sample of participants who will be followed longitudinally, worm burden and proportion of eggs unfertilised. A nested process evaluation, using semi-structured interviews, focus group discussion and a stakeholder analysis will investigate the community acceptability, feasibility, and cost-effectiveness of the interventions. Funders and governments are committed to controlling STH, but seek clear policy and technical guidance on the impact and cost-effectiveness of school- versus community-based deworming. This evaluation will be among the first to provide such policy information.


Research activity codes: 6.9 RESOURCES AND INFRASTRUCTURE (TREATMENT EVALUATION);8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: INFECTION
Title: A randomized trial to evaluate the toxicity and efficacy of 1200mg and 1800mg rifampicin daily for 4 months in the treatment of pulmonary tuberculosis
Funder: Medical Research Council

Abstract: Tuberculosis (TB) is one of the major causes of death in the world, responsible for 1.5 million deaths annually. Currently, the most effective form of control of tuberculosis is treatment of clinical disease. The current WHO recommended 6 month regimen for the treatment of TB is too long. An estimated 15% of patients worldwide do not successfully complete treatment. If treatment duration could be reduced, adherence and cure rates would improve, and treatment costs would decrease. Of the four drugs in standard tuberculosis treatment, rifampicin and pyrazinamide are responsible for most of the sterilising activity. Increasing the dose of rifampicin both results in significantly greater M. tuberculosis killing in pre-clinical studies, and also in greater early bactericidal activity in the sputum of patients with pulmonary tuberculosis. Preliminary results suggest that, unlike pyrazinamide, higher doses of rifampicin are safe. The principal objectives of the trial are: 1)To determine whether an increase in the daily dose of rifampicin from 600 mg to 1200 or 1800mg results in more rapid sterilisation of the lungs, allowing a reduction of treatment duration to 4 months. 2) To assess whether the increased dose results in an increase in serious (grade 3 or 4) adverse events. In this multicentre randomised, controlled clinical trial, 654 smear positive patients with pulmonary tuberculosis will be randomly allocated to either the standard 6 month regimen, or a 4 month regimen with rifampicin at 1200 or 1800mg daily and other drugs at standard dose. They will be followed up for 12 months after stopping treatment, with monthly clinical, sputum and laboratory examinations. If the new regimen is shown to be effective and safe, results will be presented to the WHO and to National Tuberculosis Control Programmes and to the wider academic community, to inform treatment guidelines and routine practice. If positive, the results of this trial will have major public health benefit


Research activity codes: 6.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Impact of maternally derived antibodies and infant microbiota on the immunogenicity of rotavirus vaccines in African, Indian and European infants.
Funder: Medical Research Council

Abstract: Live, attenuated, orally administered rotavirus (RV) vaccines have the potential to greatly reduce diarrhoea deaths but they work less well in countries where they are needed most. In Sub-Saharan Africa and South Asia, vaccine efficacy is 43-66% compared to >90% in high-income countries. The reasons are not understood, but likely to be complex. Serum IgA responses are lowest where RV vaccine efficacy is poor, and are used as an imperfect correlate for protection. Vaccine virus shedding in stool indicates "vaccine take", but its predictive value as a correlate of protection has not been explored in low income settings. We will address the following questions: 1. What is the role of maternally derived antibodies on RV vaccine take and serum IgA response in infants? 2. Is dysbiosis at the time of vaccination associated with poor RV vaccine take and serum IgA response in infants? 3. What is the effect of co-administered oral poliovirus vaccine (OPV) on the immunogenicity of RV vaccine in infants in low-income settings? The study will enrol birth cohorts in three countries: Malawi and India, with infant populations in whom RV vaccine efficacy is poor, and the United Kingdom, where vaccine efficacy is high. In India, two cohorts will be recruited to allow comparison of the effect of OPV and inactivated polio vaccine on RV vaccine immunogenicity in the same population. Infants will be followed from birth up to 16 weeks of age. Blood and breast milk samples will be collected to investigate the impact of maternal antibody transfer on seroconversion. Serial stools will examine gut microbiota development, early exposure to natural RV infection and RV vaccine virus shedding post immunisation. Gut and systemic inflammation at the time of vaccination will be assessed. An improved understanding of RV vaccine performance will inform strategies for delivery and design of rotavirus and other enteric vaccines in low-income settings with high burden of enteric infection.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: MRC Centre for Medical Mycology
Funder: Medical Research Council

Abstract: We will create an MRC Centre which is recognised internationally as a leading centre of excellence for research and training in Medical Mycology (the MCMM). Creation of the MCMM will enable us to establish an optimal configuration that will exploit our collective strength and will maximise our potential for fundamental and translational science, as well as for providing world-leading training in medical mycology. New posts in bioinformatics and in experimental immunology will add scope, depth and translatability to our existing research strengths. Six innovative and cross-disciplinary research themes are proposed: 1. Fungal cell surface dynamics and its impact on antimicrobial chemotherapy and host immunity; 2. Fungal components as antifungal drug targets, diagnostics, vaccine antigens and adjuvants; 3. Fungal growth, adaptation and morphogenesis in the context of infection; 4. Temporal host-fungal interactions and key mediators that influence disease establishment and progression at molecular, cellular and organismal levels; 5. Exploiting emerging technologies to generate global perspectives that broaden our mechanistic understanding of host-fungal interactions; 6. Unravelling patient susceptibility to enable directed diagnosis, treatment and prevention of fungal disease. MCMM Early Career Fellows, PhD students and clinical trainees will enable these research themes and foster interconnectivity and interdisciplinarity within and beyond the MCMM. The training of these Fellows and students will address the urgent requirement for increased capacity in basic and clinical research in this neglected field in the UK. Creation of the MMCM will also accelerate translation of our science and promote a vibrant public outreach programme, maximising the impact of the excellent mycology research that occurs in Aberdeen.


Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING);4.5 RESOURCES AND INFRASTRUCTURE (DETECTION);5.9 RESOURCES AND INFRASTRUCTURE (TREATMENT DEVELOPMENT)
Health categories: INFECTION
Title: Pre-clinical development of an influenza vaccine to induce broad protection through multiple immune mechanisms
Funder: Medical Research Council

Abstract: There is an overwhelming need for a universal influenza vaccine to protect against the next influenza pandemic as well as providing improved protection against seasonal influenza. The two most advanced approaches both rely on targeting conserved regions of the virus; inducing antibodies against the haemagglutinin stem, or T cells recognizing the internal antigens nucleoprotein (NP) and matrix protein 1 (M1). Oxford has taken the lead in clinical development of T cell boosting vaccines; Mount Sinai has been at the forefront of anti-stem antibody research. A single immunization with MVA-NP+M1 boosts T cell responses in young and older adults, and a current clinical study using both MVA and ChAdOx1 to express NP+M1 has shown increased duration of strong T cell responses following immunization, which will be important to maintain protective immunity. Mount Sinai have been able to achieve protective antibody titres against HA stem after two immunisations, but different versions of the chimeric HA (cHA) molecule must be delivered with each immunization. We now propose to collaborate to produce vaccines which employ both mechanisms of immunity in order to produce the ultimate universal influenza vaccine. We will produce and test replication-deficient viral vectors (simian adenovirus ChAdOx1 and Modified Vaccinia virus Ankara MVA) expressing both a cHA molecule derived from a group 2 influenza A virus and the NP+M1 fusion protein that has been used in clinical trials. Using a different version of cHA in each viral vector will allow us to induce protective antibody responses against HA stem at the same time as boosting and maintaining protective T cell responses against NP and M1. We will also test the use of recombinant cHA protein to boost anti-stem antibodies. We will conduct immunogencity and efficacy testing in mice and ferrets, and produce pre-GMP vaccine and/or cell banks suitable for cGMP manufacture and clinical testing.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: INFECTION
Title: Development of an infection detecting wound dressing
Funder: Medical Research Council

Abstract: NEED:140,000 patients with burns attend English and Welsh A&Es every year. Infection, a major cause of morbidity and mortality in patients with burn injuries, is implicated in ~32% of associated complications. However, diagnosis of infection in burn patients is problematic, with standard indicators of little value and clinicians routinely waiting 3 days for confirmatory tests. This clinical bottleneck undermines patient care, clinical outcomes and contributes to the inappropriate use of antibiotics and over treatment as well as missed infection diagnosis. SOLUTION & RATIONALE: We have developed an infection responsive wound dressing which gives a clear visual indication of wound infection, directly at point-of-care. This technology responds to key cytotoxic virulence factors from predominant burn wound pathogens: Staphylococcus aureus, Pseudomonas aeruginosa, Enterococcus faecalis, ("SPE-group"; up to 80% of infections). Colour change is triggered at bacterial concentrations two orders of magnitude lower than their cytotoxicity threshold, providing early warning before major tissue damage can occur, whilst distinguishing invasive infection from low-level background colonisation. DEVELOPMENT PLAN: The research will be conducted in four distinct phases, linked by pivotal stop/go points (Fig. 3 and 8). Phase 1 will build upon our existing data and resources to drive the iterative development of dressings and an optimised prototype. Phase 2: i) Will determine toxicological profiles and compliance with ISO10993; ii) Clinical feasibility study (using wound swabs / exudates) to ensure performance is at least comparable to existing gold standard microbiological assays. Phase 3 will see completion of toxicology and clinical feasibility studies, followed by technology transfer (phase 4) and trials of scale-up manufacture and packaging at our industry partner Paul Hartmann AG. Ultimately this will deliver a product ready for production and full clinical testing.


Research activity codes: 5.3 MEDICAL DEVICES
Health categories: INFECTION
Title: Targeting cell wall glycans: an untapped approach for therapeutics and diagnostics to combat antimicrobial resistance?
Funder: Medical Research Council

Abstract: The cell wall of Mycobacterium tuberculosis has an essential role in its pathogenesis and protection from environmental stresses and common antibiotics. The aim of the project is to undertake an integrated approach to identify probes that specifically cross-link cell wall glycans in mycobacteria and understand how this cross-linking affects the cell's chemical biology to identify new targets for TB drug targeting and diagnostics. Firstly, we will build on studies using metabolic labeling to guide the design of optimal dendrimer-based probes that covalently cross-link the cell wall glycans using bio-orthogonal 'click' chemistry. We will then investigate the effects this cross-linking has on the physiological state/chemical biology of mycobacteria. Growth kinetics will be monitored, effects of nutrient uptake, acquisition and metabolism assessed. Membrane stability will be investigated and susceptibility of cross-linked bacteria to TB drugs determined by standard kill-curves. Shot-gun proteomic studies will profile the changes in protein expression. In addition build-up/depletion of a subset of metabolites (e.g. glucose) will be monitored (GC(/LC)-MS). Guided by these results, a range of molecules that bind specifically to glycans will be screened to find purpose-built probes that will be incorporated onto the optimized dendrimer scaffold. The kinetics and quantification of probe incorporation into the cell wall (Raman, IR, fluorescence, GC/(LC)-MS advanced imaging) investigated. Specificity and sensitivity of these probes for mycobacteria will be explored through development of 'on/off' pro-fluorescent probes. A multi-disciplinary approach to will be exploited to gain a full fundamental understanding of the effects of cross-linking the mycobacterial cell wall. This will be a major advance in understanding role of cell wall glycans and anticipated that this will be useful for development of new therapies/diagnostics and challenge existing paradigms.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: INFECTION
Title: Exploiting commensal-pathogen competition to treat mucosal infection
Funder: Medical Research Council

Abstract: 1. We will use combinations of novel defined culture media, developed at the WTSI, to cultivate and profile the KanR microflora from naïve-antibiotic-treated and infected-antibiotic-treated mice. Moreover, we will treat mice with other classes of antibiotics, including the protein synthesis inhibitors chloramphenicol and tetracycline, the cell wall inhibitors beta-lactams and the DNA gyrase inhibitor Nalidixic acid, with or without infection with the corresponding antibiotic resistant C. rodentium (available in our lab). Although, we appreciate that not all bacteria can be cultured, we will characterise the potential out-competing commensals by culturing coupled with Bruker MALDI Biotyping and 16S rRNA gene sequencing. 2. We will use high concentrations of the antibiotics mentioned above to determine if they also induce AIBP C. rodentium and the status of virulence gene expression under these conditions. 3. We will use bacterial competition assays or co-infection to determine the ability of components of the murine intestinal microbiota, which expand while C. rodentium declines, to out compete/kill C. rodentium in vitro and in vivo. Real time bacterial colonisation will be monitored using multimodality imaging (bioluminescent imaging with integrated microCT) during bacterial competition and killing assays (prophylactic or therapeutic treatments of mice with components of the microbiota). 4. Selected bacterial taxa that are antagonistic to C. rodentium will be tagged using a bioluminescent reporter (e.g. click beetle luciferase). We will monitor colonisation of these strains following inoculation of naïve mice or mice that were previously treated with the relevant antibiotics (with and without C. rodentium infection). 5. We will identify, fractionate, enrich and test the efficacy of possible intestinal metabolites during infection in vivo using LC-MS and NMR.


Research activity codes: 6.2 CELLULAR AND GENE THERAPIES
Health categories: INFECTION