NIHRDataInsights/HRCSData huggingface dataset:
Title: Structure guided design of a transmission-blocking malaria vaccine targeting Pfs48/45
Funder: Medical Research Council

Abstract: This project combines the expertise of the Higgins and Biswas groups, allowing us to conduct a work plan which progresses from structural characterization of an important parasite surface protein through to the testing of designed immunogens in a pre-clinical setting. We will produce Pfs48/45 in stable Drosophila s2 cells. Existing hybridomas will be used to make monoclonal antibodies. New monoclonal antibodies will be generated by immunizing mice, fusing splenocytes to make hybridomas, selecting clonal colonies in semi-solid media and screening for Pfs48/45 reactivity by ELISA. Fab fragments will be produced by papain cleavage and Pfs48/45:Fab complexes will be assembled and purified by size exclusion chromatography. The structure of Pfs48/45 will be determined by x-ray crystallography and key antibody epitopes will be mapped by crystallography and by hydrogen-deuterium exchange mass spectrometry. Stabilised versions of Pfs48/45 will be generated using the PROSS-design algorithm. Novels immunogens will be made by grafting key epitopes from Pfs48/45 onto scaffold proteins and will be optimsed using Rosetta-based modeling. These immunogens will be produced in E. coli and used to immunize mice. The sera will be tested for the ability to prevent oocyte development in mosquitos using a membrane-feeding assay with parasite-infected blood. Pfs230 domains will be generated in transiently transfected stable Drosophila s2 cells and will be tested for binding to Pfs48/45 by surface plasmon resonance. Complexes will enter into crystallization trials. In addition, existing Pfs48/45 antibodies will be used to immuo-purify Pfs48/45:Pfs230 complexes from cultured gametocytes. These will be studied by electron microscopy, initially using negative stain and a T12 microscope, and then by electron cryo-microscopy using a Talos Arctica microscope with a K2 detector. Imaging processing will be done using RELION to obtain three-dimensional reconstructions.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: MICA: Addressing the burgeoning problem of tuberculosis: Exploiting phenotypic hits to identify new protein targets for drug discovery
Funder: Medical Research Council

Abstract: Despite the existence of treatments for tuberculosis (TB), TB continues to present a major healthcare challenge, accounting for nearly 9 million new infections and over 1 million deaths p.a.; indeed, this global health threat is increasing given the increased susceptibility of HIV-infected individuals to TB, the limited efficacy of the BCG vaccine and most worryingly, the growing prevalence of drug-resistant strains of Mycobacterium tuberculosis, the microorganism causing the disease. Treating TB requires a drug cocktail that has to be taken for at least six months, extending to two years for infections caused by multi drug-resistant strains of M. tuberculosis. A largely successful campaign by the WHO to stem the rise of TB has not diminished the urgent need for better drugs, acting against new cellular targets, to alleviate the devastating impact of this disease. The principal aim of this MICA is to expand the pipeline of new targets for future TB drug-discovery programmes. In achieving this objective, we will also develop new tool compounds, which will allow us to gain detailed insight into the fundamental biology of M. tuberculosis. To this end, hits from GSK DDW's most recent high-throughput phenotypic screening campaigns will be prioritised according to their potency and favourable physicochemical properties for future development in hit-optimisation and lead-identification programmes. These hits will then be subjected to a combination of genetic, chemical proteomic, metabolomic and structural studies to first identify and then to validate their associated cellular targets and ultimately to determine their mode of action. The guiding principle of this multidisciplinary, academic-industrial initiative is to focus on high-quality, potent compounds hitting diverse targets to deliver the best possible starting points for future TB drug-discovery initiatives.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Universal protection against Streptococcus pneumoniae by recombinant glycoconjugate vaccines
Funder: Medical Research Council

Abstract: S. pneumoniae Polysaccharide Conjugate Vaccines (PCVs) are effective but have limited serotype coverage and are expensive. We propose that a "PCV plus" vaccine consisting of selected S. pneumoniae proteins recombinantly coupled to S. pneumoniae capsules will resolve these limitations, creating a cheap vaccine that would be of most impact to LMIC countries in which S. pneumoniae remains a significant cause of severe disease. We will use protein glycan coupling technology (PGCT) to make recombinant glycoconjugate pneumococcal vaccines. Our hypothesis is that intelligent protein antigen selection can identify carrier proteins for a "PCV plus" vaccine made by PGCT that induces broad serotype-independent protection against S. pneumoniae infections. To identify the best protein antigens for novel S. pneumoniae vaccines we will systematically identify protein candidate antigens capable of inducing IgG and/or Th17 responses using proteome expression technology. An expression library of 1400 conserved S. pneumoniae proteins will be constructed, pooled and used to vaccinate mice. We will identify up to 50 new vaccine candidates by screening sera from vaccinated mice against a protein array to discover antibody-inducing antigens and by using an in vitro assay and CD4 cells to identify antigens inducing Th17 responses. Candidate vaccine proteins will be coupled to serotype 4 S. pneumoniae capsule to produce recombinant glycoconjugates using a high throughput PGCT expression vector. Proteins that are efficiently coupled to capsule will be tested in mice to identify the glyconconjugates that induce the most effective cross-protective immunity against heterologous capsular serotypes and during mucosal infection, whilst maintaining serotype specific immunity. Overall these studies will provide an unbiased screen of S. pneumoniae proteins to identify the best proteins for inclusion in a 'PCV plus' vaccine produced by PGCT for future testing in phase 1 trials.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Building and dismantling polymicrobial pathogen communities in cystic fibrosis.
Funder: Medical Research Council

Abstract: Chronic infections are caused by diverse communities of microbes that inhabit spatially-structured host environments. Inter-microbe interactions mediate virulence, persistence and antimicrobial resistance (AMR). Thus, improved diagnostic and R&D tests for the likely clinical impact of antimicrobial compounds require testing platforms that recapitulate diverse infection communities in structured tissue. Further, future treatments for chronic infection (e.g. bacteriophage) must be tested in such models to gain reliable predictions of their clinical potential. I have developed a clinically valid, high-throughput model of polymicrobial infections of the lungs of people with cystic fibrosis (CF): ex vivo lung tissue cultured in artificial mucus. I will characterise infection communities in this model, revealing how biodiversity mediates AMR and virulence. I will study clinical isolates of key lung pathogens (P. aeruginosa, S. aureus, B. cenocepacia, H. influenzae, S. milleri + whole CF sputum samples) in single and polymicrobial infections. I will assess how the model could be developed into a clinically predictive platform for AMR profiling and the activity of novel antimicrobial/antivirulence drugs. I will use hypothesis-driven experiments about microbial communities in structured tissue to reveal key drivers of AMR in CF infection, the likely triggers of acute pulmonary exacerbation, and how these may be neutralised. My model uses pig lung tissue from a commercial butcher and human lung from an NHS biobank. I will define how well pig lung recapitulates human tissue infections and promote its wider adoption in academia and industry to increase the clinical validity and 3Rs compliance of basic research and R&D testing. Through consultancy work with colleagues, I will explore the potential for ex vivo lung to underpin tests of novel therapeutic agents (antibiotics and phage) on realistic infection communities in structured tissue.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: The rates and routes of transmission of multidrug resistant Klebsiella clones and genes into the clinic from environmental sources.
Funder: Medical Research Council

Abstract: Klebsiella pneumoniae (Kp) is a leading cause of multidrug resistant hospital-acquired infections globally, and is responsible for an increasing public health burden in the community. In order to control the spread of Kp through targeted surveillance and intervention policies it is necessary to identify the sources of emergent community and health-care associated infection from the interlinked and varied niches encompassing "the environment". To address this, we will sample from multiple clinical, community, agricultural, veterinary and environmental settings in and around a single town, Pavia, in Northern Italy, and supplement these data with matched samples from France and elsewhere. We will use whole genome sequencing of community (mixed-colony) samples to assay accessory gene abundance and distribution. This contrasts with the more common approach based on phylogenetic analysis of single colonies, which would be of limited utility over broad environmental scales due to the complexity of transmission chains, environmental dormancy, and high rates of recombination. This gene-centric approach provides a much more efficient means to understand ecological adaptation, the distribution of resistance and virulence genes, and to identify key environmental reservoirs from which clinical clones emerge. A key deliverable of this project will be the establishment of a pan-genome database ('pangenomium') that will integrate with both existing Kp genome community resources established by project partners (BIGSdb-kp, and wgsa.net). We will also develop mathematical models to further explore gene flow between environmental compartments, and will use the Oxford Nanopore Minion TM platform to characterise AMR plasmids, and understand their distribution and transfer, using hybrid assemblies.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY)
Health categories: INFECTION
Title: Impact of alcohol-focused interventions on treatment outcomes amongst HIV patients in Tanzania and South Africa: A feasibility study
Funder: Medical Research Council

Abstract: Hazardous or harmful alcohol use is common in eastern and southern Africa, including among people living with HIV (PLWH) who drink alcohol and use anti-retroviral therapy (ART), and is associated with poorer ART adherence and lower retention in care and treatment. We hypothesise that effective alcohol reduction interventions delivered in HIV clinics could help increase ART adherence and improve treatment outcomes among PLWH who drink at harmful or hazardous levels. Our long-term goal is to implement a cluster randomised trial of an intervention, comprising individual and health facility elements, to improve treatment outcomes among PLWH on ART who engage in hazardous or harmful drinking in Tanzania and South Africa. The proposed study will collect information required to prepare for the main trial. Our specific objectives are to determine the prevalence of harmful and hazardous drinking among PLWH in Tanzania where this information is lacking; and develop and adapt the intervention, and evaluate its feasibility and acceptability in both Tanzania and South Africa. We will interview 300 randomly selected patients using ART from four HIV clinics in Tanzania regarding their alcohol use. We will also conduct a literature review of alcohol reduction interventions, a survey of 40 health workers (HWs) at four ART clinics in each country, and in-depth interviews (IDIs) with (a) key stakeholders (including HWs, ministry of health officials, and treatment supporters), and (b) ART patients to assess their attitudes, patterns of alcohol use and perceptions of the treatment received at the HIV clinics. Results obtained will be presented in a workshop and used to develop a theoretical framework which will form a basis for developing the final intervention package. The feasibility and acceptability of the intervention will then be assessed in 20 patients in up-to-four clinics per country. Final results will be used to develop the main trial protocol.


Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION;5.6 PSYCHOLOGICAL AND BEHAVIOURAL;6.5 RADIOTHERAPY AND OTHER NON-INVASIVE THERAPIES
Health categories: INFECTION
Title: Mechanisms for acquisition and transmission of successful antibiotic resistant pneumococcal clones pre- and post-vaccination
Funder: Medical Research Council

Abstract: To understand the molecular mechanisms of emergence, persistence and transmission of antibiotic resistant pneumococci arising before and after the introduction of conjugated polysaccharide vaccines (PCV). To this end, mouse models will be used to study the transmission, colonization and disease capability of antimicrobial resistant pneumococcal lineages. The overall aim being to identify the specific drivers of antibiotic resistant clones and their role in invasive pneumococcal disease and the host immune response in selection and transmission of antibiotic resistant pneumococci.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: The impact of Host restriction of Escherichia coli on Transmission dynamics and spread of antimicrobial Resistance
Funder: Medical Research Council

Abstract: The prevalence of antimicrobial resistance (AMR) is rapidly increasing worldwide, including in bacteria colonising healthy human and animal populations. The recent reports of plasmid mediated colistin resistance, potentially associated with colistin usage in agriculture, further raise fears of infections that have become untreatable due to AMR. The commensal flora of humans and animals is a reservoir of AMR encoding genes and Escherichia coli in particular can carry multiple AMR determinants. Antimicrobial resistance transmission within E. coli appears to be dominated by certain lineages. However, to what extent these are restricted to certain host species is unknown. Such host restriction may be an important determinant of the likelihood of transmission of resistant E. coli between different reservoirs, such as between animal and human hosts. The identification of determinants that allow disentanglement of the different modes of resistance transmission (i.e. bacteria vs mobile genetic elements such as plasmids) is crucial for a more targeted design of interventions to prevent and reduce transmission of resistance. The proposed research aims to identify determinants of host restriction of E. coli and their potential association with antimicrobial resistance transmission and prevalence. We propose a One Health approach using mixed methods, including whole genome sequencing of a large collection of E. coli isolates from human, animal and environmental sources in different geographic areas across Europe and in Vietnam, experimental models to study the role of host restriction determinants in transmission and bacterial fitness, and mathematical modelling. The research aims to produce a risk-assessment, estimating the contribution of different transmission routes and predicting the effect of interventions on a single route on the overall prevalence in the different compartments. The consortium is uniquely placed to perform this research.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Escherichia coli ST131: a model for high-risk transmission dynamics of antimicrobial resistance
Funder: Medical Research Council

Abstract: Objective 1: Determine the role of MGEs, genomic adaptions and fitness in the transmission success of ST131 clade C. The central hypothesis of objective 1 is that genomic islands containing certain VFs, plasmids with blaCTX-M-15 and transposons (i.e. ISEcp1) have been acquired by clade C in a specific and sequential fashion resulting in enhanced fitness and colonization that gave the subclades C1 and C2 the ability to outcompete other antimicrobial resistant clones. Hence, Objective 1 will serve as a model to predict how successful multidrug resistant clones can rapidly expand among bacteria. It might provide essential information for predicting the next clonal wave of multidrug-resistant ExPEC. Objective 1 will use NGS, fitness, adherence and invasiveness studies to identify the contributions of accessory genomes, GIs, recombination events, MGEs (plasmids and transposons) towards the evolutionary success of clade C. The UK team will undertake a longitudinal analysis of the changes and evolution of the core and accessory genomes using WGS data from collections accrued over 15 years, and data from international partners in this consortium. Key changes in the bacterial core genome and the plasmid sequences will be explored to understand host-plasmid adaptations. The UK team will investigate the effect of genetic shifts, fitness and the role of host-plasmid adaptations to the success of ST131 clade C via detailed growth analysis (via BioLog) and basic infection models Galleria mellonella, by measuring larval survival, the degree of host melanisation (oxidative stress) response and cellular damage (lactate dehydrogenase release). Co-inoculation of strains and re-isolation of bacteria from larvae will allow fitness cost to be assessed between isolates with differing resistance mechanisms or other specific genetic traits. The UK team will also compare the distributions of such changes in ST131 isolates recovered from non-human sources.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Prevention and Restriction of Antimicrobial Resistance in Pneumococci by Multi-Level Modelling
Funder: Medical Research Council

Abstract: The major aim of this consortium is to develop strategies for risk assessment, prevention and reduction of antimicrobial resistance (AMR) by understanding the drivers and mechanisms of AMR development and the consequences on pneumococcal fitness in diverse environments. We will model of the impact of antibiotic consumption on the pneumococcal evolutionary dynamics of carriage and transmission in the Mae La cohort, to quantify the relative selective effect of different antibiotics. We have identified transmission events and will now begin to explore the diversity within the swabs to obtain a deeper understanding of the amount of variation and change during carriage and transmission. In the Canadian cohorts, we will fully characterise AMR in population-based samples of pneumococcal isolates causing invasive diseases in two distinct Canadian geographic locations, and investigate the molecular determinants in gain and loss of AMR. Total transcriptomes of selected strains and host cells under different experimental conditions will be obtained by RNA-Seq to identify environmental, immunological and pharmacological drivers of AMR emergence. The specific transmission rates occurring before and after antibiotic treatment will help to decide how to act to limit the prevalence of antibiotic resistance. Some vaccines have had disproportionate effects on drug-resistant lineages within the target species. Our new data may inform our view of whether vaccine introduction, and antibiotics usage promote the spread of resistant bacteria through different mechanisms, including notably the clearing out of susceptible competitors in donors or recipients. This is important in identifying who should be the target of infection control measures, and how these measures should be designed. For instance, if antibiotics make individuals more likely to donate resistant strains to others, they could be treated with combination therapy or higher doses to clear even the resistant bacteria.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Predicting cell-cell horizontal transmission of antibiotics resistance from genome and phenome
Funder: Medical Research Council

Abstract: We propose to disclose candidate drug targets controlling the horizontal cell-cell transmission of anti-microbial resistance (AMR) and to predict AMR and its transmission dynamics from bacterial genome composition. We will integrate leading expertise from bacteriology, -omics and mathematical biology in the development of an integrated theoretical-empirical framework of plasmid borne transmission of AMR cassettes. We will employ massive-scale experimental evolution of Escherichia coli and Salmonella enterica gene deletion and overexpression collections, where adaptation requires transfer of AMR carrying conjugative plasmids. In addition, we will select for, identify and functionally dissect de novo mutations that promote horizontal transmission during long-term experimental evolution. Both approaches will disclose cellular functions controlling horizontal AMR transmission that are candidate targets for helper drugs delaying AMR development and spread. Second, we will sequence vast swaths of the genotype space inhabited by clinical bacterial isolates and disclose variants likely to alter transmission properties. DNA sequence data will be complemented by data on transcriptome, proteome and antibiotics resistance, allowing causally cohesive reconstruction of the history of antibiotics resistance. Third, we will integrate the omics data into a mathematical framework capable of predicting AMR transmission in clinical isolates, thereby laying the foundations for a future personalized medicine that tailors antibiotic choice to infection.


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