NIHRDataInsights/HRCSData huggingface dataset:
Title: Epidemiological and genetic investigations into carbapenem resistance caused by horizontal gene transfer within hospitals.
Funder: Medical Research Council

Abstract: Objective 1: Enhanced epidemiological tracking using spatial-temporal outbreak analysis, incorporating antibiotic resistance mechanism profiling to allow accurate modelling of spread of CPE around hospitals. Conventional CPE outbreak tracking relies on manual interpretation of microbiology data and patient bed movements to track and identify clusters. This project will enhance the hospital level outbreak picture by using spatial-temporal data analysis on R to make use of data readily available at ICHNT. Integrating this data will provide a novel, responsive and live updated system to predict outbreaks and track CPE transmission, and allow comparison of resistance mechanism without being reliant on specific bacterial species. Objective 2: Use of whole genome sequencing (WGS) to enhance conventional typing mechanisms, to investigate whether spread of CPEs is clonal in "hospital strains" of bacteria. Using strains identified as potentially healthcare acquired at ICHNT, bacterial DNA will be extracted, purified and prepared for Illumina Sequencing. Sequences will be assembled and compared to establish multi-locus sequence type (MLST) and resistance genes. Comparison to existing sequencing data from previous ICHNT outbreaks will be performed to look at bacterial strain evolution over time. Objective 3: Investigate whether there is evidence of inter-species transfer of plasmids driving polyclonal outbreaks, using blaIMP as a model of an emerging CPE. IMP carbapenemase is an emerging CPE strongly associated with plasmid transmission, with colonising isolates seen in a diverse range of bacteria at ICHNT since 2018. Additional long read MinION sequencing will be performed on a selection of blaIMP isolates to establish whether spread is due to conserved plasmid transmission between species. Data from both WGS and MinioN will be analysed to reconstruct potential outbreaks, and will ultimately be fed back into the spatial-temporal models described.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Influenza Vaccines in the Elderly ?Why don't they work
Funder: Medical Research Council

Abstract: The hypotheses to be tested in a cohort of over 65 admitted to GSTT with laboratory confirmed influenza are: 1 The influenza antibodies (Ab) profile at admission predicts severity of outcome and reflects vaccine exposure 2 Nanopore sequencing can be used as a tool to confirm infecting influenza strain and to correlate sequence variation at key viral antigenic sites with serological profiling 3 Biomarkers (CRP and MxA) assessed at admission can provide prognostic information. Study population and sampling: Serum and whole blood will be collected at admission/recruitment and at four weeks. Case note review and follow up will complete the assessment of clinical outcomes. Verification of vaccination history will be obtained from GP records. Severe influenza is defined as admission to ITU or death or pneumonia. Rapid testing for biomarker detection using a licensed PoC device (FebriDx RPS Diagnostics) will be recorded on admission samples. Serology: Influenza serological work will be carried out at PHE and will focus on measurement of influenza strain specific anti HA Ab using Haemagglutination Inhibition, total neutralising Ab, Neuraminidase Inhibiting Ab (ELLA) and anti-HA stem Ab using serum from patients, and comparing the results between these samples and to the infecting strain. Subtyping and sequencing of infecting strains: RNA will be extracted from clinical samples followed by RT-PCR with a single set of primers for the eight influenza gene segments. The PCR amplicons will be then purified and library preparation and sequencing by using the 1D2Sequencing Kit (Oxford Nanopore) for MinION or GridION platforms. Analysis will be done using by in-house bioinformatics pipelines developed by the CIDR bioinformatics team. Nanopore will be compared with influenza sequences derived by Illumina platforms at PHE. Statistical methods: Pair wise comparisons will be calculated. Multivariable logistic regression model will be carried out by KCL statisticians


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: E Ochodo, Stellenbosch University, Evidence synthesis for building a translation pipeline to eliminate infectious diseases
Funder: Medical Research Council

Abstract: While much scientific progress has been made towards development of interventions to aid elimination of the major infectious diseases in Africa-HIV, tuberculosis (TB) and malaria-the incidence and prevalence of these diseases remains high. One barrier to effective control of these diseases is the suboptimal translation of promising interventions and diagnostic tests into policy and practice. Multiple influencing factors exist between the decision to introduce an intervention and its use in practice. However, currently, synthesis and translation of these different forms of evidence are done as haphazardly if at all, and we need innovative methods to synthesize and integrate these different forms of evidence. We see the broader base of evidence of scale-up being supported by a pipeline of evidence synthesis from different fields to inform technical policy, programmatic guidance and to inform optimum implementation and revisions to existing policies. This is a methodological research project that aims to formally develop a pipeline approach to translating evidence into policy and practice through evidence synthesis and recommend methods for improving translation of evidence into policy and practice. We will develop syntheses of technical evidence on effectiveness or accuracy with application of absolute effects at country level; and develop methods to summarise relevant programmatic (service delivery) information on feasibility, acceptability, economic evaluation and qualitative research at global, regional and national levels. Ultimately, through this project, we aim to establish a research group and a sub-regional directive or coordinating hub for evidence synthesis and research translation in Kenya. To our knowledge no such hub exists in Kenya. This project is timely and has potential for great impact. Under new leadership, there is an explicit shift in the World Health Organization (WHO) to devolve policy making to regional levels.


Research activity codes: 4.3 INFLUENCES AND IMPACT
Health categories: INFECTION
Title: M. Claassens, University of Namibia - Hotspots, hospitals and households: enhanced drug-resistant tuberculosis case finding in Namibia (H3TB)
Funder: Medical Research Council

Abstract: BACKGROUND Poor case management, pharmacokinetic variability and on-going transmission have fostered the MDR-TB epidemic leading to a global estimated number of >500,000 new MDR-TB cases per year. Namibia is a high TB burden country with an incidence rate of 446/100,000 in 2016; ~11,000 new cases per year. 3.9% of new cases and 8.7% of previously treated cases have MDR-TB. Whole genome sequencing has been applied to interrogate the complete genetic code of M tuberculosis and can be used to infer relationships between identified strains. OBJECTIVES 1) Characterise the MDR-TB epidemic, in terms of clinical, epidemiological, geospatial, social network and laboratory data, in order to identify transmission hotspots 2) Evaluate the feasibility of targeted case finding intervention strategies 3) Develop a transmission model to investigate the impact of case finding intervention strategies on MDR-TB incidence. METHODS Individuals with GeneXpert MTB/RIF rifampicin-resistant samples and a positive M tuberculosis culture from two regions in Namibia will be included in a transmission hotspot identification study. Clinical, epidemiological, geospatial, social network and laboratory data (GeneXpert MTB/RIF, culture, drug sensitivity tests) will be collected and whole genome sequencing performed. The results in conjunction with a systematic review and meta-analysis will inform the design of case finding interventions which will be evaluated through a mixed-methods feasibility study at high transmission areas (hotspots, households and hospitals). Data from these studies and the TB programme will be used to develop a transmission model, including a health economics component. IMPACT The project will strengthen MDR-TB diagnosis, surveillance and control, inform case finding policy in Namibia and regionally, inform resource allocation by identifying high transmission areas and create preliminary data to design a large-scale MDR-TB case finding intervention.


Research activity codes: 4.4 POPULATION SCREENING
Health categories: INFECTION
Title: KC Jambo, Malawi College of Medicine - Defining changes in nasal immunity that favour propensity for pneumococcal colonisation in HIV-infected adults
Funder: Medical Research Council

Abstract: Streptococcus pneumoniae is a leading cause of morbidity and mortality in infants, immunocompromised individuals and the elderly. Pneumococcal carriage precedes disease and is important for transmission. Surveillance data from Malawi demonstrates persistently high pneumococcal carriage among antiretroviral therapy (ART)-experienced HIV-infected adults despite the introduction of pneumococcal conjugate vaccine (PCV)13 vaccine as routine childhood vaccine in Malawi in 2011, implying that the herd immunity benefits of vaccination are not robust in this setting. Due to the implementation of HIV "test and treat" strategy, the number of HIV-infected adults on ART will expand tremendously over the next 10 years. An increase in the pneumococcal transmission reservoir will threaten the public health benefits of pneumococcal vaccination. The factors behind this persistently high pneumococcal carriage remain unknown. I hypothesise that dysregulated local nasal innate immunity promotes increased propensity to pneumococcal carriage in HIV-infected adults. I propose to recruit 50 HIV-uninfected and 50 ART-naïve HIV-infected adults, and follow them up for 12 months. Nasopharyngeal swabs and nasosorption samples will be collected monthly, while blood and nasal cells will also be collected at recruitment and 12 months. As per national "test and treat" guidelines, all ART-naïve HIV-infected individuals will be initiated on ART. Pneumococcal carriage incidence will be compared between the study groups. Experiments will investigate the relationship between cytokine profiles, nasal cell phenotypes and nasal transcriptome signatures to pneumococcal carriage incidences. This work will generate information that will allow choices in optimal HIV therapy and optimal vaccination strategies to impact pneumococcal transmission and disease in high transmission settings.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: N Govella, Ifakara Health Institute, Integrating intervention targetable behaviours of malaria vectors to optimize interventions selection and impact
Funder: Medical Research Council

Abstract: Malaria burden in Tanzania has been reduced by more than 50% over the past 15 years. Vector control with insecticide-treated nets (ITNs) and, indoor residual spraying, account for most of these reductions. Despite these gains and sustained community-wide use of ITNs, new malaria cases continue to occur across the country, but with regional variation in prevalence ranges from 0 up to 24%. Underlying drivers for geographic heterogeneity in transmission remain unclear, and will limit Tanzania's efforts to eliminate malaria by 2030. Tanzania is climatically heterogeneous countries, and such climatic variations most likely affect the mosquito and human behaviours that allow malaria vectors to survive by attacking people outdoors or by feeding on animals. New technologies like insecticide vapour emanators and veterinary endectocides could be used to respectively target these behaviours. However, lack of information about where each of these measures may be optimal limits potential for effective geographic targeting of these complementary vector control tools. I propose to integrate surveys of intervention-targetable behaviours of mosquitoes and humans into the existing nationally-representative vector surveillance platform in Tanzania and use this to identify what human and mosquito behaviours drive persisting malaria transmission. Specifically, I will quantify intervention-targetable behaviours of malaria vectors and characterize both environmental and anthropological determinants of how those behaviours vary across 32 locations in diverse ecological settings in mainland Tanzania. These data will be used to model and predict which supplementary vector control tools are likely to be most effective in different ecological zones, and provide NMCP with a framework for rational selection of interventions to optimize vector control impact.


Research activity codes: 5.6 PSYCHOLOGICAL AND BEHAVIOURAL
Health categories: INFECTION
Title: Senescent CD8+ T and NK cells contribute to immunopathogy duting cutaneous leishmaniasis
Funder: Medical Research Council

Abstract: Leishmania (Viannia) brasiliensis causes a wide spectrum of cutaneous disease ranging from self-healing cutaneous leishmaniasis (CL) to tissue destructive mucocutaneous leishmaniasis (MCL) in humans. During infection CD4+ and CD8+ naïve T cells are driven to expand into different subsets including memory compartments which are crucial to infection control and tissue damage observed during CL. Although Leishmania-reactive memory T cells have been characterised in blood from CL patients, little is known about the differentiation/function of these cells in the skin/lesion site. Factors such as persistent antigen stimulation and inflammatory state have been found to play a key role in directing the development of NK cells as well as CD4+ and CD8+ differentiation into effector memory (EM) T cells (CD28-CD27-CD45RA-) and also EM T cells that re-express CD45RA (CD28-CD27-CD45RA+; EMRA). These highly differentiated CD8+ T cells cell which exhibit terminal differentiation and senescence characteristics contribute to diminished immune responses due to their increased expression of surface inhibitory receptors, DNA damage and reduced replicative capacity. Mechanisms of memory T cell and NK terminal differentiation during leishmania infection are still unknown, however this may assist the understanding of immune response diversity during CL. In this context, the present study aims to investigate the frequency, differentiation and effector function of NK and CD8+ memory T cell from blood and skin of CL patients caused by L. brasiliensis. In this study we will investigate isolated leukocytes from the blood and biopsies taken from skin lesions of the same patients. We will perform extensive flow cytometric and immunohistological analyses of these samples. We will also investigate gene expression in skin lesions by RNAseq analyses. Age and gender matched healthy controls will be recruited from the same district of Vitoria as the patients.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Understanding the molecular basis and role of parasite dormancy in Chagas disease
Funder: Medical Research Council

Abstract: Chagas disease is caused by the insect-transmitted protozoan Trypanosoma cruzi and is the most important parasitic infection in Latin America, affecting 6 - 8 million people. After an initial acute stage, the disease can remain latent for decades before re-emerging as a chronic condition characterised by cardiomyopathy and/or digestive-tract tissue damage. Current drugs are toxic and often non-curative. Investigations into the mechanisms of disease pathology and the underlying causes of treatment failure have been confounded by the complex and long-term nature of the infection. In addition, T. cruzi has the capacity to undergo a form of dormancy, a phenomenon that may explain parasite persistence and the limited efficacy of current therapy. The mechanisms that trigger dormancy are unknown, and understanding the process represents a major challenge to the research community. We have developed a powerful range of approaches that can be applied to Chagas disease research. These include crucial advances in highly sensitive imaging procedures that allow T. cruzi infections to be followed in real time, both in vivo and in vitro, innovative high-throughput genetic modification technology, highly flexible cell sorting capacity under containment level 3, and transcriptome profiling. Our aims are to use whole genome functional screens to dissect the processes that trigger dormancy at a molecular and cellular level, to determine the biological relevance of the phenomenon in an in vivo context, and to assess its implications for drug development. This project will provide new information and tools to aid the rational design of drugs able to kill parasites that are dormant and probably metabolically quiescent. Our close collaborative links with the global Chagas disease drug development community will ensure that findings can influence strategic direction and be rapidly integrated into the discovery pipeline.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Characterising the influence of parasite variation on visceral leishmaniasis.
Funder: Medical Research Council

Abstract: Visceral leishmaniasis (VL, also called kala azar) is a neglected infectious disease that affects the world poorest, resulting in 20,000 fatalities a year. VL is caused by Leishmania protozoan parasites, transmitted by sand flies. VL treatments need considerable development; no VL-vaccine is licensed and drug therapies are subject to resistance and/or require hospitalisation and do not reliably produce parasitological cure. VL can progress to persistent skin lesions (post-kala azar dermal leishmaniasis, PKDL) after successful drug treatment that are sources of transmission, likely fuel new epidemics, but is very poorly understood. VL/PKDL manifestations and drug efficacy vary between and within countries. There are indications that this variation may be due to differences between Leishmania donovani parasites, but the role of parasite variation on disease variation is not well established. This project will investigate the influence of parasite genetic variation on VL by studying L. donovani in Sudan, Ethiopia, Uganda and Kenya. We will sequence parasites genomes from 160 patients who are undergoing detailed clinical and immunological study pre- and post-drug treatment up to 12 months. We describe parasite demographics, migration, evolutionary history and patterns of molecular evolution. We will then apply genome-based restricted maximum likelihood (GREML), a sensitive quantitative genetics method, to quantify the effects of parasite variation on traits of treatment efficacy, cellular immune responses and disease manifestations such as PKDL. Genome-wide association studies (GWAS) will be used to detect parasite genes that have the strongest effects on treatment or disease. This study has potential to uncover molecular mechanisms that parasites evolve that modulate and evade immune systems, contributing to our understanding of host-parasite interactions. Study of drug treatment efficacy will detect geographically-restricted drug resistance with high sensitivity.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Carbapenem Antibiotic Resistance in Enterobacteriaceae: Understanding Interactions of KPC Carbapenemases with Substrates and Inhibitors
Funder: Medical Research Council

Abstract: Beta-lactams are the most prescribed antibiotics; carbapenems are the most potent beta-lactams and key drugs for infections by opportunistic Gram-negative bacteria. Carbapenem resistance in Enterobacteriaceae due to beta-lactamase production is a major public health challenge. The Klebsiella pneumoniae carbapenemase (KPC) beta-lactamase is distributed worldwide and is the major cause of carbapenem resistance in this organism. KPC efficiently degrades carbapenems, which inhibit the majority of related enzymes, and slowly degrades inhibitors (diazabicyclooctanes, DBOs). The basis of these activities remain poorly understood. Here we combine molecular simulations (molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) based on recent crystal structures from our group) with structural and kinetic experiments to investigate interactions of KPC with substrates (carbapenems and the cephalosporin ceftazidime) and DBO inhibitors, aiming to identify determinants of activity against each of these ligand classes. QM/MM simulations of carbapenem breakdown will focus on degradation of the acylenzyme intermediate, aiming to establish the relationship between carbapenem turnover, interactions of the deacylating water molecule, and tautomerization of the carbapenem pyrroline ring. Extended MD and QM/MM simulations will investigate ceftazidime:KPC interactions, aiming to identify why this is a relatively poor substrate. QM/MM simulations will identify pathways by which the DBO acylenzyme is either recycled to generate intact active inhibitor or desulphated and inactivated. In each case we will investigate how these activities are affected by point variants of KPC identified in the clinic. The results will establish the basis for the unique properties of KPC enzymes and their capacity for mutation, enabling identification and evaluation of routes to carbapenems and DBOs with enhanced activity against bacteria carrying this key resistance determinant.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Evaluating multiple loci modulating susceptibility of African malaria parasites to artemisinin
Funder: Medical Research Council

Abstract: We have identified five genes (pfk13, pfap2mu, pfubp1, pfcoronin and pfk10), through testing in our laboratory or from the scientific literature, which are important for the effectiveness of artemisinin - the most important drug for treating malaria. We will establish an expanded collection of parasite isolates (100-200) from UK travellers with malaria, and also in a "cohort" of recent P. falciparum isolates from malaria patients in Ho, Ghana (50-100), being collected by our collaborator Dr Bismarck Dinko. All parasites that successfully grow in our laboratory will then be tested for drug susceptibility, focussing on artemisinin. Full genome sequence data for all parasites will be generated by co-Investigator Dr Susana Campino. The application of CRISPR-Cas9 genome to Plasmodium falciparum provides an opportunity to directly test candidate drug resistance genes in transgenic parasites growing in the culture lab. We will use CRISPR editing to test gene variants of interest in our five top candidate genes. We will also have the capacity to test any genes identified in the course of our project, or in scientific journals. Pilot work by PhD student Ryan Henrici (who completed in 2018) sucessfully generated variants of two of these genes - pfap2mu and pfubp1 - in the standard laboratory line 3D7 and found that in both cases the transgenic clones were less susceptible to artemisinin, resembling resistant Cambodian parasites in phenotype. We will extend our genome editing work to natural parasite isolates from Africa, either collected from travellers presenting with malaria in the UK, or in the parasite cohort from Ghana. Thus we will have an opportunity to look at the impact of a variety of African "background" genotypes on changes in susceptibility caused by variants of interest in our top five candidates, and in any new candidates identified in the near future.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION