NIHRDataInsights/HRCSData huggingface dataset:
Title: Understanding and modelling reservoirs, vehicles and transmission of ESBL-producing Enterobacteriaceae in the community and long term care facilities
Funder: Medical Research Council

Abstract: This summary refers to methodology for WP5, Modelling transmission dynamics of ESBL-EP. It depends on other WPs as described in the full proposal. We will initially adapt methodology previously developed to study the transmission of bacterial pathogens in hospital settings. Adapted methods will be used to analyse data from WP1-4. The transmission of ESBL-PE (whether at bacterial or gene levels) can be represented as a partially observed Markov process, where the state is defined by the number of hosts colonized at a given time point. Fitting transmission multistate Markov and hidden Markov models (HMMs) to such data will be carried out with standard software (e.g. the msm and JAGS packages within R for likelihood-based and Bayesian inference respectively) or using standard algorithms to fit HMMs. Previously described Bayesian data augmentation approaches offer more flexibility at the expense of greater computational cost; recent work has shown how these approaches can make use of WGS data without restrictive assumptions to reconstruct transmission trees. We will extend this approach to account for within-host evolution and to allow for incorporation of individual-level covariates from WP1 & 2. We will cross-validate inferences about transmission processes by using, in parallel, approaches to reconstruct transmission networks using WGS and exposure history data using a novel approach based on structured coalescent models. Such an approach employs an explicit evolutionary model, though requires more restrictive epidemiological assumptions. For objective 4, we will combine inferences from objectives 1 and 2 to inform both compartmental and individual based multi-setting models. Compartmental models will account for interactions in the community, nursing homes, LTCFs and hospitals. These models will be developed by extending existing individual-based model code. Compartmental models will be implemented in R, and individual-based models in C++ (with interface to R).


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Partnership against Biofilm-associated Expression, Acquisition and Transmission of AMR
Funder: Medical Research Council

Abstract: The research objectives of this consortium are to i) determine how P. aeruginosa adapts during biofilm formation on surfaces coated with antimicrobials, ii) how AMR mutations are acquired and evolve within mature biofilms, iii) how population dynamics within biofilms affect the transmission of AMR, and iv) translate these findings into clinical practice. To achieve this we will first screen for combinations of antibiotics and antimicrobials that select for/against antibiotic resistance using in vitro models that mimic clinical situations and enable prediction of in vivo antibacterial biomaterial performance, including flow and blood serum components. Surfaces tested will include glass, and other more relevant biomaterials such as polymethylmethacrylate, stainless steel, polyethylene, and polyurethane. Antimicrobials that represent different modes of inhibition/killing and chemical classes will be tested using microtiter and agar plate models to facilitate large scale screening of antibiotic-antimicrobial combinations, and knock-out libraries to identify AMR-related genes. Effective combinations will be chosen for in-depth investigations on their effect on transcriptional and evolutionary adaptations, biophysical properties during adhesion and of mature biofilms, and also the population dynamics of resistant and susceptible genotypes using Macro- and micro-flow chambers. Based on the screening outcome, and the obtained mechanistic understanding, we will then study clinical specimens isolated from patients. As clinical examples we will focus on central venous catheters which are impregnated with chlorhexidine and silver sulphadiazine and are treated with multiple antibiotics when infected, or alternatively endotracheal tubes that are coated with sulfadiazine. These findings will aim to provide clinical recommendations for improved administration of antibiotics/antimicrobials in combination with medical device materials to mitigate against biofilm-associated AMR


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: MICA: Host-directed therapeutics to combat bacterial infections
Funder: Medical Research Council

Abstract: Globalisation has increased the risk of pandemics, and the rise of antibiotic-resistant microbes threatens to render existing drugs useless. Of concern is the mounting prevalence of infections caused by multidrug resistant Gram-negative bacteria, in particular Klebsiella pneumoniae. Shockingly, the increasing isolation of strains resistant to "last resort" antimicrobials has narrowed, and in some settings completely removed, the treatment options against these infections. Not surprisingly, Klebsiella has been singled out by the UK government, WHO and the CDC as an "urgent threat to human health." Unfortunately, we cannot identify candidate compounds in late-stage development for treatment of multidrug Klebsiella infections; this pathogen is exemplary of the mismatch between unmet medical needs and the current antimicrobial development pipeline. Therefore, it is an urgent priority to develop effective therapeutics based on new targets and concepts. Host-directed therapeutics for infectious diseases are receiving increasing attention. By targeting host factors crucial in the infection biology of a pathogen it can be enhanced innate host resistance to infection leading to reduced morbidity, mortality, and end-organ damage. Interference with signalling pathways hijacked by pathogens is thought to apply less selective pressure for the development of resistance than traditional strategies targeting the pathogen. In this proposal, we will provide compelling pre-clinical rationale for host-directed therapeutics against K. pneumoniae infections. We will demonstrate that by antagonizing the activation of the Src kinase by Klebsiella we will decisively influence the outcome of host-Klebsiella interactions thereby limiting pathogen survival. The excellent safety, tolerability and pharmacology of the Src inhibitor may anticipate a fast-track transition from the pre-clinical stage to further clinical development of the inhibitor to treat Klebsiella infections.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Effectiveness of bi-treated long lasting insecticidal nets and deployment strategy for control of malaria transmitted by pyrethroid resistant vectors
Funder: Medical Research Council

Abstract: We propose a cluster randomised trial which compares four vector control interventions to prevent malaria in areas where vector mosquitoes are resistant to pyrethroids and the standard long-lasting insecticide treated nets (LN) are unable to control malaria adequately. These interventions are based on novel bi-treated LNs incorporating mixtures of insecticides or insecticide synergists to improve efficacy. The proposed trial will be a four-arm, single blinded, non-inferiority cluster-randomized trial with the following arms: 1. Control arm: Olyset Plus LN (Sumitomo Chemicals) is a LN combining a synergist PBO and pyrethroid permethrin incorporated in the polyethylene fibres on all 5 panels. 2. Intervention arm 1: Permanet 3.0 (Vestergaard) is a mosaic LN consisting of polyester on the 4 side panels coated with pyrethroid deltamethrin. PBO is restricted to the top panel made of polyethylene fibres and incorporating also deltamethrin. 3. Intervention arm 2: Olyset Duo is a bi-treated polyethylene LN incorporating permethrin and an insect growth regulator pyriproxifen (PPF) that sterilises mosquitoes that contact the net. 4. Intervention arm 3: Interceptor G2 is a mixture LN made of polyester and coated with a wash-resistant formulation of chlorfenapyr (CFP) and alpha-cypermethrin pyrethroid. The proposal will address the following questions: 1/ Do new generation of LN that include a pyrethroid and a novel insecticide (PPF or CFP) provide similar or better protection to the PBO-synergist LN against malaria transmitted by pyrethroid resistant vectors? 2/ Does mosaic PBO-LN and PBO-LN on all panels provide the same protection? 3/ Which LN (CFP, PBO or PPF) is more effective at preventing malaria and managing resistance? Evaluation of the effectiveness of each LN will be based 1/ on malaria prevalence in children under 15 years, 2/ malaria incidence and transmission and 3/ selection of insecticide resistance. Cost effectiveness of each LN will also be compared.


Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: INFECTION
Title: Short enhanced anti-tuberculosis and anti-thrombosis treatment for children with tuberculous meningitis
Funder: Medical Research Council

Abstract: Nearly a million children develop tuberculosis (TB) each year and it is acknowledged that young children are at a high risk of developing the most severe forms of disease such as tuberculous meningitis (TBM). TBM is associated with significant mortality and functional impairment and the current treatment regimen advised by the WHO in children is to give four anti-TB drugs for two months (isoniazid (H), rifampicin(R), pyrazinamide(Z) and ethambutol (E)) followed by two drugs (H and R) for ten months:2HRZE10HR. There is emerging evidence that it may be possible to achieve similar, or better, outcomes using a shorter more enhanced regimen. Aspirin may also have a role in the treatment of TBM due to its anti-inflammatory and anti-thrombotic properties and be associated with improved functional status. The SURE trial is designed as a 4-year phase III, part-blinded factorial randomised controlled trial for the treatment of TBM in children. The first randomisation (1:1) will be a non-inferiority open-label design to evaluate whether a 6 month intensive (at revised higher dosages) regimen (6HRZL) is non-inferior to the current 12 month WHO-recommended regimen (2HRZE10HR). The second (1:1) will be placebo-controlled, blinded superiority design to evaluate the efficacy of low-dose aspirin on functional status. 400 children will be recruited from 8 centres across Africa and Vietnam. The trial will also address other important questions including cost-effectiveness and acceptability. The primary endpoint for the first randomisation is all-cause mortality at 12 months post randomisation; and for the second randomisation is functional status (measured by a modified Rankin score) at 12 months post randomisation. Should the shorter regimen be at least as good as the longer regimen, and/or should the provision of aspirin be safe and associated with improved neurological outcomes, then we would anticipate these would translate rapidly into international guidance.


Research activity codes: 6.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Correlates of risk in children exposed to multidrug-resistant tuberculosis
Funder: Medical Research Council

Abstract: BACKGROUND Of the estimated 60 million children with TB infection, 1 million each year develop TB disease. Of these one quarter die. If it were possible to identify, for example by using a blood transcriptomic signature, which children with TB infection were at highest risk of TB disease progression, treatment could be targeted. In addition if it were possible to identify a change in transcriptomic signature with drug therapy, this may have implications for patient care and for drug development. Finally, the highly immunogenic virus, CMV, generates a type I interferon response, a pattern of immune response also seen in patients with TB disease. Exploring the role of CMV in the risk and pathogenesis of childhood TB would provide insight into the immunology of dual infection but also potentially contribute to TB vaccine design and alternative interventional strategies. OBJECTIVES 1. To identify a blood RNA transcriptomic signature that can identify which MDR-TB-exposed children are at increased risk of TB disease progression 2. To identify a blood RNA transcriptomic signature in children with TB infection that changes with antimicrobial therapy 3. To evaluate the impact of CMV viraemia on the RNA transcriptomic signature of children with TB infection 4. To evaluate the impact of CMV infection on the risk of developing TB infection and disease in young children following exposure to TB METHODOLOGY The TB-CHAMP trial has already been funded (MRC/WT/DfID) to investigate the management of child MDR-TB contacts. The trial will recruit 1500 children and follow them up for 2 years. Children will be randomised to daily levofloxacin or placebo for six months. Regular blood samples will be taken. For this Fellowship samples will be analysed for their RNA expression profile and CMV status. Bioinformatic analysis will be used to identify baseline signatures that are associated with disease progression and changes on treatment. The impact of CMV will be explored.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Unravelling post-transcriptional regulatory networks in pathogenic S. aureus
Funder: Medical Research Council

Abstract: The emergence and expansion of antibiotic-resistant Staphylococcus aureus (including methicillin-resistant S. aureus, MRSA) in hospitals and the community is a global public health concern. S. aureus is an extremely versatile pathogen, due in part to its capacity to rapidly alter its transcriptome in response to stress. While transcription factors dictate which genes are expressed during stress, substantial regulation also occurs post-transcriptionally. Regulatory RNAs (ncRNAs) and RNA-binding proteins are now recognized as key players in controlling virulence, host cell interactions and antibiotic resistance in bacterial pathogens. By directly binding to their mRNA target, they decide the fate of the molecule by control how efficiently the mRNA is translated and/or degraded. We hypothesize that riboregulators play a key role in shaping gene expression profiles during stress. However, for the majority of these factors we lack understanding of their function. To gain mechanistic insights into how MRSA rapidly alters gene expression during stress, we will map the landscape of post-transcriptional regulation in S. aureus during human infection using innovative high-throughput methods developed in my group and by our collaborators. Because immune evasion is critical for S. aureus survival in the early stages of infection, we will focus our analyses on post-transcriptional events during entry into the blood stream and in response to phagocytic cells. Our preliminary data have already uncovered many targets for 89 ncRNAs, including interactions with transcripts encoding toxins and multi-drug efflux pumps, demonstrating the feasibility of our approach. We envisage that the insights into post-transcriptional regulatory networks derived from this work may lead to the design of novel approaches for treating or preventing infectious diseases.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Formation and function of the parasitophorous vacuole membrane in Plasmodium falciparum-infected erythrocytes
Funder: Medical Research Council

Abstract: The proposed research aims to understand the formation of of the membrane of the parasitophorous vacuole (PVM) and the essential functions of the proteins present in this membrane during the growth of the malaria parasite Plasmodium falciparum in erythrocytes. During entry into the erythrocyte, the parasite becomes surrounded by a membrane that forms the PV, the PV membrane (PVM), that envelops the parasite until the very last stages of the erythrocytic cycle. As the parasite grows, the PVM expands to accommodate the growing parasite. The PVM separates the parasite from the cytosol of the erythrocyte, but also forms a significant barrier to the export of parasite proteins to the host cell that are required for the survival of the parasite and the uptake of haemoglobin and nutrients from the erythrocyte. The proposed research addresses the following questions: what is the origin of the phospholipids that make up the PVM when it is made and when it expands and how does the parasite phospholipid transfer protein PFA0210c affect this process; what are the functions of the proteins in the PVM; and how does the PVM allow survival of the parasite inside the erythrocyte. These questions will be addressed using a combination of genetic techniques newly adapted for use in Plasmodium parasites (Cas9-mediated gene modification and inducible gene removal using the rapamycin-inducible diCre system), biochemical approaches, and automated EM microscopy that allows 3D models of parasites to be produced. Together, the proposed experiments will provide insight into the function of the PVM and will reveal the essential functions of PVM proteins. Furthermore, this research could reveal entirely new targets for use in anti-malarial drug development.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Molecular mechanisms of enterobacterial resistance to complement
Funder: Medical Research Council

Abstract: Complement (C') resistance is a major virulence determinant of Gram-negative bacteria (GNB). Although the basis of C' resistance has historically been intensively investigated, many features of the resistant phenotype remain elusive and have not been addressed in recent years, even though new molecular and microscopic techniques have yielded novel insights into the organisation of the outer membrane (OM). We will employ cutting-edge molecular, structural, biophysical and microscopy-based approaches to determine bacterial surface topography that defines C'-resistant pathogens. Resistance results from the capacity of target GNB to avoid deposition of terminal C' (C5b-9) complexes onto the OM by preventing C' pathway activation, degradation of early C' components or elaboration of an OM surface preventing insertion of C5b-9 into the bilayer. We will prepare high density transposon mutant libraries of Escherichia coli and Klebsiella pneumoniae C'-resistant isolates by Transposon Directed Insertion Sequencing (TraDIS) to determine gene products that contribute to the resistance phenotype. Mutants and complemented derivatives will be generated as determined by outcomes of TraDIS screens, to examine the contribution of individual gene products to resistance. Activation of C' by wild type and mutant surfaces will be examined by quantification of binding of early and late C' components and of C' inhibitor proteins. Spatiotemporal patterning of OM surface constituents will be determined by microscopic imaging of protein assemblies with novel fluorescent ligands, lipopolysaccharide and capsules with antibodies, hydrophobic regions susceptible to C5b-9 attack with fluorescent probes and C5b-9 neoepitopes with antibodies. Contour maps will be constructed to provide a detailed topography of the GNB surface. Mutants defective in synthesis of key resistance determinants will be examined in rodent models of systemic infection to determine their contribution to pathogenesis.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Structure-function relationships of the influenza virus RNA polymerase: influence on virulence, host restriction and innate immune responses
Funder: Medical Research Council

Abstract: Our research programme will uncover the role of the influenza virus RNA polymerase in virulence, host restriction and innate immune activation, and aid the development of novel antivirals and improved vaccines through investigating the structure-function relationships of the influenza virus transcriptional machinery. Specifically, we will determine how the transcriptase and replicase functions of the polymerase are regulated through interactions with host RNA polymerase II and dimerization. We will investigate the high-resolution structures of vRNPs and the replicative intermediate complementary RNPs (cRNPs) and will carry out a structural analysis of the vRNA in vRNPs. To identify accessible 'sensitive' sites in the polymerase that could be targeted by small molecule inhibitors, we will use a set of nanobodies that bind strongly to the polymerase and inhibit its function. We will investigate the role of the ANP32 family of host proteins, underlying polymerase mediated host restriction of avian influenza viruses in humans, and the mechanisms of influenza virus-induced host shut-off. To address how influenza viruses activate innate immune responses, we will investigate the molecular mechanisms by which the influenza virus polymerase generates mini viral RNAs (mvRNAs), that act as strong inducers of interferon expression and could underlie the high virulence of 1918 pandemic virus and avian influenza virus infections in humans. To meet these objectives we will use an inter-disciplinary approach, combining methods such as x-ray crystallography, cryo-electron microscopy, SAXS, next generation sequencing, bioinformatics, bio-imaging, single-molecule analyses (smFRET), biochemical and virological methods, including reverse genetics for generating influenza virus mutants. The results will be fully exploited, in collaboration with industrial partners, towards developing antivirals targeting the viral RNA polymerase and the development of improved influenza vaccines.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Targeting the IL-33-inflammasome axis in therapy for cerebral malaria
Funder: Medical Research Council

Abstract: Cerebral malaria (HCM) is the most severe complication of malaria infection, being responsible for approximately 300,000 deaths each year. The majority of individuals that die from HCM are treated with anti-malarial drugs, which is the only current treatment for the condition, but which is ineffective in 15-25% of cases. Thus, there is an urgent need to develop better treatments for CM to reduce the burden of this devastating syndrome. Our preliminary data strongly suggest that rIL-33 is a novel and highly effective potential adjunct immunotherapy for treatment of CM through its capacity to inhibit NLRP3 inflammasome-mediated neuroinflammation. Indeed, adjunct treatment with the inflammasome inhibitor MCC950 phenocopies the protective effects of rIL-33 in improving the recovery of mice with CM. These data, therefore, underline the central importance of the IL-33-inflammasome axis in determining the treatment success of CM. In this application we propose to definitively define, using a validated murine model of CM and an established in vitro human brain tripartite culture system mimicking parasite sequestration and monocyte-mediated parasite killing within the brain microvasculature, the mechanism through which adjunctive administration of rIL-33 and inflammasome inhibitors improve the recovery from established CM. Furthermore, we will perform highly resolved and quantitative analyses of IL-33 expression and inflammasome activity within plasma and post-mortem brain samples from individuals with CM and in case controls samples from individuals with asymptomatic malaria or non-CM causes of death. These investigations will reveal the relationship between impaired IL-33 function, dysregulated inflammasome activation, and neuroinflammation in determining the development and resultant treatment failure of CM. We anticipate that our results will support the design of clinical trials to study the adjunct activity of rIL-33 and inflammasome inhibitors in treatment of CM.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.1 PHARMACEUTICALS
Health categories: INFECTION