NIHRDataInsights/HRCSData huggingface dataset:
Title: Investigation of LA-MRSA in China and the UK
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The aim of the proposed research is to investigate livestock-associated MRSA (LA-MRSA) in China and the UK. LA-MRSA is an increasing problem in both China and the UK. The ST398 lineage is responsible for the majority of LA-MRSA carriage in European and North American farm animals, while in Asia the ST9 lineage is the dominant LA-MRSA type. This study will determine the prevalence and population structure of LA-MRSA in the two counties, and use functional genomics to investigate the genetic basis of the broad host species specificity demonstrated by LA-MRSA. The proposed research is divided into 4 work packages: WP 1: Measurement of the prevalence of LA-MRSA in pig farms in China in a cross-sectional survey. Isolates from the survey will be sequenced to determine the population structure and molecular epidemiology of LA-MRSA in China. This WP also includes a survey of human MRSA isolates from hospitals in the same region. WP2: A case control study, to compare pig farms where LA-MRSA is present with those where it is absent, will be performed with a greater depth of sampling and further sequencing of MRSA and S. aureus (MSSA) in order to identify potentially out-competing methicillin susceptible (MSSA) lineages, and husbandry and management factors that may be associated with the presence of LA-MRSA. WP3: Generation of transposon (Tn) mutant libraries of representative strains from the major lineages of LA-MRSA (ST398 MRSA in the UK and ST9 in China), and host (1 human and 1 porcine) specific lineages, and use these Tn mutant libraries in conjunction with Tn-seq to identify genes that may be associated with host colonisation, using in vitro assays as a proxy for infection/carriage. WP4: In addition to conventional next generation sequencing chromosome conformation metagenomics (Hi-C and meta3c) will be used to look at the diversity in the staphylococcal flora both in pigs carrying LA-MRSA and those free from LA-MRSA from the same farms.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY)
Health categories: INFECTION
Title: Determining the clinical and environmental impact, burden and cost of extensively drug resistant Enterobacteriaceae in China (DETER-XDRE-CHINA)
Funder: Biotechnology and Biological Sciences Research Council

Abstract: To meet the objectives we have devised four technical platforms as describe: Sampling platform. We are sampling in three regions (Shandong, Zhejiang and Guangdong) from five sectors. These workpackages (WP) are: primary and secondary clinical samples (WP1), normal flora fecal samples (WP2), farm animals (WP3), retail meat and (WP4), environment. We will study carbapenem resistant Enterobacteriaceae (CRE) and Enterobacteriaceae possessing the mobile colistin resistance mechanism, MCR-1 (MCRPE). Our statistical advisor (Hood, CU) has powered our study based on our pilot data and predicted positive samples. We will sample every three months and collect and analyze at least 17,280 samples. Microbiology Platform. Samples will be processed to assess 1. The prevalence of CRE and MCRPE in platform 1 samples and 2, the dominant Enterobacteriaceae. Microbiology analysis includes bacterial identification by MALDI-TOF MS and antimicrobial susceptibility testing according to EUCAST guidelines. Bacteria will be stored frozen until further required. We will also screen for resistance genes and MLST by PCR and sequencing. Molecular Platform. Data from platform 2 will determine the isolates to be whole genome sequenced. Sequencing will be primarily done on MiSeq sequencers based in Beijing and Cardiff. We aim to sequence between 2200-2400 throughout the study. We will use several software packages including, 1) whole genome mapping analysis: FASTQC, BWA, SAMTOOLS, PICARD, GATK, MUMER, MAUVE, etc; 2) whole genome assembly analysis: VELVET, SOAPdenovo, SPAdes, CA Assembler etc; 3) whole genome annotation and antibiotic resistance analysis tools and database: NCBI BLAST, MetaGeneMark, ARDB, CARD, ARG-Annot, SRST etc; 4) Phylogenetic analysis: Bionumerics, FastTree, Harvest suite, etc. Mathematical Modeling. We will apply ARIMA models on our three different sample areas with different sample sources and examining CRE and MCRPE variations in different seasons.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Accelerate CHNUK AMR discovery: Establishing joint China/UK training and research platforms enabling highthroughput fragment based inhibitor discovery
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The synchrotrons at Harwell (UK) and Shanghai (China) and the Drug Discovery unit at Dundee are powerful technology hubs. In particular Diamond Light Source is developing the first synchrotron beamline with an integrated high-throughput fragment based lead discovery (FBLD) platform and Dundee has established expertise in medicinal chemistry and drug discovery. We plan to integrate these hubs with AMR centres of excellence in China and the UK, deliver state of the art training to these researchers (and the wider AMR community) and exploit FBLD capabilities to identify novel chemical probes. These new chemical probes, alongside high throughput structural biology and mechanistic insight, will all importantly, help validate a range of novel AMR targets and provide the structural insight to build new effective inhibitors for these and the panel of well validated targets in cell wall and protein biosynthesis. Specialist workshops in China and the UK will deliver training and outreach to the wider community. To optimise and develop workflows at the interfaces between target production, fragment screening and medicinal chemistry and aid high-throughput characterization of novel targets two posts covering computational chemistry and structural biology are proposed. We will hold workshop(s) in UK, and China to attract new China academic and industry partnership and be guided by medicinal chemistry at Dundee and antibiotic discovery industry experts during the collaboration to prioritise chemical approaches. Two PDRAs are required, based at Harwell, one to support protein production and crystallography the other in silico modelling and in support of the X-ray crystallography-based FBLD platform. They will be involved in construct designing, cloning, protein production and purification, crystallization, Xchem fragment screening and data processing and analysis chemical docking and design. Moreover, the PDRAs will be involved in Harwell-based workshops and ongoing support.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Pathways to optimising antibiotic use in Anhui: Identifying key determinants in community and clinical settings
Funder: Biotechnology and Biological Sciences Research Council

Abstract: 1.1: Microbiological sampling (Objectives 2, 4, 5, 10): 1,000 patients will be recruited for the COPD study in order to collect 100 S.pneumoniae, and 278 (555) patients in order to collect 100 (200) E.coli for the cUTI study, based on these assumptions: 40% of patients recruited to cUTI study and 25% of patients recruited to COPD will yield a pathogen; 90% of pathogens isolated from urine will be E.coli and 40% of pathogens isolated from sputum will be S.pneumoniae. In E.coli, resistance to nitrofurantoin, fosfomycin and co-amoxiclav will be <5%, resistance to cephalosporins and fluoroquinolones 50-60% (Qiao L-D, Chen S, Yang Y et al, 2013); in S.pneumoniae, penicillin resistance will be 12.5% and erythromycin 90% (Kim S-H, Song J-H, Chung D-R et al, 2012) 2.4: Direct Observations at pharmacies (Objectives 2, 6, 11): An observer is at each site for two 7-day periods, each spaced over 4 consecutive seasons (92 person-days of observations over 16 periods in 2x2x4 settings). All encounters in observation days are eligible for observation, using a structured checklist. 3.1 Prospective population cohort survey (Objectives 1, 2, 8, 9): Cases will be households, selected through cluster-randomization with 3 steps: (1) divides all counties in the Province into north, middle & south regions; (2) randomly selects 6 counties from each region, then 1 township and community from each county & 1 administrative village & 1 street from each selected township or community; (3) randomly draws 1 household from each administrative village (or street) as a starting point, then every 5th household using a random walk method. Baseline survey uses a structured questionnaire. A local informant completes case detection in cohort households bi-weekly for 12 months using a symptom checklist. Cases are reported by text message for follow-up in person or by phone using structured questionnaires. Data analysis will use descriptive statistics & multivariate modelling.


Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: INFECTION
Title: Extending bicyclomycin treatment of multi-drug resistant Gram-negative pathogens
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Our research programme aims to repurpose an old antibiotic, bicyclomycin, for treatment of multi-drug resistant (MDR) Gram-negative infections. This stems from recent work demonstrating its ability to rapidly kill Gram-negative bacteria when used in combination. Bicyclomycin is a Streptomyces natural product that was discovered in the 1970s and has a narrow bacterial spectrum, poor oral absorption, and little lethal activity. Consequently, this compound, along with many others, was set aside in favour of more active agents that were available at the time. Bicyclomycin has now become a promising candidate for redevelopment as members of the research team have shown that combining bicyclomycin with a bacteriostatic inhibitor of transcription (e.g. rifampicin) or translation (e.g chloramphenicol) converts bicyclomycin from a bacteriostatic agent to a highly lethal agent against multiple Gram-negative species. This discovery of bicyclomycin lethal synergy was surprising, because with most, if not all, other antimicrobial combinations, bacteriostatic inhibitors of gene-expression antagonise rather than stimulate the lethal activity of bactericidal agents. We have evidence that indicates that in the absence of a suitable partner antibiotic, a protein that protects against the lethal activity of bicyclomycin can be expressed. A small-molecule inhibitor of this protective protein combined with bicyclomycin would create a novel, highly lethal combination therapy for MDR Gram-negative infections. To achieve this we need to: (1) determine whether lethal synergy is observed in an in vivo model of infection; (2) establish a robust, high-titre platform the production of bicyclomycin by its natural Streptomyces producer, and develop methods to produce novel derivatives by both pathway engineering and synthetic chemistry; and (3) characterise the protective mechanism using proteomics and subsequent gene deletions to inform a screen for inhibitors of this process.


Research activity codes: 6.1 PHARMACEUTICALS
Health categories: INFECTION
Title: An integrated approach to understand the emergence and spread of extensively resistant Gram-negative bacteria in China
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Combatting antimicrobial resistance is a global challenge. In China, this manifests in the rapidly rising rates of resistance in the major nosocomial pathogens such as E.coli, Klebsiella and Acinetobacter spp. Current epidemiological studies suggest that pan-drug resistant strains already exist and will thwart any currently available antibiotic. In this proposal, we outline strategies to undertake the generation of the first comprehensive genomic database of clinical isolates of the three major pathogens. This will facilitate our next approach which focusses on the development of novel computational tools to reconstruct the acquisition and spread of AMR elements throughout the different gram-negative pathogens. This data will be biologically validated using both Chinese clinical isolates and a K.pneumoniae model system to identify the genetic factors and drivers required for resistance development and plasmid acquisition and maintenance. Our multidisciplinary approach (computational to biological) will allow us to construct an integrated model for resistance acquisition to last-line agents and the proliferation of epidemic clonal lineages. This will represent the first such high-quality microbial genomic database ever and will constitute a precious resource for the development of future diagnostic and prognostic tools in China where the rapid detection and stratification of antibiotic therapy is paramount to meet the increasing demands on its healthcare system.


Research activity codes: 5.9 RESOURCES AND INFRASTRUCTURE (TREATMENT DEVELOPMENT)
Health categories: INFECTION
Title: Molecular mechanisms underlying Campylobacter jejuni's unusual swimming style
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The aim of this research is to understand how Campylobacter jejuni swims: although it uses a flagellum, its swimming is considerably different to the flagellar model organisms, E. coli and Salmonella. The work combines electron cryo-tomographic imaging and collaborations in genetic manipulation, cell biology, crystallography, and biophysics, with the ultimate goal of developing a quantitative model of this swimming. Because C. jejuni motility is required for virulence (and a number of other important pathogens from the Helicobacter and Arcobacter genera use the same mechanisms), it presents itself as an excellent target for drug development in the era of antimicrobial resistance. All electron cryo-tomographic data will be collected using established protocols that have already been published. This proposal describes four aims. Aims 1 to 3 are fairly independent; aim 4 integrates results into a model: Aim 1: Use electron cryo-tomography to determine the structures of active and inactive motors in C. jejuni, identify the protein(s) responsible for inactivation, and locate those protein(s) in the structures. Methods will be developed to separate active and inactive motors for structure determination. Differences between structures of the wild-type motor, and motors with genes deleted or tagged will enable location of proteins. Aim 2: Use electron cryo-tomography, genetics, and modelling, to test the hypothesis that the C. jejuni flagellar 'hook' that couples the flagellum to the cell body has evolved to alter the ratio of rotation (and therefore thrust) between the flagellum and counter-rotation of the helical cell body. Aim 3: Use electron cryo-tomography and genetics to make headway into understanding how C. jejuni makes itself into a helical shape, essential for proper swimming. Aim 4: Use fluorescent labelling of C. jejuni and develop mathematical models to fully understand C. jejuni with an integrative model.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Optimising forest benefits whilst minimising impacts of emerging zoonotic diseases: co-developing an interdisciplinary tool for forests in India
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Vast numbers of poor people in Low and Middle Income Countries (LMICs) depend on healthy forest ecosystems for their livelihoods and food security. In India, around 300 million people depend on forests that are badly degraded. Forest habitats in these countries are a major source of food, fuel, livestock fodder and other non-timber forest products but also of emerging infections. Upsurges in zoonotic diseases (e.g. malaria, Leishmaniases) have been linked to deforestation or re-afforestation and to forest usage in LMICs but the social and ecological mechanisms underlying these changes are unknown. Advancing the global One Health initiative, involving stakeholders across public health, animal health and forestry, this project develops a novel interdisciplinary framework and decision-support tool to understand how forests can best be used to enhance livelihoods whilst minimising exposure to zoonotic disease. The framework is developed initially for the tick-borne Kyasanur Forest Disease Virus that causes debilitating and fatal haemorrhagic human disease in forests in India. The tool will be framed by cross-sectoral, multi-scale mapping of stakeholder knowledge, human sensitivity to disease impacts and forest-user needs for decision-support. The links between forest structure and (a) the human behaviour, priorities and perceptions of risk that govern exposure and (b) the distribution and infection rates of wildlife host and tick that govern disease hazard will be quantified, along fragmented forest gradients. This research will generate spatial decision-support tools that help disease managers to better target risk communication, vaccination and prevention measures as well as guidance for individual forest user groups on forest locations and habitats, seasons and activities that pose the most risk of exposure. Wider application of this inter-disciplinary framework to emerging forest zoonotic diseases in LMICs will be explored with the global research community.


Research activity codes: 3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING
Health categories: INFECTION
Title: Assessing treatment with miltefosine as an intervention strategy for visceral leishmaniasis in Brazil
Funder: Biotechnology and Biological Sciences Research Council

Abstract: We have identified a genomic locus, the miltefosine sensitivity locus, MSL, which is potentially a major determinant of miltefosine efficacy for the treatment of Visceral Leishmaniasis. In this proposal we shall investigate the presence or absence of the MSL in L. infantum in Brazil, as this could inform on whether a new clinical trial with stratified patients might be viable and whether a PCR-based diagnostic test for the MSL should be developed. The molecular basis by which the MSL confers susceptibility of the parasite to miltefosine will be investigated. We will also study the environmental basis for the loss of the MSL in Brazilian L. infantum. Sandflies, the insect vector that transmits Leishmania, take food from plants. We shall test the hypothesis that Brazilian trees of the family Fabaceae fed on by the sandfly contain a natural product(s) that selects for loss of the MSL via genome rearrangement in the parasite. Identification of the plant(s) and natural product (s) involved would help define the range of MSL-containing L. infantum in Brazil, though Geographic information system (GIS) mapping of the specific natural product-containing trees. To achieve this we shall 1. Determine the prevalence of the MSL in Leishmania infantum circulating in Brazil by PCR analysis of DNA taken from infected phlebotomine flies, VL patients and domestic dogs (zoonotic reservoir). Also, to identify plants on which infected phlebotomine flies have fed. 2. Identify the molecular mechanism by which the MSL confers susceptibility to miltefosine by CRISPR-Cas9 directed genetic modification of L. infantum. 3. Test if there is a statistical association between natural products identified in specific plants and loss of MSL across geographical regions. This will combine GIS data on plant locations with identification of miltefosine-like natural products by mass spectrometry.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Evaluation of a novel microbiological diagnostic test for latent tuberculosis infection in Ethiopia (Micro-LTBI)
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Background Efforts to identify and treat people with latent tuberculosis (TB) infection are impeded by the lack of a gold standard diagnostic test for this condition. Very recently, it has been reported that DNA of M. tuberculosis complex (MTBC) can be detected in CD34+ pluripotent haematopoietic stem cells isolated from peripheral blood of sensitised healthy TB contacts (n=7, Europe), using qRT-PCR. Research Objectives To determine whether: a) qRT-PCR consistently detects MTBC DNA in CD34+ peripheral blood mononuclear cells (PBMC) of a larger cohort of sensitised healthy TB contacts living in Ethiopia; b) MTBC strains isolated from human and bovine index cases of active TB in urban and rural Ethiopia are genetically identical to those detected by qRT-PCR in CD34+ PBMC of associated contacts; c) Chemoprophylaxis renders MTBC DNA undetectable in CD34+ PBMC of Ethiopian adults who were qRT-PCR-positive at baseline. Study design We will conduct cross-sectional studies enrolling 200 asymptomatic contacts of infectious TB cases in humans and cattle. The novel qRT-PCR assay will be used to detect MTBC DNA in participants' PBMC. Where this is found, amplicon libraries will be generated and sequences compared to those of MTBC isolates from associated human / bovine index cases. We will also conduct a prospective study, in which results of the novel qRT-PCR assay will be compared pre- vs. post-chemoprophylaxis in 40 people with latent TB infection. Laboratory techniques MTBC-specific DNA in CD34+ PBMC will be quantitated by qRT-PCR. PCR-based methods will also be used to selectively amplify SNP-rich regions (amplicons) in MTBC genomic DNA detected in CD34+ PBMC of TB contacts. Amplicon sequences will be compared with those identified in MTBC isolated from index cases. Application of results This research could lead to the development of a more specific test for latent TB infection, with potential to revolutionise global TB control.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Drinking-water under a "One Health" lens: quantifying microbial contamination pathways between livestock and drinking-water
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Background: Diarrhoeal disease risk remains the fourth leading cause of years of life lost globally, but the role of livestock in contributing to this burden remains unclear. Objective: To develop and validate livestock-related hazard assessment protocols including affordable microbial source-tracking methods, deliver preliminary evidence regarding drinking-water contamination by livestock and its implications for human health, and develop a related multi-country research plan for a future, follow-up longitudinal survey component. Study design: Water quality and livestock hazard module embedded in ongoing longitudinal health and demographic surveillance system. Participants: Household members aged 6 months of over from 200 rural households in Siaya County, Kenya. Outcomes: Source and point-of-consumption drinking-water contamination with E. coli and cryptosporidium; Fortnightly prospective prevalence of reported diarrhoea. Planned analysis: Multinomial logistic regression of E. coli and cryptosporidium counts in drinking-water in relation to livestock ownership, sanitary risk inspection scores, and hazard maps, controlling for confounders; log linear model of prospective 2-day diarrhoea prevalence in those aged >5 months in relation to E. coli and cryptosporidium in stored water, controlling for confounders. Immediate outputs: validated livestock hazard assessment tools; preliminary evidence on livestock, water contamination and diarrhoea risks; local capacity-building, particularly in microbial source tracking methods Long-term research plan: Development of a multi-country protocol and research network for a water quality and livestock hazard module, to be embedded in longitudinal health and demographic surveillance systems such as INDEPTH surveys


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