NIHRDataInsights/HRCSData huggingface dataset:
Title: Mapping resistance to Campylobacter in the chicken
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Campylobacter has long been considered to be a commensal in the chicken, and therefore at first consideration it would seem unlikely that there could be resistance to colonisation. However, we believe that rather than being a commensal, Campylobacter is actually an accomplished pathogen. It can induce typical innate immune responses (albeit that these are time- and magnitude-limited), it can be partially controlled by vaccine-induced adaptive immunity, and genetic resistance to colonisation exists in chickens. We have identified four Campylobacter resistance QTL in inbred lines 61 and N. Our overarching hypothesis is that QTL controlling resistance to Campylobacter are also circulating in commercial chickens, and that some of these will be in common with those identified in the inbred lines. For example, of the 4 QTL we identified for resistance to colonisation with Salmonella, two are circulating in commercial chickens. We will refine the Campylobacter resistance QTL in the inbred lines, identify candidate genes and nucleotide changes and analyse the functional consequences of this sequence variation. We will also perform whole genome association/genomic selection (WGA/GS) for Campylobacter resistance in commercial lines and then independently validate the WGA/GS results. This dual approach is required as we cannot apply a simple candidate SNP polymorphism approach in the commercial lines, based on the inbred line data, as we have no evidence that there is the same underlying linkage disequilibrium (LD) between the causal mutation and the SNP in the commercial lines. The overall aim is to identify markers (SNPs), candidate genes and ultimately causative mutations for resistance/susceptibility to colonisation with Campylobacter in chickens. The resistance-associated genotypes will inform commercial breeding programmes to reduce the incidence of Campylobacter contamination of poultry carcasses and thereby levels of this food-borne zoonosis in humans.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: Determining bacterial RNA polymerase functionalities required for sigma factor specific escape from antibiotic action.
Funder: Biotechnology and Biological Sciences Research Council

Abstract: For more than a decade, genomic approaches have been used with only limited success to identify new potential antibiotic targets essential for bacterial viability. The bacterial RNA polymerase (bRNAP); is a validated target and is an attractive target for antimicrobial therapy given (i) RNAP is an essential enzyme in transcription ; (ii) bRNAP-subunit sequences are conserved (permitting broad-spectrum activities); and (iii) bacterial and eukaryotic RNAP-subunit sequences are less well conserved (permitting therapeutic selectivity). Currently there is only one class of clinical antibiotics that target bRNAP, rifamycins (Rif). However, emergence of bacterial strains resistant to rifamycins has greatly compromised treatment of many bacterial pathogens including Mycobacterium (tuberculosis), Staphylococcus (MRSA) and Listeria. There is therefore an urgent need to develop new antibiotics to treat infections caused by Rif-resistant and multidrug-resistant bacteria. A detailed mechanistic understanding of transcription, in particular knowledge of the various mechanisms by which RNAP-associated antibiotic resistance arise is of immense importance. These findings will guide essential steps in the development and use of future therapeutic agents. Knowledge of intrinsic resistance mechanisms is of growing importance in developing new antimicrobial strategies. Here we will study one intrinsic resistance mechanism associated with bRNAP function. The intrinsic resistance mechanism relies on the association of the bRNAP with one of its sigma factors, and how this form of bRNAP holoenzyme confers tolerance to antibiotics will be dissected biochemically and genetically using purified components and readouts of the various stages of the transcription process. Outcomes are expected to enlarge our understanding of the mechanisms operating for gene specific expression by bRNAP as well as provide a basis to rationalise intrinsic mechanisms of antimicrobial resistance in bacteria.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Olfactory mechanisms underlying behavioural manipulation of mosquitoes by malaria parasites
Funder: Biotechnology and Biological Sciences Research Council

Abstract: There is considerable evidence that pathogens manipulate the behaviour of their vectors to enhance pathogen transmission. For example, malaria-infected mosquitoes take larger blood meals than uninfected ones, and take multiple blood meals. We have recently demonstrated that P. falciparum-infected An. gambiae females were significantly more attracted to human odours than uninfected females. This was the first demonstration of a change in An. gambiae behaviour in response to olfactory stimuli caused by infection with P. falciparum. Despite the clear impact on the epidemiology of vector-borne diseases, parasite-mediated behaviour of haematophagous insects in response to host odours, and the chemistry and olfactory mechanisms underlying the behavioural responses, have not been elucidated. The hypothesis of this study is that P. falciparum manipulates the olfactory system of infected An. gambiae mosquitoes, causing them to be more attracted to human hosts. We propose to build on our preliminary study to quantify, using olfactometer studies within BSL-3 laboratories at LSHTM, the behaviour of An. gambiae females infected with human malaria parasites, P. falciparum, and compare these responses to uninfected females, and determine whether the responses depend on the lifecycle stage of the parasites. Electrophysiological experiments will be done to examine whether P. falciparum infection has an effect on the olfactory system. New compounds (or blends) could be identified, using sophisticated analytical chemistry techniques, which could be exploited to develop a synthetic lure for application in surveillance or trapping programmes specifically targeting P. falciparum infected An. gambiae s.s. females. This study represents a novel piece of biology exploring the olfactory mechanisms by which parasites enhance their transmission success. This is, to our knowledge, the first study to examine this type of behavioural manipulation by a parasite.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: The impact and social ecology of bacterial zoonoses in northern Tanzania
Funder: Biotechnology and Biological Sciences Research Council

Abstract: With growing recognition of the widespread over-diagnosis of malaria in many parts of Africa, increasing attention is being given to other causes of human febrile illness. Preliminary studies in northern Tanzania indicate that febrile disease caused by the zoonotic diseases, leptospirosis, Q-fever and brucellosis, result in 11 times as many cases of febrile admissions as malaria. These pathogens can infect and be transmitted among a wide range of host species. However, almost nothing is known about transmission patterns among animal hosts, which host species are responsible for human disease, or the key social, economic and behavioural determinants of human disease risk in different agro-ecological settings. This study aims to address the overarching question: what are the origins and determinants of human disease risk for bacterial zoonoses? In addition, the research will determine how risk factors vary among different livestock-owning communities and explore the effectiveness of different control and prevention strategies in these communities. The project will integrate several different disciplinary approaches, including social behavioral studies, human febrile illness surveillance, and linked human-animal epidemiological studies (cross-sectional and case-control studies), to generate data for incorporation into models of human disease risk. These models, together with an understanding of community risk perception and knowledges, will allow us to identify appropriate strategies for disease control and prevention. The project brings together medical, social science, veterinary and ecology research groups working together to conduct the first integrated research into this group of bacterial zoonoses in Africa.


Research activity codes: 2.3 PSYCHOLOGICAL, SOCIAL AND ECONOMIC FACTORS;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION
Title: The Type III secretion system 'translocation stop' activity of EspZ
Funder: Biotechnology and Biological Sciences Research Council

Abstract: 'Attaching & effacing' (AE) E. coli exert a substantial burden on human and animal health and use Type III secretion to colonise intestinal epithelia and induce pathology. The locus of enterocyte effacement (LEE)-encoded Type III secretion system of such pathogens mediates injection of tens of bacterial effectors into enterocytes. These orchestrate cellular pathways in a manner requiring exquisite temporal and spatial control. Our data indicate that the LEE-encoded effector EspZ is modified upon entry into host cells and is integrated into the host cell plasma membrane where it functions as an inhibitor of further effector translocation. Ectopic expression of EspZ in eukaryotic cells renders them refractory to infection, and cells infected with AE pathogens are resistant to super-infection in an EspZ-dependent manner. Bacteria lacking EspZ cause cell damage, likely owing to accumulation of effectors to toxic levels. Our yeast-2-hybrid analysis has indicated that EspZ may interact with a constituent of the translocation pore (EspD), however the molecular mechanism by which it arrests Type III secretion is not known. We propose to define the kinetics of EspZ translocation, its insertion into the host cell plasma membrane and the onset of 'translocation-stop' activity. We will map the protein-protein interaction sites of EspZ and its partner proteins, and determine the role of the partner proteins and interacting residues in its 'translocation-stop' activity. The electrophoretic mobility of EspZ shifts on entry into cells and we propose to define the nature and consequences of post-translational modification. We will also evaluate the impact of mutation and over-espression of espZ on intestinal persistence of enterohaemorrhagic E. coli in calves and Citrobacter rodentium in mice. Unravelling the mode of action of EspZ will have major implications for the design of novel strategies to control infections by pathogenic E. coli.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Role of AKT1 & SIVA1 in resistance to avian salmonellosis
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Avian resistance to systemic salmonellosis is largely mediated by the SAL1 locus. Analysis of the segregation of SNPs in the progeny of a sixth generation back-cross of inbred lines that differ in resistance (6 and 15I), as well as F(13) inter-cross lines, has fine-mapped the QTL to a 0.4Mb region encoding AKT1 and SIVA1. In murine and human cells, these proteins have opposing effects on apoptosis and induction of innate immunity. In mammalian cells, Salmonella activates AKT via injection of SopB. This delays apoptosis and promotes net intracellular replication in vitro and in mice, as evidenced by studies with sopB mutants, null mice and specific inhibitors. By contrast, SIVA1 is pro-apoptotic and is proposed to control Salmonella via release of heterophil extracellular traps upon cell death. No evidence exists that these mechanisms are relevant in chickens and a need exists to unravel how resistance-associated SNPs exert their effect. We propose to define the kinetics of AKT1 and SIVA1 activation upon Salmonella infection using specific antisera, and associate this with the fate of infected cells ex vivo and in chickens by flow cytometry and immuno-staining. We will examine if levels or activities of AKT1 and SIVA1 explain the differential resistance of lines 6 and 15I. Net replication of Salmonella in such birds will be quantified in cells and tissues by fluorescence dilution, and visualised relative to AKT1 activation and apoptosis. We will further define if AKT1 plays a protective role in avian responses to Salmonella by use of sopB mutants, inhibitors and siRNA-mediated knock-down. Toward marker-assisted selection, we will survey the frequency of informative SNPs in a population of Hy-Line layers directly related to that exposed to a recent fowl typhoid outbreak. Birds of defined genotype will be challenged to associate genetic variation with AKT1/SIVA1 levels or activation, host responses and Salmonella replication.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Biological function of Candida albicans Ece1 and role in host-microbe interactions
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The ability of a host organism to discriminate between commensal and pathogenic microbes is essential to health. Recently, we identified an epithelial signalling mechanism instrumental in identifying the commensal-pathogen switch of Candida albicans (C.alb) a major life-threatening fungal pathogen of humans. This activation mechanism targets the hyphal form of C.alb, resulting in induction of proinflammatory cytokines and subsequent protection against mucosal fungal infection. We have now identified the C.alb hyphal protein (CaEce1p) targeted for epithelial recognition of the commensal-pathogen switch. This proposal will (i) characterise the biological function of CaEce1p in C.alb using a combination of C.alb microarrays, bioinformatics and phenotypic analyses, (ii) determine the importance of CaKex2p for CaEce1p processing, localisation and function in C.alb using ECE1-GFP labelled C.alb strains and CaEce1p specific antibodies by fluorescence and electron microscopy, and (iii) ascertain the importance of CaEce1p processing and localisation for epithelial cell activation. This project will provide essential new understanding to basic fungal biology and the mechanisms that underpin C.alb-host interactions in health. It will also identify CaEce1p as a new target for the development of new drugs, vaccines, adjuvants, diagnostic tests and biomarkers for fungal infections.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Susceptibility of broiler chickens to Campylobacter: impacts of the gut environment and immune status on colonisation
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Chicken is the main source of human Campylobacter and this threat must be reduced. The proposed work will determine mechanisms behind the delay before broiler chickens become Campylobacter-positive in housed flocks. The project is in partnership with poultry producers to identify cost-effective control measures to protect chickens against Campylobacter. Past work suggested that maternal antibodies provide chicks with some protection against Campylobacter in early life. However, this was done in isolation and other protective factors were not studied. Campylobacter-negative chicks can have gut bacteria that inhibit C. jejuni. In most flocks, the 'protective bacteria' were not present when birds reached 3-4 weeks of age and flocks rapidly became Campylobacter-positive. We will determine whether maternally-derived antibodies and/or gut microbiota and/or gut architecture is the most important in determining broiler susceptibility to Campylobacter. We will study Ross 308 birds, the most common type in the UK. The field studies will relate changes in naturally acquired maternal anti-Campylobacter antibodies and gut microbiota with events in flock management, like diet change and with the presence of Campylobacter. State of the art techniques will be used to determine microbiota. Laboratory experiments will test field-generated hypotheses in a controlled manner. B-cell deficient breeders will be produced by surgical bursectomy. This creates B-cell- and thus antibody-deficient hens. These will be used to form breeding flocks producing progeny deficient in maternal antibodies. We can then determine definitively the role of maternal antibodies in the resistance of chicks to Campylobacter. We will use modelling to investigate dynamics of chicken gut microbiota and its impact and maternal antibodies as direct and proximal drivers of colonisation in commercial chicken production. These models will be used to identify targets for mitigating Campylobacter colonisation.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: The molecular basis of action of the toxin Microcin B17 on DNA gyrase
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Finding new molecules that are potential leads for antibacterial agents is a significant challenge. There are relatively few validated antibacterial targets; the considerable efforts of genomics/proteomics have largely failed to deliver many new targets. Nature has already revealed what the good targets are, and among these is bacterial DNA gyrase. The fluoroquinolones, which target gyrase, have been spectacularly successful, but resistance problems have now rendered them considerably less effective. Therefore we need new agents with comparable properties. Microcin B17 (MccB17) acts on gyrase in a similar, but distinct, way to quinolones; its binding site and exact mode of action are different. By establishing the molecular basis of MccB17's action and by exploring novel small molecules that are fragments/analogues of MccB17, we believe we can provide insight into novel gyrase-inhibitor interactions that will subsequently contribute to the development of new anti-bacterial agents. Our approach entails: producing novel microcin analogues, by genetic and chemical means, that can be assessed for their potential as novel inhibitors and utilised in the analysis of MccB17 action; and defining the MccB17 binding site by identifying novel mutations in gyrase, performing toxin-target cross-linking studes, and structural analysis by crystallography and NMR.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: drosophila model to investigate the tripartite relationship between symbiont, trypanosomes and tsetse flies
Funder: Biotechnology and Biological Sciences Research Council

Abstract: The presence of Sodalis glossinidius in the midgut of tsetse has been linked to increased establishment of trypanosomes in the insect's midgut. This suggests that Sodalis is changing the status of the tsetse gut allowing trypanosomes to establish. The central hypothesis of this study is that the symbiotic interaction of Sodalis with the tsetse host results in the fly being more susceptible to trypanosome infection. The most likely explanation for this is that tsetse immunity is compromised by the Sodalis symbiosis. Tsetse are very difficult and expensive insects to work with due to their slow reproductive rate and complex symbiont biology. We take the novel approach of using drosophila as a model system for tsetse biology. This overcomes a number of tsetse research problems and opens up the opportunity to use the vast molecular genetic toolbox provided by drosophila research. Unusually for insect symbionts Sodalis is amenable to culture and genetic manipulation. Therefore we will use a unique Sodalis/drosophila experimental symbiosis to investigate 1) how Sodalis establishes a symbiotic relationship with drosophila and 2) how the symbiotic interaction of Sodalis with tsetse results in the fly becoming more susceptible to trypanosome infection. This project will use transcriptomic (RNAseq- Sodalis and microarray - drosophila), proteomics and genomics information to identify bacterial and insect genes involved in the establishment and persistence of symbiosis using parallel analysis of symbiont and host gene expression in cells. Candidate genes which may make the tsetse fly immune-incompetent to trypanosomes will be validated in the drosophila model and tsetse gut using functional genetics. The work will provide fundamental understanding of the tsetse biology as a disease vector but will also provide insight into novel ways to target important vector of animal, plant and human disease.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Metal-sensing in Salmonella: A model for targeting a network that differentiates metals
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Five transcriptional regulators that detect metals have been characterised in S. Typhimurium (CueR, GolS, Fur, MntR and Zur). Metal-effectors and operator-promoter targets can be predicted for a further five deduced sensors (hypothetically ZntR, NikR, RcnR, ModE and ArsR) exploiting sequence similarity and gene context. Predicted DNA-binding sites and metal-specificities will be validated by experiment, establishing which metals each sensor responds to under steady state conditions (generations of growth under maximum and minimum permissive concentrations of each metal). One additional CsoR/RcnR homologue plus five further MerR-homologues are also encoded in the genome and will be analysed to discover which ones are metal sensors. Recombinant proteins will be expressed and purified to determine affinities (of the tightest sensory site in the first instance) for the metals that each sensor detects, affinities for the metals detected by the other sensors and affinities for DNA. This part of the programme will be aided by a linked PhD student, also funded by our industrial partners. In addition to advancing knowledge of the individual components of the set of metal sensors in a micro-organism of relevance to food production and processing, this programme will quantify the abundance of each metal sensor in vivo under each steady state metal condition to enable the generation of integrated mathematical models to describe metal-specificity of metal-sensing. An attractive feature is that some intracellular parameters (the buffered available concentration of metals for example) can be treated as common functions for all of the sensors, assisting the mathematical modelling.


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