Rational selection of targets for control of bacterial pathogens of food-producing animals

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

This project brings together scientists with expertise in diverse animal models and bacterial genetics to identify factors important for colonisation, host-specificity and pathogenesis. Although complete and partial genome sequences exist for the pathogens under study, the role of the encoded products in persistence, pathogenesis and protection needs to be evaluated. High-resolution comparative genomics and high-throughput in vivo and in vitro screens have identified bacterial determinants which are predicted to be important for these processes. We aim to determine how they function and examine their effect on innate and/or acquired responses in naïve or resistant hosts. The work will be integrated with studies on pathogen recognition (theme 1) and resistance (theme 2) and be exploited to develop and refine intervention strategies.

Publications

10 25 50
 
Description This main aim of the research was to identify key colonisation factors and the mechanisms by which pathogens modulate innate responses in order to develop vaccine-based interventions. This work brings together scientists with expertise in diverse animal models and bacterial genetics to identify factors important for colonisation, host-specificity and pathogenesis. Although complete and partial genome sequences exist for the pathogens under study, the role of the encoded products in persistence, pathogenesis and protection needs to be evaluated. High-resolution comparative genomics and high-throughput in vivo and in vitro screens have identified bacterial determinants which are predicted to be important for these processes. The aim of this work is to determine how they function and examine their effect on innate and/or acquired responses in naïve or resistant hosts. The work will be integrated with other studies on pathogen recognition and resistance to develop and refine intervention strategies:

Highlight findings:

High resolution evolutionary genetic analysis has identified livestock as a reservoir for emergent strains of human methicillin-resistant S. aureus, in addition to the discovery that endemic livestock strains originated in humans. The studies also identified mobile genetic elements specific to host species implying a role in host-adaptation. Whole genome sequence analyses have also tracked the emergence, evolution and spread of hospital-associated MRSA in the UK.

Demonstrated that a subset of enterohaemorrhagic E. coli (EHEC) O157 strains encoding Shiga toxin (Stx) 2a, as opposed to Stx1 or Stx2c, are excreted from cattle at higher levels and are more likely to be associated with serious human infection. We have also identified bacteriophage-encoded factors that control EHEC binding and replication. including a new class of small RNA regulators. A £2m FSA grant was awarded to further define the genetic basis to EHEC O157 super-shedding in cattle and to test refined vaccines (FS101055), building on BBSRC- and industry-funded vaccine work on H7 flagellin and key adhesins.

Machine-learning has been used to analyse complex pangenome data in order to predict the human infection potential of cattle E. coli O157 isolates. We demonstrated that only a minor subset of bovine strains is likely to cause human disease, even within previously defined pathogenic lineages. The approach was tested across isolates from the UK and USA and verified with cattle and food isolates traced from human outbreaks. The work highlights the tremendous potential of machine learning to interrogate complex sequence datasets to predict host and virulence as long as the sequence data is stored with this additional information (metadata). This work has now been supported by further BBSRC grant funding and a similar approach is being adopted to predict phage sensitivity from E. coli isolate sequence data.

By using transposon-directed insertion-site sequencing we assigned roles to almost 3000 Salmonella genes in intestinal colonisation of chickens, pigs and cattle, providing key information for the control of animal and zoonotic disease. The method yields rich functional annotation of pathogen genomes with minimal animal use and attracted BBSRC & Zoetis uplift funding to define the role of Salmonella genes in entry and persistence in the bovine lymphatic system and Staphylococcus genes influencing ruminant mastitis. We also devised a method for tracking the fate of tens of bacterial strains during mixed infections based on massively-parallel sequencing of polymorphic regions of the genome. This represents an advance of the 3Rs, as it avoids the need to separately infect animals with single strains, for example when evaluating cross-protective efficacy of vaccines.

With support from BBSRC and Zoetis we have evaluated subunit vaccines for control of Campylobacter in poultry. This has identified protective antigens and primed BBSRC strategic LoLa funding to develop improved glycoconjugate vaccines for Campylobacter and other pathogens found in poultry. The basis of natural and vaccine-mediated immunity to avian pathogenic E. coli has also been examined, revealing a key role for B cells and priming BBSRC uplift projects with leading teams in the US and EC on avian resistance to E. coli.

We have discovered that the major clone of Staphylococcus aureus causing disease in rabbits evolved through a single host-jump event from humans that occurred over 30 years ago. Comparative genomic analysis revealed that in contrast to S. aureus strains causing disease in humans, ruminants and poultry, mobile genetic elements do not play a major role in this host adaptation. A single non-synonymous mutation in a gene (dltb) involved in D-alanine modification of the cell wall was required and sufficient to confer infectivity for rabbits in an abscess model of infection. The study establishes a new paradigm for the minimal number of genetic events required to support a bacterial host switch event and has broader implications for understanding the emergence of new pathogenic clones. A related study explored the emergence of a major MRSA clone affecting pigs with results reflecting differences in antibiotic usage in human medicine and agriculture.

We have demonstrated that the S. aureus superantigen (SAg) staphylococcal enterotoxin-like toxin X (SElX) contributes to immune evasion by inducing unregulated T-cell proliferation, and by inhibition of phagocytosis by neutrophils. We observed that the capacity to bind neutrophils appears to be central to the SElX-dependent toxicity observed in a necrotising pneumonia infection model in rabbits. We report the first example of a staphylococcal SAg with two independent immunomodulatory functions acting on distinct immune cell types.

The grouping has made important progress on understanding the pathogenesis of Lawsonia intracellularis, an important pig pathogen, towards improving diagnostics and understanding of vaccine-based protection. Specifically, Notch-1 signalling and enhanced SOX9 expression along crypts suggest an expansion of progenitor cells and provide a potential basis for understanding the development and maintenance of disease.
L. intracellularis was shown to impact on MUC2 production, altering the mucus barrier and enabling cellular invasion. By examining the integrity of the intestinal barrier and quantifying a range of intestinal markers, the impact of different vaccine preparations can be compared to wild type strains. The Lawsonia work is in collaboration with commercial partners.

Development of diagnostic tests for important but under-studied bacterial diseases of pigs caused by Erysipelothrix rhusiopathiae and Actinobacillus pleuropneumoniae. Serotypes 1a, 1b and 2 constitute 88.3% of isolates investigated. Current serotype 2 based vaccines should protect against these isolates. Oral fluids can be used for detecting acute outbreaks of erysipelas in pig herds and using a combination of IgA, IgG and DNA detection gives the best prediction on herd exposure to the bacterium. In routinely vaccinated marine mammals, the humoral Erysipelothrix rhusiopathiae decreases over time perhaps indicating reducing the vaccination intervals in older animals (after 6-8 years of vaccination). A multiplex serology assay capable to detect antibodies against ApxI, ApxII, ApxIII and ApxIV has been developed and is used for assessing exposure status to Actinobacillus pleuropneumoniae in pigs.

We have described a novel family of antimicrobial peptides that are expressed in the avian reproductive tract and egg (ovodefensins). A BBSRC LINK project with AB Vista is examining the ability of such factors to act as growth promoters in poultry as alternatives to antimicrobials. This extends in silico characterisation of the ovodefensin family and BBSRC Sparking Impact support, jointly with ISP2.
Exploitation Route There are multiple sub-projects under this programme theme, several with commercial partners. The main impact of this research is the development of improved diagnostic tests and an understanding of markers that are critical for disease, for example in defining which strains in animals are more of a threat to human health. The work therefore is of value to public health bodies in defining zoonotic threat and the commercial sector for diagnostics and vaccine development.
Sectors Agriculture, Food and Drink,Environment,Pharmaceuticals and Medical Biotechnology

 
Description This research brought together scientists with expertise in diverse animal models and bacterial genetics to identify factors important for colonisation, host-specificity and pathogenesis. Although complete and partial genome sequences exist for the pathogens under study, the role of the encoded products in persistence, pathogenesis and protection needs to be understood. We have used comparative genomics, machine learning and high-throughput and resolution in vivo and in vitro screens to identify bacterial genes which are predicted to be important in the disease process and zoonotic threat. Our focus has been primarily on bacterial pathogens, many with zoonotic potential and included Salmonella serovars, Escherichia coli, Staphylococcus species, Campylobacter spp. Listeria monocytogenes, Mycobacterium bovis and paratuberculosis, Rhodococcus equi and Legionella pneumophila. There have been significant advances in vaccine development and testing, many involving commercial parties, particular with Mycobacterium, E. coli, Staphylococcus and Lawsonia. Our work has exploited antigens that activate natural pattern recognition receptors to induce stronger responses to these and linked antigens. The research has also helped identify novel candidate vaccine antigens that are now being tested in formulations. Specific commercial collaborations are entered under partnerships. Significant progress has been made in understanding the epidemiology of disease outbreaks based on both short and long read next generation sequencing. The work has enabled insights into the adaptation of pathogens over short timeframes and on transition between hosts. The research has identified factors required for host adaptation that have diagnostic value and provide insights into selective pressures operating in different host species. These then translate to targets for interventions such as vaccines. The work therefore aligns well with our studies of resistance traits in livestock with on-going work examining genetic engineering and breeding for resistance or resilience in farmed species. Our work has also examined the distribution of antibiotic resistance genes between animal and human isolates, contributing to the debate over issues of antimicrobial use in livestock. BBSRC strategic investment at Roslin via this and other Institute Strategic Programmes has sustained expertise and facilities that have attracted substantial inward investment at Easter Bush. This has recently included £15M Gates Foundation funding to establish the Centre for Tropical Livestock Genetics & Health to implement genetic gain and treatments in support of farmers in low- and middle-income farmers, including to control endemic and zoonotic diseases. It has also driven dozens of productive collaborations with industry via contracts and leveraging schemes, leading to £10M private equity investment to form Roslin Technologies to commercialise our research and construction of a new £32M Innovation Centre adjacent to the Institute to engage and grow businesses. Moreover, the expertise supported by this funding has attracted major investment in Agri-Tech Centres at Easter Bush funded by InnovateUK (Centre for Innovation Excellence in Livestock & Agri-EPI). These Centres will increase national capacity for infectious challenge in farmed animals, gene editing and collection of novel phenotypes and be linked to stakeholders throughout the food supply chain.
First Year Of Impact 2013
Sector Agriculture, Food and Drink,Environment,Healthcare
Impact Types Economic

 
Description University of Edinburgh Research into use of Software to tackle food poisoning
Geographic Reach National 
Policy Influence Type Citation in other policy documents
 
Description AMR3 - Tackling AMR in the environment - The dynamics of antimicrobial resistance gene prevalence on a commercial pig farm: implications for policy
Amount £200,000 (GBP)
Funding ID NE/N020162/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 07/2016 
End 06/2018
 
Description BBSRC ANIWHA call 2
Amount £428,690 (GBP)
Funding ID BB/M028305/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 09/2018
 
Description BBSRC Future Leader Fellowship
Amount £304,886 (GBP)
Funding ID BB/P007767/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 05/2017 
End 03/2019
 
Description BBSRC LINK
Amount £336,000 (GBP)
Funding ID BB/K00638X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2013 
End 09/2016
 
Description BBSRC LINK with AB Vista
Amount £830,000 (GBP)
Funding ID BB/M020738/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2015 
End 08/2018
 
Description BBSRC Responsive mode
Amount £450,000 (GBP)
Funding ID BB/K005642/1 (A novel bacterial defence system against antimicrobial peptides: Implications for host colonisation in the foodborne pathogen Campylobacter jejuni) 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 12/2013 
End 12/2016
 
Description BBSRC Responsive mode
Amount £500,000 (GBP)
Funding ID BB/J014850/1 (The Type III secretion system 'translocation stop' activity of EspZ) 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2013 
End 12/2016
 
Description BBSRC Responsive mode
Amount £500,000 (GBP)
Funding ID BB/M021114/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2015 
End 08/2018
 
Description BBSRC Sparking Impact & AB Vista
Amount £14,765 (GBP)
Funding ID The development of novel egg peptides as antimicrobial feed additives for poultry 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2013 
End 07/2013
 
Description BBSRC Strategic LoLa scheme
Amount £5,700,000 (GBP)
Funding ID BB/N001591/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2017 
End 03/2021
 
Description BBSRC US partnering award
Amount £36,000 (GBP)
Funding ID BB/K021257/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2013 
End 05/2017
 
Description BBSRC US-UK Parterning Scheme
Amount £48,900 (GBP)
Funding ID BB/L026732/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2014 
End 07/2018
 
Description BBSRC-ANIHWA 'Understanding mucosal immunology and co-infections in the chicken to drive vaccine strategies'. UK-EC collaboration with INRA and LMU
Amount £428,690 (GBP)
Funding ID BB/M028305/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2015 
End 07/2018
 
Description BBSRC-NIFA
Amount £417,191 (GBP)
Funding ID BB/M028208/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 09/2018
 
Description BBSRC-SFI-Tackling a multi-host pathogen problem - phylodynamic analyses of the epidemiology of M. bovis in Britain and Ireland
Amount £448,073 (GBP)
Funding ID BB/P010598/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 09/2020
 
Description BMGF grant
Amount £2,050,805 (GBP)
Funding ID BMGF OPP1108042 and OPP1126862 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 05/2014 
End 04/2017
 
Description Carnegie Research Incentive Grant
Amount £9,886 (GBP)
Organisation Carnegie Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 02/2018 
End 07/2018
 
Description European Commission H2020-INFRAIA-2016-1
Amount € 10,000,000 (EUR)
Funding ID EU project 731014 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 04/2017 
End 03/2022
 
Description Food Standard Agency mitigation of risk from EHEC O157
Amount £2,063,845 (GBP)
Funding ID FS101055 
Organisation Food Standards Agency (FSA) 
Sector Public
Country United Kingdom
Start 01/2014 
End 08/2017
 
Description Food Standards Scotland Open Tender
Amount £120,000 (GBP)
Funding ID CRF:MRI/104/17 
Organisation Government of Scotland 
Department Food Standards Agency (FSA), Scotland
Sector Public
Country United Kingdom
Start 07/2017 
End 06/2019
 
Description Impact Acceleration Account
Amount £19,259 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2015 
End 07/2016
 
Description KTN Scholarship
Amount £30,000 (GBP)
Organisation Boehringer Ingelheim 
Sector Private
Country Germany
Start 10/2016 
End 10/2021
 
Description Machine-learning to predict and understand the zoonotic threat of E. coli O157 isolates
Amount £421,490 (GBP)
Funding ID BB/P02095X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
End 09/2020
 
Description Medical Research Council AMR Theme 1
Amount £1,600,000 (GBP)
Funding ID MR/N002660/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 10/2015 
End 09/2018
 
Description Study of effects of ageing on M cells
Amount £450,000 (GBP)
Funding ID BB/M024288/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2015 
End 10/2018
 
Description The Houghton Trust, Small Project Grant Scheme
Amount £10,000 (GBP)
Organisation The Houghton Trust 
Sector Charity/Non Profit
Country Unknown
Start  
 
Description The capacity and pathogenic potential of bacteria that internalise into plant tissue
Amount £37,462 (GBP)
Organisation Food Standards Agency (FSA) 
Sector Public
Country United Kingdom
Start 04/2014 
End 03/2016
 
Description University of Edinburgh Principals Career Development Scholarship
Amount £66,000 (GBP)
Funding ID Mode of action of lymphostatin from attaching & effacing Escherichia coli 
Organisation University of Edinburgh 
Sector Academic/University
Country United Kingdom
Start 10/2015 
End 09/2018
 
Description Welcome Trust Pathfinder
Amount £129,709 (GBP)
Funding ID 204521/Z/16/Z 
Organisation Wellcome Trust 
Department Wellcome Trust Bloomsbury Centre
Sector Academic/University
Country United Kingdom
Start 01/2017 
End 06/2018
 
Description Wellcome Trust Collaborative Award
Amount £2,021,766 (GBP)
Funding ID 206815/Z/17/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2018 
End 03/2022
 
Description Wellcome Trust Collaborative award
Amount £1,200,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 01/2017 
End 12/2021
 
Description Wellcome Trust Pathfinder Award
Amount £129,709 (GBP)
Funding ID 204521/Z/16/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2017 
End 11/2018
 
Description Wellcome Trust re-entry Fellowship to Dr Deborah Hoyle
Amount £349,434 (GBP)
Organisation Wellcome Trust 
Department Wellcome Trust Bloomsbury Centre
Sector Academic/University
Country United Kingdom
Start 06/2015 
End 06/2019
 
Description commonwealth studentship
Amount £70,000 (GBP)
Organisation Government of the UK 
Department Commonwealth Scholarship Commission
Sector Public
Country United Kingdom
Start 01/2013 
End 12/2015
 
Title Strategy for quantifying individual bacterial strains during mixed infections 
Description We devised a novel strategy to follow the fate of individual bacterial strains during mixed infections. Specifically, we wished to follow the fate of multiple Salmonella enterica serovars during colonisation of the bovine host. These are indistinguishable by culture, and while they can be specifically detected by serology, quantification of numbers of each serovar during mixed infection would involve analysis of many hundreds or thousands of individual colonies. We devised a method based on massively-parallel sequencing of a polymorphic allele (rpoB), whereby sequence reads can be used to identify the strain present (based on single nucleotide polymorphisms specific to each strain) and the number of sequence reads can be taken as a measure of the abundance of the cognate strain. Using this method we were able to simultaneously define the fate of 12 different S. enterica strains during infection of cattle, including as they colonised the gut over time and spread from the gut to the lymphatic system and other tissues. This 3R approach should allow phenotypes to be derived with reduced use of animals in experiments and could, for example, be used to see if vaccine-induced responses are effective in control of all the different members of a bacterial population present - in this case toward a pan-serovar cross-protective vaccine. A manuscript reporting these findings was published in late 2017 (Vohra et al). Though a direct output of BBSRC responsive-mode funding, the project was underpinned by core-strategic grants from 2012 and 2017 (e.g. via the involvement of core-funded staff in animal studies) and a BBSRC US-UK partnering award, where the ideas for following serovars based on massively-parallel sequencing of rpoB and ileS were jointly developed. 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? Yes  
Impact Too early to say, but the method has the potential to reduce animal use in evaluating the cross-protective efficacy of vaccines or treatments as it enables many strains to be tested at once in a single animal rather than in separate groups that each receive a single strain. 
 
Description Bovine TB antibody collaboration 
Organisation University of California, Davis
Country United States 
Sector Academic/University 
PI Contribution Development of a bovine TB serological assay
Collaborator Contribution Supplement of beads and proteins and samples
Impact Not appliable
Start Year 2016
 
Description Collaboration with AB Vista 
Organisation AB Vista
Country United Kingdom 
Sector Private 
PI Contribution We are researching the activity of ovodefensins, naturally-occurring egg peptides with antimicrobial properties. With BBSRC LINK funding we are exploring the activity of diverse ovodefensins from multiple avian species, dissecting their structure and mode of action, and exploring their capacity to act as growth promoters and novel therapeutics.
Collaborator Contribution AB Vista have made a substantial cash contribution to the LINK project (c. £460k) and also provide access to natural populations of broilers for feed trials using diets supplemented (or not) with Trichoderma-expressed ovodefensins. They also support analysis of the impact of such diets on intestinal microbiota and metabolites.
Impact Commercially sensitive and to be disclosed following scrutiny for Intellectual Property.
Start Year 2012
 
Description Collaboration with Kansas State University 
Organisation Kansas State University
Country United States 
Sector Academic/University 
PI Contribution Kansas State University are partners in this BBSRC US-UK Partnering Award related to Salmonella and E. coli infections in food-producing animals.
Collaborator Contribution Sharing of expertise & materials.
Impact None yet from this specific partner.
Start Year 2014
 
Description Collaboration with Mahidol University 
Organisation Mahidol University
Department Department of Immunology
Country Thailand 
Sector Academic/University 
PI Contribution We collaborated with Professor Sunee Korbsrisate, including co-supervision of a Thai PhD student (Chayada Sitthidet) funded by the Royal Golden Jubilee scheme. Miss Sitthidet spent 9 months working in our laboratory, and contributed to joint research linked to the project on the basis of actin-based motility of Burkholderia species. This productive collaboration has led to other papers not directly liked to the project on Type III secretion, cell fusion mediated by Burkholderia, the induction of neutrophil extracellular traps by B. pseudomallei and the role of macroautophagy in control of the pathogen.
Collaborator Contribution Sharing of expertise, ideas and materials. Joint students.
Impact Publications related to the molecular basis of virulence of Burkholderia species.
 
Description Collaboration with Professor Dave Kelly, University of Sheffield 
Organisation University of Sheffield
Country United Kingdom 
Sector Academic/University 
PI Contribution This is a joint project led by Professor Dave Kelly at the University of Sheffield. Our component involved testing the ability of Campylobacter mutant strains lacking specific genes to colonise the intestines of chickens relative to the parent strain. Additionally, we established a Galleria mellonella 3R model to evaluate virulence of the strains.
Collaborator Contribution Provision of strains & expertise.
Impact Phenotypes for a series of mutant strains lacking specific genes, singly and in combinations, from chicken and Galleria models.
Start Year 2012
 
Description Collaboration with Professor Gad Frankel, Imperial College London. 
Organisation Imperial College London
Department Department of Bioengineering
Country United Kingdom 
Sector Academic/University 
PI Contribution This was a joint project, where Prof. Frankel was the lead Principal Investigator. Our component was to evaluate the phenotype of an espZ mutant of E. coli O157 in cattle relative to the isogenic parent strain.
Collaborator Contribution Provision of strains for testing in cattle.
Impact We anticipate that the data arising from our in vivo studies with the E. coli O157 espZ mutant will be included in a future publication.
Start Year 2011
 
Description Collaboration with Public Health England 
Organisation Public Health England
Country United Kingdom 
Sector Public 
PI Contribution Provision of animal and human STEC for sequencing, working with PHE to analyse strain phylogeny and epidemiology. We have contributed through further analysis of long read strain sequences to understand changes in strains that occur during outbreaks. We have co-upervised 2 PhD students on STEC bioinformatics projects.
Collaborator Contribution Reduced rate sequencing of STEC, analysis of data, provision of metadata. Co-publication
Impact Publications as in main list
Start Year 2013
 
Description Collaboration with Texas Tech University 
Organisation Texas Tech University
Country United States 
Sector Academic/University 
PI Contribution Partner in this BBSRC US-UK Partnering Award related to Salmonella and E. coli infections in food-producing animals.
Collaborator Contribution We hosted a visiting postdoctoral research fellow (Marie Bugarel from TTU) in 2015 and provided training in methods to study the basis of Salmonella virulence (inc. mutagenesis, cell-based assays & in vivo models). Drs Bugarel and Loneragan were co-authors on our manuscript describing the use of massively-parallel sequencing of polymorphic alleles to track the fate of Salmonella enterica serovars following inoculation of cattle.
Impact A manuscript relating to a novel method to follow the fate of Salmonella enterica serovars during mixed infections was published in Applied and Environmental Microbiology in late 2017. This arose, in part, from the collaboration funded by a BBSRC US-UK partnering award (see tools), with resources from BBSRC- and Zoetis-funded project (BB/K015524/1) and core strategic grants to the Roslin Institute awarded in 2012 and 2017.
Start Year 2014
 
Description Collaboration with USDA Nebraska 
Organisation U.S. Department of Agriculture USDA
Country United States 
Sector Public 
PI Contribution Exchange of STEC sequence information. Analysis of PacBio long read sequencing of human and cattle isolates
Collaborator Contribution Exchange of STEC sequence information. Carrying out of PacBio sequencing. Discussion of feedlot trials for E. coli O157 vaccine
Impact Publications are provided in main list
Start Year 2014
 
Description Collaboration with United States Department of Agriculture 
Organisation U.S. Department of Agriculture USDA
Country United States 
Sector Public 
PI Contribution USDA are partners in this BBSRC US-UK Partnering Award related to Salmonella and E. coli infections in food-producing animals. We have shared expertise, ideas & materials. A co-Investigator at the Roslin Institute (Professor John Hopkins) visited USDA researchers to transfer his expertise in surgical cannulation of lymphatic vessels, to allow the team to gain access to Salmonella and immune cells as they migrate from the intestines of cattle.
Collaborator Contribution Shared expertise, ideas & materials.
Impact Not at this stage.
Start Year 2014
 
Description Collaboration with Zoetis 
Organisation Zoetis
Country United States 
Sector Private 
PI Contribution The project was a BBSRC Industrial Partnership Award with Zoetis (formerly Pfizer Animal Health) to understand the role of bacterial and host factors in colonisation of the bovine lymphatic system by Salmonella. We analysed the nature and consequences of Salmonella interactions with immune cells in the gut and lymphatic system of cattle, assigned phenotypes to thousands of Salmonella genes during lymph node colonisation and analysed the relative ability of different Salmonella serotypes to enter and persist in the lymphatic system using a novel strain tracking method. The data aid the design of strategies to control Salmonella in cattle, both to benefit bovine health and reduce the impact of zoonotic infections.
Collaborator Contribution Zoetis provided $250 toward project costs and also hosted meetings of a Salmonella Research Cluster that also involved academics at Texas Tech University, Kansas State University and the US Department of Agriculture. In turn this helped to form the basis of a BBSRC US-UK Partnering Award (BB/L026732/1).
Impact See key findings.
Start Year 2012
 
Description Collaboration with the Quadram Institute 
Organisation Quadram Institute Bioscience
Country United Kingdom 
Sector Academic/University 
PI Contribution This is a joint project with the Quadram Institute, where the lead Principal Investigator is Dr Rob Kingsley. The BBSRC contribution to our component of the project is £123,594. It is envisaged that we will evaluate the virulence of variants of Salmonella enterica serovar Typhimurium in porcine models, both to quantify the magnitude and duration of intestinal colonisation in orally challenged pigs and the ability of strains to induce secretory and inflammatory responses in a porcine surgical model.
Collaborator Contribution The Quadram Institute will select Salmonella strains for testing in vivo, based on analysis of their genome sequences, transcriptomes and the phenotypes of the strains in cell-based assays.
Impact None at this stage. We await strains for testing.
Start Year 2015
 
Description Molecular immunology of sheep paratuberculosis 
Organisation Moredun Research Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Collaborative work has investigated the host response to Mycobacterium avium subspecies paratuberculosis, the causative agent of Johne's disease, to explain the molecular basis for the development of the different pathological forms of the disease. Previous collaborative work with the Moredun Research Institute led to the hypothesis that differential T cell activation was critical for the development of paucibacillary and multibacillary paratuberculosis. Analysis of similar diseases in humans (tuberculosis and leprosy) supported this hypothesis. Consequently, initial studies focussed on the identification of cytokine receptor and transcription factor genes of sheep that, in humans and mice, are known to influence T cell polarization and tuberculosis/leprosy pathology. This was extended to identify the transcript variants of these genes. Assays were developed to allow accurate quantification of these genes in the ileo-caecal lymph node (the primary immune inductive site of paratuberculosis lesions) of pathologically-defined animals. These experiments measured the expression of specific transcript variants; linking IL23 and IL25 receptors, and the GATA3, RORC2 and RORA transcription factors, with paucibacillary and multibacillary disease. These data showed that the two disease forms were not just a result of a simple switch from Th1 to Th2 but that sheep with multibacillary disease had a broad immune dysfunction. To examine this immune dysfunction, we performed Illumina Truseq analysis on these same samples. This showed that paucibacillary and multibacillary disease are different stages of the same process. The inflammatory response of both diseases is an acute phase response (chronic inflammation) and not an acute inflammatory response. Animals with both forms of pathology also show a large increase in the expression of immunoglobulin genes. The major difference between paucibacillary and multibacillary animals is that there is a significant reduction in the expression of most genes associated with T cell function and activation. Perhaps the most surprising result was that all diseased animals showed a large reduction in the expression of transcripts associated with mast cells, and this was supported by subsequent histochemistry.
Collaborator Contribution The Moredun Research Institute provided biological material from diseased sheep. These sheep were clinical cases with naturally-acquired paratuberculosis. They had been culled for clinical reasons and subjected to post-mortem examination, including a full pathological/bacteriological examination. This had been done for more than 100 animals and 18 animals were chosen for the molecular immunology studies. These included animals with defined paucibacillary (tuberculoid) and multibacillary (lepromatous) pathologies. Coolleagues were also fully involved in discussions of the data and also in editing manuscripts.
Impact 1. Nicol, L., A. G. Gossner, C. Watkins, F. Chianini, R. G. Dalziel and J. Hopkins. (2016). Variations in IL-23 and IL-25 receptor gene structure, sequence and expression associated with the two disease forms of sheep paratuberculosis. Veterinary Research 47; 27. PMID: 26861902, doi: 10.1186/s13567-016-0314-4. 2 Nicol, L., H. Wilkie, A. G. Gossner, C. Watkins, R. G. Dalziel and J. Hopkins. (2016). Variations in T cell transcription factor gene structure and expression associated with the two disease forms of sheep paratuberculosis. Veterinary Research 47:83. PMID: 27530627.doi: 10.1186/s13567-016-0368-3. 3. Gossner, A. C. Watkins, F. Chianini and J Hopkins. (2017). Pathways and genes associated with immune dysfunction in sheep paratuberculosis. Scientific Reports (revision under review).
Start Year 2013
 
Description SAC-collaboration 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution Characterization of bacterial strains
Collaborator Contribution Providing of relevant UK bacterial strains
Impact Several publications
Start Year 2013
 
Description Study of M cell immunobiology and their role in mucosally-acquired infections 
Organisation Tohoku University
Department Graduate School of Medicine
Country Japan 
Sector Academic/University 
PI Contribution Dr. Atsushi Kobayashi worked within my research group for 2 years here at The Roslin Institute.
Collaborator Contribution Dr. Dr. Atsushi Kobayashi brought his expertise here for two years and worked as a visiting scientist in my research group.
Impact Several publications: DNA RESEARCH 19, 407-422, (2012); doi:10.1093/dnares/dss022 Mucosal Immunology 5, 216-225; doi: 10.1038/mi.2011.68 Mucosal Immunology 6, 1027-1037; doi:10.1038/mi.2012.141 Mucosal Immunology 6, 666-677; doi:10.1038/mi.2013.30
Start Year 2011
 
Description Study of M cell immunobiology and their role in mucosally-acquired infections (RIKEN) 
Organisation RIKEN
Department RIKEN Center for Integrative Medical Sciences (IMS)
Country Japan 
Sector Hospitals 
PI Contribution We provided the ageing and prion disease pathogenesis mouse models.
Collaborator Contribution Prof. Hiroshi Ohno and his colleagues provided expertise in M cell immunobiology.
Impact Several publications: DNA RESEARCH 19, 407-422, (2012); doi:10.1093/dnares/dss022 Mucosal Immunology 5, 216-225; doi: 10.1038/mi.2011.68 Mucosal Immunology 6, 1027-1037; doi:10.1038/mi.2012.141 Mucosal Immunology 6, 666-677; doi:10.1038/mi.2013.30 Prof. Ohno is also a named collaborator on the following BBSRC grants: BB/J014672/1 BB/M024288/1 and BBSRC Japan Partnering Award
Start Year 2007
 
Description UG collaboration 
Organisation University of Glasgow
Country United Kingdom 
Sector Academic/University 
PI Contribution Research idea development, sourcing of samples and sample preparation
Collaborator Contribution Sequencing of samples
Impact There are no outputs yet.
Start Year 2015
 
Title IMMUNOGENIC OMPOSITIONS CONTAINING ESCHERICHIA COLI H7 FLAGELLA AND METHODS OF USE THEREOF 
Description Immunogenic compositions containing Escherichia coli O157:H7 flagella including fusion proteins and methods using the immunogenic compositions are disclosed. Inducing an immune response in an animal to Escherichia coli O157:H7 flagella will result in prevention of colonization by Escherichia coli O157:H7 in the animal or a reduction in the amount of Escherichia coli O157:H7 infecting the animal. The immune composition will prevent or reduce the attachment of Escherichia coli O157:H7 to cells within the animal. 
IP Reference WO2009050474 
Protection Patent granted
Year Protection Granted 2015
Licensed No
Impact A commercial partner has supported further research due to the IP and still working to achieve wider scale commercialisation
 
Description Annual Roslin Institute Open Doors Day 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The annual Roslin Institute Open Doors day was held on 14 October 2017 and was attended by 491 people. It involved 81 members of staff and students and showcased a wide range of research arising from BBSRC strategic investment, including (but not limited to), food safety, influenza, genetic improvement, DNA, imaging and the ethical treatment of animals in research.
Year(s) Of Engagement Activity 2017
 
Description Feature for BBC2 Food Detectives programme 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Professor Stevens took part in a BBC2 Food Detectives programme which featured Campylobacter in chickens. He helped to design a survey of Campylobacter contamination in a sample of fresh chicken obtained from Scottish retailers and interpret the findings. This were close to Food Standards Agency findings, which were broadcast as part of an interview with Prof. Alice Roberts. The interview took place at The Roslin Institute and included a lay description of Campylobacter, the importance of chickens as a reservoir of infection and strategies by which consumers can protect themselves. It also highlighted BBSRC-funded work at Roslin to mitigate the problem based on genetic selection (this project) and vaccines (other BBSRC projects held by Prof. Stevens).
Year(s) Of Engagement Activity 2016
URL http://www.bbc.co.uk/programmes/b077rgd4
 
Description International workshop on Shiga toxin-producing Escherichia coli at The Roslin Institute 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact A two-day international workshop was held at The Roslin Institute on Shiga toxin-producing Escherichia coli (STEC), funded partly by this award (for travel of US collaborators) and partly by the Food Standards Agency of Scotland via a £2m award for collaborative research by a consortium led by Professor Gally. The workshop attracted leading academics working on E. coli O157 and other STEC from the US (Jim Bono, Guy Loneragan, Tom Edrington), Canada (Tim McAllister, Kim Stanford), Germany (Christian Menge), Belgium (Eric Cox), Sweden (Erik Eriksson, Lena-Mari Tamminen, Robert Soderlund) and the United Kingdom (Claire Jenkins, Tim Dallman, Dominic Mellor, Norval Strachan [Chief Scientific Advisor for FSA Scotland]). The workshop shared the latest advances in understanding of the biology of E. coli O157 and other STEC, including epidemiology, genomics, virulence, super-shedding and control strategies.
Year(s) Of Engagement Activity 2017
 
Description Keeping bugs at Bay: a Public Engagement Activity at the Roslin Institute 2014 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact This activity aims to teach people how the immune system fights bugs.
Year(s) Of Engagement Activity 2014
 
Description Keeping bugs at Bay: a Public Engagement Activity at the Royal Highland Show 2015 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact This activity aims to teach people how the immune system fights bugs.
Year(s) Of Engagement Activity 2015
 
Description Media interviews for Nature Ecol evol paper 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Talking to various media including print and radio regarding our Nature Ecology and Evolution publication
Year(s) Of Engagement Activity 2018
 
Description Newspaper article on infection threat from unpasteurised milk products 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The article was written by myself and Dr Deborah Hoyle in response to an outbreak of E.coli O157 for which the epidemiology strongly pointed to the source being an unpasteurised soft cheese from a local producer, the outbreak resulted in the death of a three year old girl. The causative organism was not found in the company's product and the article discussed key issues around unpasteurised and minimally processed food, especially with an increase in artisan food producers, what are the risks and how should they be controlled, or not?
Year(s) Of Engagement Activity 2017
URL http://www.heraldscotland.com/news/health/15565022.Health_warnings_on_unpasteurised_cheese__should_b...
 
Description Open lecture on African trypanosomes in cattle to Royal Society of Biology Scottish Branch 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Dr Liam provided an overview of his research on African trypanosomes in cattle to members of the public and the Royal Society of Biology, who convened for the annual symposium of the RSB Scottish Branch on 14 October 2017 at Roslin. The event coincided with the annual Roslin 'Open Doors' day and featured BBSRC-funded research.
Year(s) Of Engagement Activity 2017
 
Description Pig practitioner workshop - Germany 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Update on Erysipelothrix due to outbreaks in pigs and chickens
Year(s) Of Engagement Activity 2019
 
Description Press release and TV news item 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Press releases and one TV news report about our vaccine research and machine learning prediction of the human health threat of specific E. coli strains
Year(s) Of Engagement Activity 2013,2016
 
Description Press release on the development of a method to simultanoeusly analyse multiple Salmonella strains in animals 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Press release on work arising from this US-UK collaboration to understand the risk to food safety and animal welfare posed by Salmonella enterica serovars in cattle.
Year(s) Of Engagement Activity 2018
URL https://www.ed.ac.uk/roslin/news-events/latest-news/novel-sequencing-study-salmonella-cattle
 
Description Prison visit (Shotts) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Presented a workshop at Shotts prison to a small group working on a prison magazine.
Year(s) Of Engagement Activity 2014
 
Description Public lecture entitled Confronting the Microbial Menace in Our Food'. Professor Mark Stevens 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The inaugural lecture of Professor Mark Stevens was held on 30 October 2017 on his BBSRC-funded research to identify bacterial and host factors influencing the ability of Salmonella, Campylobacter and E. coli to colonise farm animals and cause disease. It was attended by children from local schools, members of the public, students at The Roslin Institute and wider University of Edinburgh and posted online.
Year(s) Of Engagement Activity 2017,2018
URL https://media.ed.ac.uk/media/Inaugural+lectureA+Confronting+the+microbial+menace+in+our+food/1_x5k5e...
 
Description Public lecture on Campylobacter in chickens 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Public talk on 'Chickens and the enemy within' at The Roslin Institute Open Doors Day in 2012. This highlighted the problem of Campylobacter infections in people, the role of poultry as a reservoir, and research at Roslin to control the problem via genetic selection and vaccination in poultry and to understand the molecular basis of virulence of the organism.
Year(s) Of Engagement Activity 2012
 
Description Public lecture on microbes and antimicorbial resistance by Professor David Gally, U3A event Centre for Life, Newcastle 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Professor David Gally delivered a public lecture at the Centre for Life, Newcastle, organised by the University of the Third Age for their Microbes and Antibiotics Day on 9 October 2017. BBSRC-funded research at the Roslin Institute featured in his presentation.
Year(s) Of Engagement Activity 2017
 
Description The Human Body activities at a BBC-sponsored Edinburgh Festival event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Researchers from The Roslin Institute joined colleagues from across the University's College of Medicine and Veterinary Medicine in the grounds of George Heriot's School in central Edinburgh to deliver family-friendly activities about 'The Human Body' on 15 August 2017. The event was part of a series of science-themed activities hosted by the BBC at the Edinburgh Festivals to support BBC Learning's 'Terrific Scientific' campaign, which aims to inspire children and young people to engage with science. Our staff and Ph.D students ran interactive activities about their research on lungs and skin, including inflating and examining real pig lungs, comparing healthy and diseased organs, and a chance for visitors to use their craft skills to make a model of their skin. Other activities at the event included anatomy face and body painting and a chance to see dissections of animal brains and hearts close-up. An estimated 1,400 family visitors were engaged, with great questions about our research and what it's like to work as a scientist.
Year(s) Of Engagement Activity 2017
URL https://www.ed.ac.uk/roslin/community-engagement/public-events/events-archive/the-human-body-bbc-at-...