Microbial Survival in the Food Chain
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
The ‘Microbial Survival in the Food Chain’ theme aims to understand the genetic basis by which three major foodborne pathogens; Campylobacter, Salmonella and Listeria are able to survive and adapt to food chain relevant stresses. We will use a combination of large scale transposon mutant libraries, transcriptomics, Chip-Seq and targeted evolution experiments as well as classical molecular microbiology to identify genes and mutations that allow survival in the food chain. We will further define the genotype-phenotype linkage by using ‘Genome Scale Metabolic Reconstruction’ models which will help identify the key pathways involved in survival.
We have been and will continue to refine transposon mutagenesis techniques to allow all genes in a genome to be assayed for impacts on any particular stress – our enhanced TraDIS method includes outward facing, inducible promoters allowing the impact of over and under-expression of essential genes on fitness to be assayed for the first time. This approach will be applied to all three pathogens of interest.
The ability of strains to survive in a range of food chain relevant stresses including different temperatures, desiccation, acid stress, salt stress, nitrite stress, biocides will be investigated as well as biofilm formation on relevant surfaces (including organic and inorganic).
We have developed a biofilm evolution model which will allow us to investigate biofilm specific pathways of adaptation to stresses which will reveal context specific genes involved in adaptation.
We will use both well understood reference strains and epidemiologically relevant representative isolates (decided in conjunction with work in theme 1 of this ISP) to ensure data is as applicable as possible to real-world scenarios.
We have been and will continue to refine transposon mutagenesis techniques to allow all genes in a genome to be assayed for impacts on any particular stress – our enhanced TraDIS method includes outward facing, inducible promoters allowing the impact of over and under-expression of essential genes on fitness to be assayed for the first time. This approach will be applied to all three pathogens of interest.
The ability of strains to survive in a range of food chain relevant stresses including different temperatures, desiccation, acid stress, salt stress, nitrite stress, biocides will be investigated as well as biofilm formation on relevant surfaces (including organic and inorganic).
We have developed a biofilm evolution model which will allow us to investigate biofilm specific pathways of adaptation to stresses which will reveal context specific genes involved in adaptation.
We will use both well understood reference strains and epidemiologically relevant representative isolates (decided in conjunction with work in theme 1 of this ISP) to ensure data is as applicable as possible to real-world scenarios.
Planned Impact
unavailable
Organisations
- QUADRAM INSTITUTE BIOSCIENCE (Lead Research Organisation)
- Unilever (Collaboration)
- UNIVERSITY COLLEGE LONDON (Collaboration)
- NORFOLK AND NORWICH UNIVERSITY HOSPITAL (Collaboration)
- University of Sydney (Collaboration)
- AB Agri Ltd (Collaboration)
- Nestlé (Global) (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- Public Health Agency of Canada (Collaboration)
- Procter & Gamble (Collaboration)
- Nationwide Children's Hospital (Collaboration)
- UNIVERSITY OF BIRMINGHAM (Collaboration)
- Child Health Research Foundation (Collaboration)
- Utrecht University (Collaboration)
- Chilled Food Association (Collaboration)
- UK HEALTH SECURITY AGENCY (Collaboration)
- PUBLIC HEALTH ENGLAND (Collaboration)
- SRI International (inc) (Collaboration)
- GAMA Healthcare (Collaboration)
- COMSATS Institute of Information Technology (Collaboration)
- Norfolk and Norwich University Hospitals NHS Foundation Trust (Collaboration)
- OXFORD BROOKES UNIVERSITY (Collaboration)
- Government of Canada (Collaboration)
- University of Ljubljana (Collaboration)
- South China Agricultural University (Collaboration)
- Edith Cowan University (Collaboration)
- George Washington University (Collaboration)
- GlaxoSmithKline (GSK) (Collaboration)
- UNIVERSITY OF ESSEX (Collaboration)
- Government Medical College Nagpur (Collaboration)
Publications
Abd El Ghany M
(2021)
Functional analysis of colonization factor antigen I positive enterotoxigenic Escherichia coli identifies genes implicated in survival in water and host colonization.
in Microbial genomics
Aleksandrowicz A
(2024)
FdeC expression regulates motility and adhesion of the avian pathogenic Escherichia coli strain IMT5155.
in Veterinary research
Baker D
(2020)
CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes
Baker DJ
(2021)
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.
in Genome medicine
Bawn M
(2022)
Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella.
in Microbial genomics
Bloomfield SJ
(2023)
Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK.
in Microbial genomics
Bloomfield SJ
(2023)
Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics.
in Food microbiology
| Title | Video: TraDIS - Transposon Directed Insertion Site Sequencing |
| Description | This video illustrates the TraDIS method developed. Using TraDIS-Xpress the genes involved in bacterial growth in diverse conditions are quickly identified and can be compared. This vast amount of genomic information provides us with a more fuller understanding of the biology of the bacterial cell which in turn will help us identify new ways to combat pathogenic bacteria, encourage beneficial commensal bacteria or optimise bacteria used in medical or industrial processes. TraDIS-Xpress is just one of a number of very powerful cutting-edge technologies being developed at the Quadram Institute These technologies are promising some very exciting times ahead for our investigation of the human intestinal microbiome human health and food safety. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2020 |
| Impact | No impacts yet due to the video only being released at the point of report submission. In the first week of publishing the video, it had 56 views. |
| URL | https://vimeo.com/390489066 |
| Description | This project set out to understand how three important bacteria which cause food borne disease, Salmonella, Listeria and Campylobacter survive and adapt to stresses in the food chain. We aimed to develop models to study bacterial behaviour in biofilms (communities of bacteria adhered to a surface) which will mimic real world conditions. We also aimed to expand genomic methods to allow us to identify which genes are important in stress (using transposon mutagenesis, 'TraDIS') and to understand how these genes function in a cell by making genome scale metabolic models. We have achieved all our main objectives and generated significant new information, developed, and validated new tools as well as opening new research questions and avenues and securing uplift funding. Significant knowledge generated 1. Biofilm evolution and biology. Most bacteria survive in adhered groups or communities we call biofilms. However, little is understood about how bacteria within biofilms behave and how they respond to stress. We have established a model to study this in the laboratory and studied how a range of food chain relevant conditions (temperature, pH, preservatives) impact evolution of Salmonella biofilms and documented collateral resistances and sensitivities which emerge under stress. We found that development of bigger, 'stickier' biofilms are not necessarily protected from antimicrobial stress, that biofilms are highly sensitive to exposure to low concentrations of antimicrobials, and that selection of resistance often carries a large cost to other phenotypes (biofilm formation and virulence). This alters current understanding of biofilm biology and how AMR is selected. We published a series of papers describing this work with Salmonella and have expanded the model to work with Listeria to study responses to biocides used in food production (with UKHSA) and Campylobacter as well as other species in collaboration with various partners (beyond the remit of this project). The biofilm evolution model has been the basis for new collaborations in multiple joint PhD projects including government agencies or industry partners. 2. Predicting evolution in the real world. We have linked laboratory results with real world epidemiological data about genotypes selected - we have compared genes under selection in Salmonella in the laboratory with isolates sequenced globally and we link our data which lets us know what a mutation does to how these changes are important in the real world. We have also studied population structures of Campylobacter using long read sequencing methods we have established and explored how many different types of Campylobacter are present within food and people during infection. This work helps understand which strains are successful in transiting from food to fork and has been the basis for multiple publications. 3. Understanding risk from different types of bacteria. We have studied how different variants of Salmonella are able to survive stresses in the food chain and found that different serovars have significantly different abilities to survive heat, pH and desiccation. This work has been published and is important to developing risk assessments as not all serotypes of Salmonella are equal. 4. Campylobacter regulation. We have studied the role of two novel campylobacter genes in survival on surfaces and to oxidative shocks in a range of strains - this explains why some strains are better adapted to survive in the food chain than others. We have also made multiple transposon mutant libraries in Campylobacter which has allowed us to define the core set of genes needed by all strains as well as identifying those which give different properties to different strains. We have defined the metabolic requirements for Campylobacter in different growth conditions which, with our genomic information has allowed us to publish genome scale metabolic models which allow us to explain how gene content relates into phenotypes. New research areas As well as addressing our core objectives we have opened new areas of research 1. We have expanded work into Pseudomonads and begun a programme studying how these organisms cause spoilage of food. We have shown how biofilms formed by organisms from this group take up DNA from their environment and use twitching motility to colonise new surfaces. 2. We are studying how bacteria respond differently to stress in the food chain when in different lifestyles (e.g. cell wall deficient, in a biofilm, in different rates of growth). 3. We have established mixed community models of biofilms to understand how consortia differ in their responses to stress compared to monospecies to mimic real world conditions in a more realistic manner. 4. We have studied the potential for various plant produced molecules to act as replacement food preservatives or antimicrobials to replace current toxic chemicals 5. We have demonstrated that different species of amoebae are important for the survival and pre-adaptation of virulence of Campylobacter and represent a novel model to study Campylobacter-host interactions. Advances in resources, methods, and skills To deliver our research agenda we have produced important new technical capacities 1. Functional genomics. We developed an improved method to study the role of all genes in a bacterium in stress survival (TraDIS-Xpress) which relies on making large libraries of transposon mutants and studying which are better or worse at surviving in a condition of interest. We have made TraDIS mutant libraries in key foodborne pathogens for this project (E. coli, Salmonella, Campylobacter), as well as developing and improving a competency protocol to transform Listeria (a gram-positive microbe) and then screening our extensive panel of Listeria strains to identify strains suitable for mutagenesis. We have extended the approach to other species (Acinetobacter, Pseudomonas, Bilophila, various Staphylococci and Streptococci) which has allowed cross-fertilisation of the technology into other projects and applications including microbiome work. This has resulted in numerous publications industry funding and partnerships, and we have submitted patent applications with more in preparation and have also completed market research with a view to launching a spin out company. We have established QIB as a hub of expertise in this technology and academic collaborations with groups around the world have resulted. This platform has also been the basis for us partnering on two successful UKRI engineering biology awards (a Hub and a Mission award), in both TraDIS will be used across the consortia as a central technology platform. 2. We have developed CRISPR gene silencing for Campylobacter which is an important technical achievement as genomics in this organism is not simple, now allowing us to selectively silence genes and study the resulting impacts 3. We have established a hub of imaging expertise supported by uplift funding which now allows state of the art imaging of microbial behaviour in food chain relevant conditions 4. We have made genome scale metabolic models that allow us to understand how bacteria work and which genes are needed for different processes in a cell or community. This gives us a greatly improved ability to explain interactions between species and is now being applied to mixed community models which represent the food chain better 5. We have developed bacterial single cell sequencing methods and used these to track the evolution of AMR within populations of Salmonella at unprecedented detail in a collaboration with the Earlham Institute |
| Exploitation Route | Understanding how Campylobacter, Listeria and Salmonella survive in the food chain and respond to common preservative conditions will help us target where we could develop interventions to prevent contamination of food and subsequent infection. Understanding how biofilms evolve will help inform eradication and control strategies and inform risk of development of AMR. The TraDIS-Xpress platform has been widely used to identify numerous potential targets or optimise bacterial strains in a wide range of applications. |
| Sectors | Agriculture Food and Drink Energy Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| Description | Our work has had multiple impacts beyond the traditional academic routes, examples of these and the different sectors impacted are given below. Informing policy and public services We provided expert advice to the UK government for reviews of the UK AMR strategy on two separate occasions with multiple group leaders providing evidence to parliament as well as background material. We have also provided advice to the WHO/FAO on multiple occasions including joining expert working groups producing guidance documents and informing policy on the impact of disinfection on AMR and Campylobacter in the food chain. As well as providing expert evidence one of our GLs has been appointed to the FSA Advisory Committee for the Microbial Safety of Food ensuring consistent input from our science into this group. Our work was cited by the European Food Safety Authority as identifying a knowledge gap in the role of biofilms in AMR in the food chain as well as providing new methods to help study this. We have also provided advice to UK government about UK research strategy going forward. These activities helped ensure our scientific opinion was provided as policies are being formulated. Impacts on health Our publications with Salmonella Typhi produced data which helped shape improved guidelines for treatment of infection Our technical expertise and informatics capabilities were rapidly employed to help the UK response to SARS COV2 allowing QIB to sequence over 60,000 genomes which directly informed local and national health policy. We also proactively engaged with partners in Pakistan, Zimbabwe and the Lebanon and helped their public health responses via either generating data or providing training. Contribution to the knowledge economy We have generated important new intellectual property and methodologies which have resulted in the filing of three patents around some our work with novel oligosaccharides and functional genomics. This has helped underpin one spin out company (Arkvax) with another in progress. These new technological developments have also allowed us to attract significant industrial partnerships and funding into the institute demonstrating the importance of this work beyond academia. We have made significant efforts to engage with industry to ensure our work aligns with real-world problems, and to provide a route to translation from our science. In the ISP period we have initiated over 10 new projects with industry. These include iCASE partnerships, joint funding from Innovate UK and significant direct contract funding. The partner companies range from SMEs to large household name multinationals (e.g. Unilever, Nestle, DuPont, Proctor and Gamble). Projects relate to our expertise in genomics and biofilms being used to help industry develop new antimicrobial products, new DNA extraction methods, reduce antibiotic use in animal husbandry and ensure project safety. To further engagement and delivery of impact of our science into the food industry QIB GL's have initiated the BBSRC and FSA-funded UK Food Safety Research Network (BB/X002985/1). This has positioned QIB in a strong leadership role to broker cross-disciplinary research projects between food businesses, academics, and government departments, with the goal of improving the safety of UK food supplies. This network leadership role has placed QIB as a highly visible research convenor with food industry and government partners and has led to multiple speaking engagements as invited keynote or expert panellist at food industry symposiums. Engagement with the public We have extensively engaged with the public with showcases of our research and how it relates to people's everyday lives being made at major science festivals as well as delivering webinars to a global audience, producing two podcast series, and providing expert commentary for numerous pieces in the media and advice to documentary makers. We have completed over 80 separate engagement activities during this ISP. Global reach We have demonstrated global reach from our research with new research partnerships initiated with academics or governmental bodies in North and South America, Europe, Asia, and Australasia. Activities include global surveillance of AMR to guide policy (e.g. collaborations with Brazil, Zimbabwe), and work to maintain population health (e.g. work studying impacts of Campylobacter in Bangladesh or Typhoid in the pacific islands). We have visited multiple nations to engage with partners, an example being our securing funding for and running a workshop on AMR in the food chain hosted in China where we took a delegation of relevant researchers from QIB and the UK. Nucleation of new research areas In the current ISP we have opened up new research areas, which include the impact of spoilage on food waste (where we have supported successful fellowship application), the role of microplastics as vectors of food borne pathogens, the impact of AI on AMR and study of how genome rearrangement impacts bacterial persistence. We expect all these areas to progress in our future work defining new fields of activity important to society. |
| First Year Of Impact | 2019 |
| Sector | Agriculture, Food and Drink,Chemicals,Healthcare,Government, Democracy and Justice,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Societal Economic Policy & public services |
| Description | Appointed WHO/FAO expert advisor about foodborne antimicrobial resistance |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Description | BBSRC AI network proposal development workshop |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.ukri.org/events/help-build-an-ai-in-the-biosciences-network-proposal-workshop/ |
| Description | Communicable Disease Research Centre Reference Group, Fiji |
| Geographic Reach | Australia |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Links through this committee have led to the appointment of external lecturers at FNU. |
| URL | https://www.fnu.ac.fj/college-of-medicine/research-cmnhs/research-centres/cdrc/ |
| Description | EU Report (Refresh) on the valorisation of putrescible waste |
| Geographic Reach | Europe |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://eu-refresh.org/viability-bio-based-chemicals-food-waste |
| Description | Engagement with Canadian Government - knowledge exchange on Campylobacter jejuni fluoroquinolone resistance in agriculture |
| Geographic Reach | North America |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | Evidence for EU EFSA opinion piece |
| Geographic Reach | Europe |
| Policy Influence Type | Citation in systematic reviews |
| URL | https://efsa.onlinelibrary.wiley.com/doi/full/10.2903/j.efsa.2021.6651 |
| Description | Evidence for UK AMR review |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Guideline Title | British infection association guidelines for the diagnosis and management of enteric fever in England |
| Description | Evidence for updating clinical guidelines on enteric fever |
| Geographic Reach | National |
| Policy Influence Type | Citation in clinical guidelines |
| Description | Expert Advice to Food Standards Scotland |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | Expert Advice to UK Government (FSA) |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | Expert Advice to UK Government (FSA) |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | The ACMSF committee members all have a part in influencing the FSA on using scientific evidence and expert advice on matters pertaining to foodborne pathogens. This in turn influences regulatory bodies and works towards effective solutions for societal and public health challenges. The influence also has impact on effectiveness of public service delivery where applicable to topics raised to the ACMSF members |
| Description | Feedback to WHO Guidance document draft for microbiological risk assessment |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Joint Expert Meeting for Microbial Risk Assessment (JEMRA)- Assessment of pre- and post- harvest interventions for Campylobacter in chicken production |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | MRC workshop: Embedding Diversity in Research Design |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Part of WHO(FAO) expert panel assessing research needs re biocides and AMR in the foodchain |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Description | Reform Roundtable: Big Data in Health Transformation |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://reform.uk/events/role-big-data-transforming-nhs-practical-steps-forward |
| Description | Written response to Governments 5 year AMR plan |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| URL | https://publications.parliament.uk/pa/cm201719/cmselect/cmhealth/962/96202.htm |
| Description | BBSRC DTP Studentship (mixed community evolution in biofilms) |
| Amount | £96,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2020 |
| End | 09/2024 |
| Description | BBSRC IAA |
| Amount | £10,000 (GBP) |
| Funding ID | BB/S506679/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2019 |
| End | 04/2019 |
| Description | BBSRC IAA |
| Amount | £16,569 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 03/2022 |
| Description | BBSRC IAA The Quadram Institute |
| Amount | £300,000 (GBP) |
| Funding ID | BB/S506679/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2022 |
| Description | BBSRC IGP |
| Amount | £1,483,784 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2020 |
| End | 03/2021 |
| Description | Biofilm Inhibition and Pathogen Control in Food Production Environments |
| Amount | £56,878 (GBP) |
| Funding ID | 05POC24-07 |
| Organisation | National Biofilms Innovation Centre |
| Sector | Private |
| Start | 01/2025 |
| End | 01/2026 |
| Description | Copper-induced microbiota shifts and its effect on pig-gut colonisation by sil and sopE encoding Salmonella |
| Amount | £490,482 (GBP) |
| Funding ID | BB/W003155/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2022 |
| End | 12/2025 |
| Description | Development of single-cell sequencing technology for microbial populations |
| Amount | £149,610 (GBP) |
| Funding ID | BB/R022526/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 06/2019 |
| Description | Engineering biology for critical metal recovery from industrial wastestreams |
| Amount | £1,838,843 (GBP) |
| Funding ID | BB/Y008448/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2024 |
| End | 01/2026 |
| Description | Environmental niches of Salmonella Typhi |
| Amount | $100,000 (USD) |
| Funding ID | OPP1217177 |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 11/2019 |
| End | 04/2022 |
| Description | Family Larsson- Rosenquist Foundation (FLRF) Trainee Expansion program grant to Anuradha Ravi |
| Amount | $9,812 (USD) |
| Organisation | Family Larsson-Rosenquist Foundation |
| Sector | Charity/Non Profit |
| Country | Switzerland |
| Start | 05/2019 |
| End | 08/2019 |
| Description | Gates Grant |
| Amount | $1,200,000 (USD) |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 01/2019 |
| End | 12/2021 |
| Description | Genomic surveillance of SARS-CoV-2 in Pakistan |
| Amount | £10,000 (GBP) |
| Funding ID | BB/S506679/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2021 |
| End | 07/2021 |
| Description | IAA |
| Amount | £10,000 (GBP) |
| Funding ID | BB/S506679/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 03/2022 |
| Description | MRC DART iCASE Sship |
| Amount | £100,028 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 09/2021 |
| Description | Medical Research Council AMR-DART DTP studentship |
| Amount | £96,000 (GBP) |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2020 |
| End | 09/2024 |
| Description | National Biofilm Innovation Centre - Proof of Concept studies |
| Amount | £50,000 (GBP) |
| Funding ID | BLUE |
| Organisation | National Biofilms Innovation Centre |
| Sector | Private |
| Start | 03/2019 |
| End | 08/2019 |
| Description | Newton Fund Researcher Links Workshop Grant |
| Amount | £24,000 (GBP) |
| Funding ID | 2018-RLWK10-10731 |
| Organisation | British Council |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 11/2018 |
| End | 12/2019 |
| Description | Novel gene editing CRISPR Guided Vector technology to replace antibiotic use in farm animal production |
| Amount | £1,045,297 (GBP) |
| Funding ID | 104289 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2018 |
| End | 02/2020 |
| Description | Reducing the health & economic burden of Campylobacter using a live vaccine |
| Amount | $600,000 (AUD) |
| Funding ID | LP190100114 |
| Organisation | Australian Research Council |
| Sector | Public |
| Country | Australia |
| Start | 09/2021 |
| End | 10/2024 |
| Description | S. Typhi and protozoa in contaminated water in Zimbabwe |
| Amount | $100,000 (USD) |
| Funding ID | OPP1217121 |
| Organisation | Bill and Melinda Gates Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 11/2019 |
| End | 04/2021 |
| Description | Testing poultry vaccines |
| Amount | £54,000 (GBP) |
| Organisation | Bioproperties Ltd |
| Sector | Private |
| Country | Australia |
| Start | 02/2019 |
| End | 02/2020 |
| Description | The GCRF One Health Poultry HUB |
| Amount | £20,000,000 (GBP) |
| Organisation | Research Councils UK (RCUK) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2019 |
| End | 02/2024 |
| Title | Biofilm evolution model |
| Description | Development of a biofilm evolution model to study bacterial responses to stress in biofilms |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Collaborative research project with Procter and Gamble Submitted grant applications Hosted training events for collaborating groups to allow transfer of the technology |
| Title | Mixed community biofilm model |
| Description | Generation and validation of a mixed community biofilm model incorporating stable levels of multiple relevant organisms from the food chain. Allowing evolution of specific pathogens to be studied in community context |
| Type Of Material | Model of mechanisms or symptoms - in vitro |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | Allows impact of bystander organisms and interactions between multiple species to be modelled to follow evolution in a more realistic context |
| Title | NanoTraDIS |
| Description | Application of long read sequencing for identification of insert sites in transposon mutant libraries |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | New collaboration with Koch Institute |
| Title | TraDIS+ |
| Description | Development of improved approaches for transposon mutagenesis in bacteria |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | Discussion with major multinational companies about exploiting the technology platform |
| Title | Video for remote training (MinION setup and sequencing) |
| Description | Due to restrictions on international travel, we were unable to host visiting scientists for training. We filmed, edited and captioned this video to be used alongside a written SOP in order to provide remote training to individuals based internationally. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | This video enabled us to provide remote training to collaborators based in Fiji and France. With the current restrictions on international travel, we considered this the best opportunity to provide visual cues to the techniques being set up for the first time. Other researchers have been given access to this training resource to support local training. |
| URL | https://youtu.be/1rR2nPU0k0o |
| Title | Video for remote training (library prep) |
| Description | Due to restrictions on international travel, we were unable to host visiting scientists for training. We filmed, edited and captioned this video to be used alongside a written SOP in order to provide remote training to individuals based internationally. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | This video enabled us to provide remote training to collaborators based in Fiji and France. With the current restrictions on international travel, we considered this the best opportunity to provide visual cues to the techniques being set up for the first time. Other researchers have been given access to this training resource to support local training. |
| URL | https://youtu.be/ZaAhUWNcq5w |
| Title | Additional file 1 of CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes |
| Description | Additional file 1: Table S1. Barcode sequences. Table S2a. Sample metrics for the Routine dataset. Table S2b. Sample metrics for the Rapid Response dataset. Table S3. The differences between the consensus genomes of each sequencing method, for all samples with differences reported. Table S4. Reagent costs for the three methods when sequencing 96 samples (CoronaHiT-ONT and ARTIC LoCost) or 384 samples (CoronaHiT-Illumina). Table S5. Sample identifiers and accession numbers. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_CoronaHiT_high-throughput_... |
| Title | Additional file 1 of CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes |
| Description | Additional file 1: Table S1. Barcode sequences. Table S2a. Sample metrics for the Routine dataset. Table S2b. Sample metrics for the Rapid Response dataset. Table S3. The differences between the consensus genomes of each sequencing method, for all samples with differences reported. Table S4. Reagent costs for the three methods when sequencing 96 samples (CoronaHiT-ONT and ARTIC LoCost) or 384 samples (CoronaHiT-Illumina). Table S5. Sample identifiers and accession numbers. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_CoronaHiT_high-throughput_... |
| Title | Conditionally essential genes in the microbiome |
| Description | A series of experiments were completed to identify genes in Salmonella and E. coli which become conditionally essential in a microbiome model |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Novel genes identified are being explored for protection as IP |
| Title | Responses of Salmonella biofilms to stress |
| Description | A series of biofilm evolution experiments have been completed where Salmonella biofilms were exposed to various stress conditions including pH, salt, temperature, preservatives and antibiotics. Mutants were phenotyped and sequenced after exposure to allow analysis of impact of stress on phenotype and genotype |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | We have had numerous requests to learn about the model system leading to new collaborations |
| Title | TraDIS antibiotic response data set |
| Description | A series of experiments to determine the genes involved in response of E. coli to antibiotics used to exemplify our TraDIS-Xpress methodology. Responses included to ciprofloxacin, coumermycin, tetracycline, chloramphenicol, gentamicin, azithromycin, tigecycline, fosfomycin, aztreonam, cefuroxime, meropenem, piperacillin and colisin |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | A series of papers and collaborations with multiple groups |
| Title | TraDIS biofilm formation datasets |
| Description | A series of experiments were completed to identify the genes needed for Salmonella and E. coli to form biofilms over time and to identify similarities and differences between the species |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Novel genes have been the basis for successful applications for follow on PhD student funding |
| Title | TraDIS heat and pH response data set |
| Description | A series of experiments were completed to identify genes under selective pressure in response to pH, and temperature in E. coli and Salmonella |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Papers are in final preparation and discussions have started with industrial food producers about the implications of the work |
| Title | TraDIS preservative response data set |
| Description | A series of experiments have been completed studying the response of E. coli and Salmonella to common food preservatives and other biocides using TraDIS libraries |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Data is the basis for two publications and has been used in conversations with industry to inform how best to control food borne pathogens and relative efficacy of different active agents as well as mechanisms of action |
| Title | Use of hybrid assembly to characterise Campylobacter genomes |
| Description | This bioinformatic technique was used for approx 800 genomes from my research collection of Campylobacter genomes in support of genomic characterisation |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | This dataset is the base for further method development to understand population diversity of Campylobacter using novel techniques |
| Title | metabolic model for Campylobacter jejuni M1 |
| Description | A mathematical model that describes the metabolic capability of of Campylobacter jejuni M1. This was used to design a defined medium for the growth of Campylobacter jejuni M1 in strictly controlled conditions for scientific research into the ability of C. jejuni to survive in the food chain Published in https://www.frontiersin.org/articles/10.3389/fmicb.2020.01072/full |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Too early to report |
| URL | https://data.quadram.ac.uk/dipali.singh/CJM1cam_DB |
| Description | Ab Agri |
| Organisation | AB Agri Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Project to assess efficacy of different biocidal formulation in eradicating Salmonella from wheat and whole meal animal feeds |
| Collaborator Contribution | Provision of materials, strains from the relevant environment and biocides to test |
| Impact | Information for the industry about best practices, enhanced understanding of the capacity of Salmonella to form biofilms on feed and additives |
| Start Year | 2019 |
| Description | Bioinformatic pipelines for Campylobacter population structure |
| Organisation | Utrecht University |
| Department | Institute for Risk Assessment Sciences |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | This partnership is a shared interest in the population structure and strain level difference in Campylobacter. We have contributed >1,000 genomes for shared analysis and testing of novel bioinformatic pipeline approaches. |
| Collaborator Contribution | Our Risk Assessment Institute, Utrecht University |
| Impact | Outcomes thus far have been the appointment of a Master's student (Utrecht University) to the project and monthly progress meetings |
| Start Year | 2022 |
| Description | CFA - listeria control |
| Organisation | Chilled Food Association |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Project to assess the efficacy of blue light in the control of Listeria biofilms in a chilled food processing environment - we provide expertise and run and analyse experiments and genetic analysis of mutants recovered after exposure |
| Collaborator Contribution | Provision of relevant strains from factory context, materials from factory environment for testing, sourcing of blue light source for testing |
| Impact | Development of test blue light system |
| Start Year | 2019 |
| Description | Canada - UK Coalition on Listeria Genomics |
| Organisation | Government of Canada |
| Department | Canadian Food Inspection Agency (CFIA) |
| Country | Canada |
| Sector | Public |
| PI Contribution | We have assembled a multidisciplinary coalition of Canadian and UK experts that will seek to refine informatic tools and share ideas to address specific gaps on how Listeria genome and metagenome data are analysed. Our partnership will focus on finding and understanding the microbiota and genetic traits associated with biocide resistance, the formation of biofilms, and the transmission of Listeria through the food chain. The ideas and tools developed in this project will be presented and discussed with food safety stakeholders to aid in their impact. As co-chair of the coalition, we have organised and hosted a two-day project launch meeting that was held virtually between project participants. We devised a pre-event survey to identify broad research themes of interest, have synthesised the results of that survey for discussion during the launch meeting, and we have subsequently prepared and distributed summaries of that launch meeting. |
| Collaborator Contribution | Project partners have attended and participated in our November 2021 virtual launch meeting and during the pre-event activities to identify research themes that promote the application of genomic sciences towards food safety challenges. The project co-chair from Canada and an early career researcher from their team co-developed: a pre-event survey to identify broad research themes of interest, have synthesised the results of that survey for discussion during the launch meeting, and have subsequently prepared and distributed summaries of that launch meeting. |
| Impact | Disciplines: microbiology, public health, bioinformatics, food safety, epidemiology Outputs: project launch meeting summary of proposed research themes that promote the application of genomic sciences towards food safety challenges. |
| Start Year | 2021 |
| Description | Canada - UK Coalition on Listeria Genomics |
| Organisation | Government of Canada |
| Department | Health Canada |
| Country | Canada |
| Sector | Public |
| PI Contribution | We have assembled a multidisciplinary coalition of Canadian and UK experts that will seek to refine informatic tools and share ideas to address specific gaps on how Listeria genome and metagenome data are analysed. Our partnership will focus on finding and understanding the microbiota and genetic traits associated with biocide resistance, the formation of biofilms, and the transmission of Listeria through the food chain. The ideas and tools developed in this project will be presented and discussed with food safety stakeholders to aid in their impact. As co-chair of the coalition, we have organised and hosted a two-day project launch meeting that was held virtually between project participants. We devised a pre-event survey to identify broad research themes of interest, have synthesised the results of that survey for discussion during the launch meeting, and we have subsequently prepared and distributed summaries of that launch meeting. |
| Collaborator Contribution | Project partners have attended and participated in our November 2021 virtual launch meeting and during the pre-event activities to identify research themes that promote the application of genomic sciences towards food safety challenges. The project co-chair from Canada and an early career researcher from their team co-developed: a pre-event survey to identify broad research themes of interest, have synthesised the results of that survey for discussion during the launch meeting, and have subsequently prepared and distributed summaries of that launch meeting. |
| Impact | Disciplines: microbiology, public health, bioinformatics, food safety, epidemiology Outputs: project launch meeting summary of proposed research themes that promote the application of genomic sciences towards food safety challenges. |
| Start Year | 2021 |
| Description | Canada - UK Coalition on Listeria Genomics |
| Organisation | Public Health Agency of Canada |
| Department | National Microbiology Laboratory (NML) |
| Country | Canada |
| Sector | Public |
| PI Contribution | We have assembled a multidisciplinary coalition of Canadian and UK experts that will seek to refine informatic tools and share ideas to address specific gaps on how Listeria genome and metagenome data are analysed. Our partnership will focus on finding and understanding the microbiota and genetic traits associated with biocide resistance, the formation of biofilms, and the transmission of Listeria through the food chain. The ideas and tools developed in this project will be presented and discussed with food safety stakeholders to aid in their impact. As co-chair of the coalition, we have organised and hosted a two-day project launch meeting that was held virtually between project participants. We devised a pre-event survey to identify broad research themes of interest, have synthesised the results of that survey for discussion during the launch meeting, and we have subsequently prepared and distributed summaries of that launch meeting. |
| Collaborator Contribution | Project partners have attended and participated in our November 2021 virtual launch meeting and during the pre-event activities to identify research themes that promote the application of genomic sciences towards food safety challenges. The project co-chair from Canada and an early career researcher from their team co-developed: a pre-event survey to identify broad research themes of interest, have synthesised the results of that survey for discussion during the launch meeting, and have subsequently prepared and distributed summaries of that launch meeting. |
| Impact | Disciplines: microbiology, public health, bioinformatics, food safety, epidemiology Outputs: project launch meeting summary of proposed research themes that promote the application of genomic sciences towards food safety challenges. |
| Start Year | 2021 |
| Description | Canada - UK Coalition on Listeria Genomics |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | We have assembled a multidisciplinary coalition of Canadian and UK experts that will seek to refine informatic tools and share ideas to address specific gaps on how Listeria genome and metagenome data are analysed. Our partnership will focus on finding and understanding the microbiota and genetic traits associated with biocide resistance, the formation of biofilms, and the transmission of Listeria through the food chain. The ideas and tools developed in this project will be presented and discussed with food safety stakeholders to aid in their impact. As co-chair of the coalition, we have organised and hosted a two-day project launch meeting that was held virtually between project participants. We devised a pre-event survey to identify broad research themes of interest, have synthesised the results of that survey for discussion during the launch meeting, and we have subsequently prepared and distributed summaries of that launch meeting. |
| Collaborator Contribution | Project partners have attended and participated in our November 2021 virtual launch meeting and during the pre-event activities to identify research themes that promote the application of genomic sciences towards food safety challenges. The project co-chair from Canada and an early career researcher from their team co-developed: a pre-event survey to identify broad research themes of interest, have synthesised the results of that survey for discussion during the launch meeting, and have subsequently prepared and distributed summaries of that launch meeting. |
| Impact | Disciplines: microbiology, public health, bioinformatics, food safety, epidemiology Outputs: project launch meeting summary of proposed research themes that promote the application of genomic sciences towards food safety challenges. |
| Start Year | 2021 |
| Description | Capacity building of SARS-CoV-2 sequencing using ONT in Bangladesh |
| Organisation | Child Health Research Foundation |
| Country | Bangladesh |
| Sector | Charity/Non Profit |
| PI Contribution | Knowledge and in-kind contribution was set up as part of an existing collaboration to build laboratory capacity at CHRF in Dhaka, Bangladesh for SARS-CoV-2 sequencing on Oxford Nanopore Technologies using QIB published multiplexing methodology. |
| Collaborator Contribution | Contribution to science and Bangladeshi Ministry of Health by CHRF was made by sequencing and mapping SARS-CoV-2 variants circulating in Bangladesh. |
| Impact | Collaboration is multidisciplinary with the following disciplines involved: -Molecular biologists -Researchers (QIB and CHRF) -Ministry of Health (public health) -Hospital (Bangladesh clinical patient care) -National health surveillance teams (Bangladesh) |
| Start Year | 2020 |
| Description | Collaboration with Amira Roess - Department of Global Health, George Washington University, USA. |
| Organisation | George Washington University |
| Department | Department of Global Health |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | This collaboration led to a successful joint funding application to the Gates Foundation. John Wain from QIB, is a co-investigator on the grant. The QIB team will be building infrastructure within Bangladesh for nanopore sequencing and metagenomics. |
| Collaborator Contribution | This collaboration led to a successful joint funding application to the Gates Foundation. Amira Roess, from GWU, is a principle investigator on the grant. |
| Impact | This collaboration led to a successful grant application to the Gates Foundation. The application was led by Amira Roess (GWU), with partners at QIB (John Wain as the QIB co-investigator and Alison Mather, Justin O'Grady and Andrew Page, as named investigators). The grant title is: A longitudinal, source attribution study of Campylobacter emergence and transmission in rural Bangladesh to inform intervention development. Through this grant we are also part of an international consortium of Gates funded projects |
| Start Year | 2018 |
| Description | Collaboration with Amira Roess - Dept of Global Health, George Washington University |
| Organisation | George Washington University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | This collaboration stems from a successful Gates foundation grant that Amira Roess (George Mason University) is a PI for and John Wain (QIB) a Co-I titled Transmission of Campylobacter in rural Bangladesh. I, as part of the QIB research team aided in building a sequencing laboratory infrastructure fo Oxford Nanopore Technologies sequencing for genomes and metagenomes in Dhaka, Bangladesh. During 2020-2021 we have leveraged that infrastructure to build further capacity within the Dhaka laboratory to sequence SARS-CoV-2. |
| Collaborator Contribution | The collaboration, led by Amira Roess, GMU has progressed to further capacity building in the Bangladesh laboratories. This collaboration is leading to new grant application opportunities and further work on global health. |
| Impact | This collaboration is interdisciplinary with microbiologist, bioinformatiticians, field epidemiologist and molecular biologist working together on assessing the routes of transmission of Campylobacter in rural Bangladesh. |
| Start Year | 2019 |
| Description | Collaboration with Dr Aaron Jenkins - University of Sydney |
| Organisation | University of Sydney |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | We will provide expertise in nanopore sequencing and Salmonella Typhi epidemiology to help build capacity in Fiji to better understand the persistence of S. Typhi in the environment. |
| Collaborator Contribution | Our partners provide access to a field site and specimens from patients with strong epidemiological and geographical metadata. |
| Impact | Grants awarded from BMGF - Gemma Langridge (QIB) as PI - two other grants with QIB Co-Investigators with PIs from Canada and Australia |
| Start Year | 2018 |
| Description | Development of Metabolic Database for Campylobacter |
| Organisation | SRI International (inc) |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | Generation of biochemical database for establishing publicly available database for metabolic modelling of Campylobacter. |
| Collaborator Contribution | Internationally known informatics platform and infrastructure to allow public access. |
| Impact | The datasets generated for this study can be found in the https://data.quadram.ac.uk/dipali.singh/CJM1cam_MM/, https://data.quadram.ac.uk/dipali.singh/CJM1cam_DB/. Additionally, Pathway/Genome database generated in this study is available from Pathway Tool Registry. |
| Start Year | 2019 |
| Description | Enhanced biofilm and extracellular matrix production by chronic carriage versus acute isolates of Salmonella Typhi |
| Organisation | Nationwide Children's Hospital |
| Country | United States |
| Sector | Hospitals |
| PI Contribution | Phylogenetic analysis of a collection of S. Typhi strains isolated from chronic carriers and acute infection in order to understand variation in biofilm formation associated with distinct lifestyles and disease and carrier syndromes. |
| Collaborator Contribution | Demonstration that chronic carriage isolates form thicker biofilms than acute infection isolates and that of those components tested, the increase in biofilm formation by chronic carriage isolates correlated only with greater steady state levels of eDNA and DNABII proteins within the biofilm EPS. Overall, these data suggested that during carriage, chronic S. Typhi isolates may undergo pathoadaptation in the gallbladder for enhanced biofilm capabilities. Demonstration of disruption of biofilms formed by chronic carriage isolates with a specific antibody that targets the DNABII proteins supporting development of therapeutic use of this antiserum to attenuate the chronic carriage of S. Typhi. |
| Impact | Publication of research in a peer reviewed journal |
| Start Year | 2021 |
| Description | Formal invitation to Pacific Partnership for Planetary Health |
| Organisation | Edith Cowan University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Following from our BBSRC international partnership award to visit the Centre for People, Place and Planet at Edith Cowan University, we recieved this invitation to become a consortium member of the Pacific Partnership for Planetary Health. Our contribution will be designing environmental sampling strategies and new techniques for analysing metagenomics data. |
| Collaborator Contribution | Activities focused on strengthening capacity to prevent, prepare and respond to infectious disease threats |
| Impact | None yet |
| Start Year | 2023 |
| Description | GAMA Healthcare |
| Organisation | GAMA Healthcare |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Research collaboration with GAMA healthcare to research and develop improved disinfection regimes - including successful application for iCASE PhD (GAMA contributing cash) |
| Collaborator Contribution | GAMA contributing cash for stipend uplift and in kind access to reagents and facilities |
| Impact | None as yet |
| Start Year | 2019 |
| Description | GSK global health |
| Organisation | GlaxoSmithKline (GSK) |
| Department | GSK Oncology |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Deploying our transposon mutagenesis expertise in a new project to study Salmonella responses to novel antimicrobials |
| Collaborator Contribution | Contribution of a intramacrophage screen and lead compounds for analysis |
| Impact | Award of a TCOLF grant |
| Start Year | 2024 |
| Description | Global S. Infantis |
| Organisation | UK Health Security Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Knowledge exchange, long read sequencing technology and data analysis |
| Collaborator Contribution | Development of detection methods for Salmonella Infantis |
| Impact | A multi-disciplinary approach to understanding the population structure of the important broiler and human pathogen Salmonella Infantis has allowed: Publications of benefit to the Salmonella research community Development of tools to investigate the risk of importing Salmonella Infantis into the UK |
| Start Year | 2018 |
| Description | International Partnership on Campylobacter and microplastics |
| Organisation | University of Ljubljana |
| Country | Slovenia |
| Sector | Academic/University |
| PI Contribution | My research team has provided expertise, analysis and interpretation to the collaborative project on Campylobacter biofilms and microplastics in the environment. |
| Collaborator Contribution | The Biotechnical Faculty, University of Ljubljana collaborator and her team have provided expertise, sampling and testing as a contribution to the project. This is a partnership between QIB, University of Ljubljana and the Institute for Water. |
| Impact | 1. Symposium with QIB (N Janecko and B Djeghout - post doc) as invited speakers 2. Workshop of genomic and metagenomic methodologies, analysis and interpretation 3. Multi-disciplinary discussion forum with Veterinary Faculty, Biotechnical Faculty, Institute of Water in Ljubljana, Slovenia |
| Start Year | 2022 |
| Description | Investigation of antibiotic resistance in Salmonella Infantis |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Both partners have had several discussion meetings around the reporting of S. Infantis and risk assessment. QIB have supplied informatics support through Gemma Langridge and Microbiology through John Wain. The first paper has been submitted |
| Collaborator Contribution | PHE provide public health intervention experience, several genome sequences and a route to change the reporting guidelines. |
| Impact | Salmonella nomenclature in the genomic era: a time for change. MA Chattaway, GC Langridge, J Wain. Scientific reports 11 (1), 1-8 Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales. WWY Lee, J Mattock, DR Greig, GC Langridge, D Baker, S Bloomfield, ... Microbial genomics 7 (10) |
| Start Year | 2018 |
| Description | Jess Blair - efflux over time |
| Organisation | University of Birmingham |
| Department | Institute of Microbiology and Infection |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration to study the control of cellular permability across a growth phase - we have generated and shared a series of gfp-reporter vectors to help analyse gene expression |
| Collaborator Contribution | Single cell analysis of gene expression integrated with drug uptake |
| Impact | Grant application (submitted to BBSRC Sept 2018 round). Publication in revision from Plos Pathogens |
| Start Year | 2018 |
| Description | Jo Santini - plasmids |
| Organisation | University College London |
| Department | Division of Biosciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Use of our biofilm bead model to show plasmid transfer over time and as a tool to study plasmid inhibitors |
| Collaborator Contribution | Strains and plasmids to test |
| Impact | Grant application in preparation for BBSRC (April 2019) |
| Start Year | 2019 |
| Description | MRC MMB DTP studentship |
| Organisation | UK Health Security Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Training of a PhD student in high molecular weight DNA extraction and long read sequencing, working on a strain collection of interest to UKHSA. |
| Collaborator Contribution | Provision of public health expertise and a route to impact in regards to outbreak detection. |
| Impact | Poster presented at Microbiology Society Conference 2023. |
| Start Year | 2022 |
| Description | MTA with Public Health England |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Long read sequencing and metabolic analysis of Salmonella isolates provided by PHE. |
| Collaborator Contribution | Provision of Salmonella isolates, associated metadata and short read sequence data. |
| Impact | Joint publications, some used as evidence base for improving clinical guidelines |
| Start Year | 2021 |
| Description | Microbial Metabolic Modelling |
| Organisation | Oxford Brookes University |
| Department | School of Life Sciences Oxford Brookes |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Delivery of experimental data and use of modelling software developed at Oxford Brookes |
| Collaborator Contribution | Written and curated software for metabolic modelling. Collaborative development multi-disciplinary projects - biology and computation |
| Impact | Outputs: Workshops on metabolic modelling delivered in the UK (https://mudshark.brookes.ac.uk/Meetings) Training course in India 2024 on genome scale metabolic modelling Training course in Nepal 2024 on genome scale metabolic modelling |
| Start Year | 2024 |
| Description | Molecular epidemiology and genomics of Salmonella Typhimurium in livestock and wild animals |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | My research group provides expertise in sequencing and analysis of sequence data of foodborne bacterial pathogens and molecular biology for the characterisation of pathogens. My team analyses data and disseminates findings to the scientific community and other groups of interested parties by the preparation of manuscripts or oral presentations. The activity aims to contribute underpinning scientific evidence for bacterial pathogen surveillance and development of intervention strategies aimed at decreasing the likelihood that pathogens will enter the food chain. |
| Collaborator Contribution | Collaborators at PHE contribute surveillance, samples and molecular epidemiology expertise. They contribute to preparation of publication material and monitor potential use of scientific output for translation into surveillance or intervention. |
| Impact | none as yet |
| Start Year | 2015 |
| Description | NNUH Collaboration-Diagnostic Bacteriology |
| Organisation | Norfolk and Norwich University Hospital |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | This partnership is a shared research interest in the population diversity and diagnostic testing of Campylobacter and other enteric pathogens found in stool through comparative genomics and metagenomics |
| Collaborator Contribution | The NNUH partner contributes clinical specimens and expertise from a clinician's perspective as well as local public health expertise. This drives important research objectives and impacts. |
| Impact | This is a multi-disciplinary collaboration with clinicians, diagnostic laboratory staff, epidemiologists, microbiologists and bioinformaticians involved. |
| Start Year | 2019 |
| Description | NNUH plueral infection |
| Organisation | Norfolk and Norwich University Hospitals NHS Foundation Trust |
| Department | Department of Respiratory Medicine |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | Initiated a study to investigate bacterial causes of infection and colonisation of catheters in pleural patient cohort |
| Collaborator Contribution | Access to clinical samples |
| Impact | none to date |
| Start Year | 2021 |
| Description | Nestle - Molecular basis for variation in physiological resistance of Salmonella enterica during minimal heating of chilled plant protein foods |
| Organisation | Nestlé (Global) |
| Country | Switzerland |
| Sector | Private |
| PI Contribution | The outcome of this objective will be a comprehensive understanding of the phylogenetic relationship and genome sequence variation of candidate Salmonella strains with increased thermal tolerance and other Salmonella strains not implicated in outbreaks from processed foods. 10-20 representative strains will be selected and their thermal inactivation dynamics will be determined. Whole genome functional screens using saturating transposon mutagenesis and transposon insertion site sequencing (TraDIS) will be used to identify conditional-essential genes required for maximum tolerance to heat and organic acid inactivation. |
| Collaborator Contribution | Insight into industrial processes and relevance to food safety. Advice on impact of research on the food industry. |
| Impact | In progress |
| Start Year | 2018 |
| Description | Nestle iCASE |
| Organisation | Nestlé (Global) |
| Department | Nestle PTC York |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | iCASE studentship to study potential for polyphenols to act as food preservatives to replace nitrites. Study of antimicrobial action and mechanisms of a range of polyphenols |
| Collaborator Contribution | Provision of polyphenols of interest, information about food matrix conditions, support for student internship at Nestle R&D centre |
| Impact | Identification of active polyphenols from a large panel and analysis of activity under different conditions |
| Start Year | 2018 |
| Description | Niche adaptation in Pseudomonas aeruginosa |
| Organisation | University of East Anglia |
| Department | School of Medicine UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Strain collection started by me - genomic sequencing carried out by my team and initial analysis of genomes. Typing scheme used developed by me. |
| Collaborator Contribution | Hosting the PhD student; experimental work on mechanisms of AMR |
| Impact | Conference posters |
| Start Year | 2020 |
| Description | Proof-of-Concept: Clinical Diagnosis of Bloodstream Infections using Metagenomics |
| Organisation | Norfolk and Norwich University Hospital |
| Country | United Kingdom |
| Sector | Hospitals |
| PI Contribution | We proposed a proof-of-concept study of Quadram's novel clinical metagenomic bloodstream infection (BSI) method using excess blood samples from patients with confirmed bacteremia at the Norfolk and Norwich University Hospital (NNUH). Clinical metagenomic diagnosis of BSI's have been greatly challenged because the abundance of host DNA in blood greatly exceeds (and 'masks') the DNA from the infecting microbe and there is otherwise estimated to be a very low abundance of pathogen within blood samples. To address these issues, we have successfully demonstrated the application of a highly efficient host depletion process (previously developed at Quadram to support metagenomic diagnostics of respiratory infections; Charalampous et al. 2019. Nature Biotechnology) in conjunction with a whole genome amplification (WGA) step prior to nanopore sequencing. In mock specimens that contained known amounts of spiked Escherichia coli, the combination of these two methods provided sensitive detection in blood samples when microorganisms were at clinically relevant concentrations. Promisingly, these results were available within 8 hours. However, this protocol has never been tested on clinical specimens from patients with established BSI. |
| Collaborator Contribution | NNUH consultant microbiologist and project co-I identified BSI cases at NNUH during review of critical blood culture results. With support from NNUH Haematology laboratory, NNUH laboratory technicians then identified, recovered, and anonymised excess EDTA blood samples from the haematology laboratory that were previously collected from the same patient. With the view of subsequently translating metagenomic technologies into clinical practice, the co-I and their team at NNUH laboratories reviewed sequence results and provide analysis and advice on the accuracy and optimisations needed for the Quadram BSI metagenomic method. |
| Impact | Our goal to demonstrate the diagnostic capability of clinical metagenomics on BSIs while also learning from clinical partners so that we can refine essential steps of the methodology for sample collection, sample transport, and result reporting to clinicians. We have established a productive pathway with ethics clearance to receive and test excess clinical samples, and testing is now underway. |
| Start Year | 2021 |
| Description | SCAU |
| Organisation | South China Agricultural University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | Established a partnership to study mechanisms of resistance in food borne salmonella from China - we are hosting a Chinese PhD student for a year |
| Collaborator Contribution | Support for student visit and costs for a workshop in China (also supported by British Council funding) |
| Impact | Funding for workshop in China, to be held in Oct 2019. Awarded a British Society grant for this to happen (£24K to quadram for uk participane travel) |
| Start Year | 2018 |
| Description | Study of Camplybacter in central India |
| Organisation | Government Medical College Nagpur |
| Country | India |
| Sector | Academic/University |
| PI Contribution | Provision of expertise in the culturing of Campylobacter species and interpretation of patient records |
| Collaborator Contribution | Provision of appropriate field sites in rural central india |
| Impact | An initial GCRF funded meeting in Nagpul and visits to rural sites |
| Start Year | 2020 |
| Description | Studying Campylobacter in rural Pakistan |
| Organisation | COMSATS Institute of Information Technology |
| Country | Pakistan |
| Sector | Academic/University |
| PI Contribution | Provide expertise in culturing, monitoring and genome sequencing of Campylobacter species |
| Collaborator Contribution | Appropriate filed sites and metadata |
| Impact | A meeting under GCRF and set up study on Campylobacter |
| Start Year | 2019 |
| Description | UEA - PhD studentship |
| Organisation | Public Health England |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Jenny Mattock a a PhD student funded by the NIHR, UK. By linking Jenny to the this project we allowed her to explore the genetic diversity of Salmonella Infantis in South African . Jenny visited South Africa in October 2017 and was supported to extract DNA and collect meta-data |
| Collaborator Contribution | The Health Protection Resreach Unit for gastrointestinal infection has provided the student and Public Health England has provided DNA sequnce from isolates of S. Infantis from the UK |
| Impact | Poster presentations at various symposia. Multidisciplionary involvement: BioiInformatics - PHE and Quadram Institute; Microbiology - NICED and UEA PhD awarded by UEA in 2020 publication - 2021 Oct 14. doi: 10.1099/mgen.0.000658 |
| Start Year | 2017 |
| Description | UEA - PhD studentship |
| Organisation | University of East Anglia |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Jenny Mattock a a PhD student funded by the NIHR, UK. By linking Jenny to the this project we allowed her to explore the genetic diversity of Salmonella Infantis in South African . Jenny visited South Africa in October 2017 and was supported to extract DNA and collect meta-data |
| Collaborator Contribution | The Health Protection Resreach Unit for gastrointestinal infection has provided the student and Public Health England has provided DNA sequnce from isolates of S. Infantis from the UK |
| Impact | Poster presentations at various symposia. Multidisciplionary involvement: BioiInformatics - PHE and Quadram Institute; Microbiology - NICED and UEA PhD awarded by UEA in 2020 publication - 2021 Oct 14. doi: 10.1099/mgen.0.000658 |
| Start Year | 2017 |
| Description | Unilever (iCASE) |
| Organisation | Unilever |
| Department | Unilever UK Central Resources Limited |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | New iCASE studentship to explore development of skin microbiota in early life - we provide access to trial subjects and technologies |
| Collaborator Contribution | Uplift to funding for sequencing, experience in skin metagenomics |
| Impact | None as yet |
| Start Year | 2020 |
| Description | Vass - modelling |
| Organisation | University of Essex |
| Department | School of Biological Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration to model structurally the impact of novel substitutions within efflux pump proteins selected in our evolution experiments. We provided data re the phenotypes and nature of substitutions |
| Collaborator Contribution | Expert analysis of the structural impact of the substitutions and predictions re drugs likely to be impacted to be tested in the laboratory |
| Impact | Data for paper in preparation |
| Start Year | 2019 |
| Description | iCASE (Greg) |
| Organisation | Procter & Gamble |
| Department | Newcastle Innovation Centre |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Use of our bead based biofilm evolution model to study impacts of biocides on evolution of resistance |
| Collaborator Contribution | Biocides of interest and support for student visit to P&G |
| Impact | Identification of conditions impacting biofilm formation for various species and analysis of impacts of different biocides |
| Start Year | 2017 |
| Title | Oligosaccharyltransferase Polypeptide |
| Description | New enzyme to improve glycoengineering in E. coli |
| IP Reference | GB1704103.9 |
| Protection | Patent application published |
| Year Protection Granted | 2018 |
| Licensed | Commercial In Confidence |
| Impact | Improve glycoengineering in the E. coli cell |
| Title | Use of TraDIS-Xpress to study the basis for action and resistance of antimicrobials |
| Description | Development of TraDIS-Xpress technology to allow essential bacterial genes to be assayed in roles for conditional survival along with proprietary methods to make the process cheaper and faster |
| IP Reference | |
| Protection | Protection not required |
| Year Protection Granted | 2020 |
| Licensed | Commercial In Confidence |
| Impact | Two projects funded by Industrial partner to study the response to preservatives of interest (details confidential) |
| Title | AlbaTraDIS |
| Description | AlbaTradis has been developed at Quadram to analyse the outputs from large scale bacterial transposon mutagenesis experiments. It allows analysis of gene expression changes and analysis across multiple conditions for the first time |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Gretaly improved analysis capability for transposon mutagenesis |
| URL | https://github.com/quadram-institute-bioscience/albatradis |
| Title | QuaTraDIS |
| Description | The QuaTradis pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. QuaTradis provides functionality to: detect TraDIS tags in a BAM file add the tags to the reads filter reads in a FastQ file containing a user defined tag remove tags map to a reference genome create an insertion site plot file Continued updates and releases have been made since the first release in 2022 with the latest in february 2025. These have increased functionality and accuracy |
| Type Of Technology | Software |
| Year Produced | 2025 |
| Open Source License? | Yes |
| Impact | Used by groups around the world for analysis of transposon insert site data |
| URL | https://github.com/quadram-institute-bioscience/QuaTradis |
| Title | Socru: order and orientation of bacterial genomes |
| Description | Socru allows you to easily identify and communicate the order and orientation of complete genomes around ribosomal operons. These large scale structural variants have real impacts on the phenotype of the organism, and with the advent of long read sequencing, we can now start to delve into the mechanisms at work. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | Since its launch in February 2019, this software has been downloaded over 2,400 times. |
| URL | https://github.com/quadram-institute-bioscience/socru |
| Company Name | ArkVax |
| Description | ArkVax develops vaccines for animals through glycoengineering. |
| Year Established | 2020 |
| Impact | The focus of the company is the development of multicomponent poultry, pig and ruminant vaccines. The business is supported contract research for vaccine candidate from established vet vaccine companies and further funding is currently being sought from a range of investors. |
| Website | https://www.arkvax.com/ |
| Description | 30+ TV interviews (BBC, SKY, Channel 4) on Covid vaccine delivery, production and use |
| 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 | Media (as a channel to the public) |
| Results and Impact | 30+ TV interviews (BBC, SKY, Channel 4) on Covid vaccine delivery, production and use. Received 100s of questions from general public many relating to vaccine confidence |
| Year(s) Of Engagement Activity | 2020 |
| Description | Activity stand (Norwich Science Festival) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Hosted an all day stand during the Science Festival week in Norwich. Young people were encouraged to take part in the prepared activities which sparked coversations about bacteria, sequencing and science in general. Many of the audience reported positive change in opinion on bacteria. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Activity stand: Testing, testing, 1-2-3 (Norwich Science Festival) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Hosted an all day stand during the Science Festival week in Norwich. Young people were encouraged to take part in the prepared activities which sparked coversations about microbes, diagnostic tests and science in general. Many of the audience reported increased understanding of scientists' roles in mitigating against pathogens. |
| Year(s) Of Engagement Activity | 2023 |
| Description | BBC Breakfast |
| 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 | Media (as a channel to the public) |
| Results and Impact | Expert opinion of an outbreak of E. coli |
| Year(s) Of Engagement Activity | 2018 |
| Description | BBC Breakfast |
| 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 | Media (as a channel to the public) |
| Results and Impact | Interview on Antibiotic resistance, Vaccine development and Government plans |
| Year(s) Of Engagement Activity | 2019 |
| Description | BBC News |
| 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 | Media (as a channel to the public) |
| Results and Impact | Interview on Antibiotic resistance, Vaccine development and Government plans |
| Year(s) Of Engagement Activity | 2019 |
| Description | BBC News at 10 |
| 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 | Media (as a channel to the public) |
| Results and Impact | Explained consequence of an E. coli outbreak |
| Year(s) Of Engagement Activity | 2018 |
| Description | Biofilms, the good the bad and the ugly. A Webinar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A global webinar was delivered explaining why biofilms are important, why they are antimicrobial resistant and a perspective on possible treatment options. Invited by GARDP - a WHO initiative for development of new antimicrobials |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://revive.gardp.org/biofilms-what-are-they-and-why-do-we-care/ |
| Description | Blog on diversity in science |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Inspiring blog written by QIB scientist exploring their journey from school into science and the value of role models. Has led to enquiries from schools about bringing this theme in for assemblies. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://quadram.ac.uk/blogs/diversity-in-science-if-you-can-see-it-you-can-be-it/ |
| Description | Blog on scientific research |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Blog written to lift the lid on the technology being used to support our science at Quadram, and the industry collaborations associated with this. Has led to enquiries about this technology. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://quadram.ac.uk/blogs/robots-and-jigsaws-the-technology-behind-investigating-bacterial-diversi... |
| Description | Campylobacter research discussion with 2 Sisters Food Group |
| 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 | Discussion with Directors of 2 Sisters about potential areas of collaboration with the aim to investigate the diversity and spread of Campylobacter in poultry and food. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Cardiff School of Medicine Science Seminar series |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Invited keynote seminar at the University of Cardiff School of Medicine presentation entitled 'Salmonella Variants of Interest and Concern: carving a Niche in the pork industry'. Dissemination of key findings from a number of project from within my research group to an audience of approximately 50 students, postdoctoral scientists and prinicpal investigators. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Comment for Sci DEv Network. Bringing science and development together through news and analysis. |
| 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 | Media (as a channel to the public) |
| Results and Impact | Provided comment within an article called "Focus piece on: Antibiotics resistance breaks global boundaries " |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.scidev.net/global/health/opinion/antibiotics-resistance-breaks-global-boundaries.html |
| Description | Conference talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Research talk at 3rd Bacterial Cell Biology Conference, Bahamas |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.fusion-conferences.com/conference/100 |
| Description | Conjoint scientific and strategic planning session with UKHSA |
| 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 | Professional Practitioners |
| Results and Impact | Scientists from the Microbes in the Food Chain ISP meet with key counterparts in the UKHSA to further develop their long-term scientific collaboration, with the overall goal of the meeting being increased interaction and coordination between members of the partnership, and specific goals to collaborative advance scientific capabilities through increased access to the expertise, technologies and datasets across both organisations, with recognition of the unique/complementary skill sets in both and how best to leverage these to achieve mutual goals (e.g. co-development of data visualisation tools and the advancement of genomic sequencing protocols that support research and surveillance outcomes). |
| Year(s) Of Engagement Activity | 2022 |
| Description | Contribution to exhibition 'I'm a Scientist'. 2023 |
| 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 | Schools |
| Results and Impact | Contributed material for an exhibition about diverse nature of scientists displayed at Norwich Science Festival |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://norwichsciencefestival.co.uk/ |
| Description | Contributor to The Biofilm Brainhub website |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website highlighting the role of biofilms in Industry, farming and food. Aimed at the non-specialist. Recent research from my research groups on Biofilm formation by Salmonella was highlighted and a link to the primary literature provided. It is expected that this resource will increase public awareness of biofilms and the risk they play in agriculture. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://biofilmbrainhub.co.uk/ |
| Description | Created a video to explain technology allowing identification of genes allowing bacteria survive in conditions of interest and how this can relate to health and wealth |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | We have developed new technology (TraDIS-Xpress) to study bacterial behaviour and this has application in many fields. It is not easy to explain this technology and we have had various engagements with industry who are keen to access the platform but need an easier way to explain this internally. The approach is also important for students and anyone interested in bacteriology. Therefore we created and released a video (in conjunction with a paper publication) - this has recently been done but has already attracted new industrial contacts who are interested in accessing the technology as well as feedback from students who have seen the video and want to work with us. The production was supported from an IAA award |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://vimeo.com/390489066 |
| Description | Demonstration of Metagenomics with a Food Factory |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | QIB scientists provided information to a food producer on the latest generation of genome sequencing technologies and how these technologies can be used to improve surveillance activities for foodborne pathogens and how subsequent experimental studies with isolated pathogens can be used to provide evidence on the effectiveness of disinfection regimens. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Discussion with Bakkavor technical Director |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion with Bakkavor food processing company to discuss strategy to ensure safety of food in relation to Listeria contamination |
| Year(s) Of Engagement Activity | 2023 |
| Description | Discussion with CSIRO (Australia) -Microbiomes for One Systems Health FSP |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | Discussion about food spoilage with CSIRO scientists from One Systems Health FSP- from Agriculture and Food divisions in Sydney, Brisbane and Weribee, Australia which sparked interest in developing future collaborations |
| Year(s) Of Engagement Activity | 2023 |
| Description | Discussion with Cranswick Foods directors |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Full day discussion session to share information and develop collaborations on food safety |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://cranswick.plc.uk/ |
| Description | Discussion with Harbro Limited Livestock Feed company |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion with Harbro Limited Livestock Feed company Head of Technical to plan potential collaborations to investigate the impact of feed on the microbiota of pigs to promote health |
| Year(s) Of Engagement Activity | 2021 |
| Description | Discussion with Illumina Accelerator representative |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion about developing translation and potential spinout company from BBSRC CASE studentship work |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.illumina.com/company/illumina-for-startups/accelerator-program.html |
| Description | Discussion with Nestle food safety technologists |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Exploratory talks about how scientists at the Quadram Institute could collaborate with Nestle in studies aimed at investigating the impact of genetic diversity on risk to food safety |
| Year(s) Of Engagement Activity | 2018 |
| Description | Discussion with raw pet food manufacturer (Bella and Duke) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion with Head of Food Development for a raw pet food manufacturer (Bella and Duke) on the application of our work on the use of phage as biocides in the food chain |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.bellaandduke.com/lp/50-off-raw-dog-food/?utm_source=google&utm_medium=cpc&utm_campaign=D... |
| Description | Discussion with waitrose and suppliers |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | A series of meetings were held with Waitrose and technical managers interested in food safety from their key suppliers. Discussions about our skills and interests and how these relate to their issues were held and potential future collaborative projects identified. The events increased awareness of our abilities for industry and of industries needs and current challenges for us |
| Year(s) Of Engagement Activity | 2019 |
| Description | Discussions with 'Nature Menu' on potential collaborations aimed at investigating the diversity of Salmonella in raw dog food and implementation of intervention strategies |
| 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 | Discussion of previous collaboration outcomes and planning for future collaborations and investment from Natures menus in collaborative research |
| Year(s) Of Engagement Activity | 2018 |
| Description | Engagement with Food Industry |
| 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 | Industry/Business |
| Results and Impact | A number of engagement activities with a national food production industry company that included facility tours, wider meetings/discussions, research presentations over an 8 month period |
| Year(s) Of Engagement Activity | 2022,2023 |
| Description | Engagement with HEI - Slovenia |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Multiple engagement activities with the University of Ljubljana, Biotechnical Faculty that included: Symposium - "Campylobacter as an analytical target to improve food safety"; tour of facilities; workshop led by Bilal Djeghout (post doctoral researcher in my research group); multiple discussions with individual researchers at the University of Ljubljana working in the area of biofilms, Campylobacter and food safety. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Engagement with HEI - Spain |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | >20 University of Vigo participants and specific discussions the Cancer evolution and genomics research group lead by Dr. David Posada; tour of the Toralla Marine Science Station (ECIMAT-UVIGO) and discussions with marine biology focused researchers. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Engagement with New Zealand Food Safety Science & Research Centre |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I visited the New Zealand Food Safety Science & Research Centre and gave a presentation entitled "Whole genome sequencing and metagenomics for the investigation of food safety and antimicrobial resistance". A roundtable discussion with students and researchers then followed. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Exhibition (Schools and county show) |
| 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 | Schools |
| Results and Impact | Exhibition presented to 400 school children as an assembly and displayed to 3000 visitors at the Royal Norfolk County Show, and other events including display at Earlham Institute and John Innes Centre accessible science days. Children were invited to identify who they thought were scientists, resulting in excellent discussions showing improved understanding that anyone can be a scientist. |
| Year(s) Of Engagement Activity | 2023,2024 |
| Description | Exhibition on diversity in science |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Large exhibition displaying the diverse home/work lives of scientists across the Norwich Research Park, curated by a QIB scientist. Sparked engagement in person and online and has led to follow up activities being planned in two schools and at a regional county show. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Expert advisor for documentary |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Expert advisor for a cinema and TV documentary designed to raise awareness about the diminishing effectiveness of antibiotics and the consequent threat to modern hospital medicine. The film is an ambitious project supported by HBO, BBC, the Wellcome Trust and the Howard Hughes Medical Institute. |
| Year(s) Of Engagement Activity | 2020,2021 |
| Description | Expert consultation on non-typhoidal Salmonella (NTS) and broadly protective Salmonella vaccines (NTS, paratyphoid A, typhoid) |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | WHO convened this 2-day expert consultation as a forum for stakeholders to review the evidence on the epidemiology and the serovar distribution of invasive and diarrheal NTS disease, and to discuss how the geographic diversity of Salmonella serovars and the potential demand of endemic countries should be considered in the development of broadly protective Salmonella vaccines. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Expert consultations on invasive non-typhoidal Salmonella (iNTS) vaccines invited participant |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | Under a recently awarded 3-year grant by the Wellcome Trust, IVI, WHO and other global partners are collaborating to develop a Full Value of Vaccines Assessment to understand both the general and specific value of investment in an iNTS vaccine (or vaccines) and potential to combine with a Typhoid / paratyphoid vaccine. The long-term goal of this FVVA project is to pave the way for the development of safe and efficacious iNTS vaccines, licensure, policy recommendations from SAGE, WHO prequalification, Gavi financing, UNICEF purchasing and national technical advisory group recommendations for use. |
| Year(s) Of Engagement Activity | 2021 |
| Description | FSA-QIB Kitchen model |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Engagement activity attended by 8 individuals what sparked discussions of strategic collaborative activities between QIB and FSA for the understanding of Campylobacter survival in kitchen environments. This engagement aligned UK gov findings of Kitchen-Life 2 and QIB MFS ISP Themes 1-3 |
| Year(s) Of Engagement Activity | 2023,2024 |
| Description | Food Safety Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Delivered a talk to 2018 'Food Safety' annual conference 'Quadram Institute: a new vision for food safety research' |
| Year(s) Of Engagement Activity | 2018 |
| Description | Generated content for 'Food matters live' |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Display of QIB research and expertise in relation to biofilms and food safety for the 'Food matters live' 2018 conference, part of the EIT-Food network |
| Year(s) Of Engagement Activity | 2018 |
| Description | Hosted Food Safety Lead and Technical Manager from major UK meat/food producer |
| 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 | Industry/Business |
| Results and Impact | Full day session in Norwich to generate awareness of Quadram food safety microbiology research programmes and identify collaborative interests. |
| Year(s) Of Engagement Activity | 2023 |
| Description | How bacteriophage resistance shapes Salmonella populations Blog |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | A Blog highlighting published research |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://quadram.ac.uk/bacteriophage-resistance-salmonella/ |
| Description | How do bacteria evolve? |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Ran a stand at the Norwich Science Festival explaining the history of bacterial evolution and how this still happens today. Over 300 children visited the stand and took away various materials. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Industry collaboration |
| 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 | Industry/Business |
| Results and Impact | Press release describing the first implementation in the country of technology at Quadram. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://revolugen.co.uk/news/32/111/Tecan-and-RevoluGen-Enter-into-Agreement-for-96-well-Plates-for-... |
| Description | Interface event with researchers and clinicians |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Interface/network meeting between researchers and Norfolk and Norwich University Hospital Trust clinicians to facilitate joint projects |
| Year(s) Of Engagement Activity | 2019 |
| Description | International Partnering visit to UC Davis, USA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Visited Prof Andreas Baumler, Prof Renee Tsolis, Dr Sebastian Winter and Prof Bart Weimer at UC Davis, USA to meet with scientists from their labs and discuss future collaboration. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Interview for World Antimicrobial Awareness Week 2022 on AL24 News, Algerian International Channel |
| 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 | Bilal Djeghout, a post doctoral researcher in my research group gave an invited interview to the AL24 News Channel, an Algerian international TV channel broadcast during morning news segment. The channel reaches Algerian and other north African nations. The interview was conducted in Arabic via Skype for the World Antimicrobial Awareness Week 2022 and focused on general antimicrobial resistance topics. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Invited Presentation (Microbial Metagenomics - A new view on infectious disease diagnostics and food safety surveillance) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited presentation on microbial metagenomics to the Barts NHS London microbiology journal club. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited Speaker at Microbiology Society Focussed meeting (Microbiome and mucosa associated infectious disease, Dublin 2022) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk given about research to microbiome focussed meeting covering aspects of work with Salmonella, E. coli and Staphylococcus |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://microbiologysociety.org/event/society-events-and-meetings/gut-microbiome-and-mucosa-associat... |
| Description | Invited Talk at 7th Microbiome & Probiotics R&D and Business Collaboration Forum: Europe |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation re Rational design of probiotics and microbiome biotherapeutics |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited guest lecture "Listeria is a rugged foodborne pathogen that acts as a Persister and an Evictor" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Gilmour provided an invited lecture to the Institute of Food Science and Technology Eastern branch. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Invited seminar (Universite Paris-Saclay) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Invited talk in seminar series, given to researchers at Universite Paris-Saclay. 1-1 talks with postdocs and postgraduate students also took place, leading to a collaborative project on long read sequencing. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited seminar (University of Birmingham) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Invited seminar series talk on bacterial metabolism, given to researchers at the Institute of Microbiology & Infection, University of Birmingham. Resulted in several follow up communications relating to the topic. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited seminar (University of Glasgow) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Invited talk in seminar series, given to researchers at University of Glasgow. Also met with several academics across the day. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited seminar - Caltech |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | seminar presentation to research students and staff in the Biology and Bioengineering Department, California Institute of Technology which sparked questions and discussions afterwards |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited seminar speaker: Trinity College Dublin |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | Seminar: Using laboratory evolution to understand and predict antimicrobial resistance |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited seminar speaker: University of Bath |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Seminar to Bath re Predicting routes and mechanisms of antibiotic resistance |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited seminar- ASM Biofilm SIG |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | seminar presentation to the Australian Microbiology Society Biofilm Special Interest Group which sparked questions and discussions afterwards |
| Year(s) Of Engagement Activity | 2022 |
| Description | Invited seminar- Imperial College London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar given to researchers at the National Heart and Lung Institute, Imperial College London with discussion after. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited seminar- John Innes Centre |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Seminar given to researchers with discussions afterwards. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited seminar- London School of Health and Tropical Medicine |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Seminar given to researchers at the London School of Health and Tropical Medicine with discussion after. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited seminar- Newcastle University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Seminar given to researchers at the Newcastle University Biosciences Institute with discussion after. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited seminar- Texas A&M |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Seminar given to researchers with discussions afterwards. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited seminar- Universiteit Leiden |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Seminar given to researchers with discussions afterwards. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited seminar- University of Dundee |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Seminar given to researchers at the School of Life Sciences, University of Dundee with discussion after. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited seminar- Warwick University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Seminar given to researchers at the Warwick Medical School and School of Life Sciences Warwick University with discussion after. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited seminar-Cardiff University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Seminar given to researchers at the School of Dentistry at Cardiff University with discussion after. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Invited speaker at University of Exeter seminar: How do biofilms evolve? |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Attended universitry of Exeter to deliver a seminar to ecologists about 'How Biofilms Evolve'. Aiming to cross disciplines and engage with ecologists |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invited talk (University of Cambridge) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Talk given to researchers at the Vet School, University of Cambridge with discussion after. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited talk to doctoral students |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited to give a talk to 45 students from the London Interdisciplinary Biosciences Consortium as part of their annual set of talks across the BBSRC/UKRI remit. |
| Year(s) Of Engagement Activity | 2021 |
| Description | LGBTQ+ point of view talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Talk presented by group member as part of OutThinkers: Celebrating LGBTQ+ in STEMM which was held during the Norwich Science Festival. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://norwichsciencefestival.co.uk/whats-on/out-thinkers-celebrating-lgbtq-in-stemm-2021 |
| Description | LGBTQ+ video for QIB |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Filmed speech by lab member on the point of view of an LGBTQ+ scientist working at QIB in support of LGBTQ+ in STEM day. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.youtube.com/watch?v=Wm4H_OAckps |
| Description | Media interview for trade press article |
| 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 | Industry/Business |
| Results and Impact | Interviewed for trade press article in association with industry collaboration at QIB. Raised awareness of the nature of the science we perform and has led to enquiries about the technology we have in place that supports the science. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.insideprecisionmedicine.com/coronavirus-2/genomic-pathogen-surveillance-in-the-spotlight... |
| Description | Minisymposium on metabolic modelling |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Metabolic modelling projects were presented and discussed. This event led to a collaborative grant submission. |
| Year(s) Of Engagement Activity | 2019 |
| Description | NNUH grand round |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Delivered 'Grand Round' talk to NNUH hospital 'March of the Superbugs, how antibiotic resistant pathogens evolve' |
| Year(s) Of Engagement Activity | 2018 |
| Description | Norwich Science Festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Norwich Science Festival event. Raspberry pi workshop at the Norwich science festival, to introduce coding to the wider society. Raspberry Pis are low-cost, high-performance computers that people use to learn, solve problems and have fun. The Raspberry Pi Foundation provides outreach and education through Raspberry Jams to help more people access computing and digital making. They develop free resources to help people learn about computing and how to make things with computers, and train educators who can guide other people to learn. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://norwichsciencefestival.co.uk/events/raspberry-pi-jamwich/ |
| Description | Norwich Science Festival 2024 |
| 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 | Schools |
| Results and Impact | Developed and ran a stand at the Norwich Science Festival communicating the differences between 'good' and 'bad' microbes |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://norwichsciencefestival.co.uk/whats-on/nrp-explorium-2024?start_time=2024-02-21T10.30 |
| Description | Norwich Science Festival- Out thinkers |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Presentation in Norwich Science Festival - Out thinkers- celebrating LGBTG+ in STEM, which sparked questions and discussion afterwards. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://norwichsciencefestival.co.uk/whats-on/out-thinkers |
| Description | Opening and Keynote presentation - Why should the food industry care about genomics? |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Dr Gilmour gave the opening and keynote presentation at the Food Genomics Summit to introduce the potential food industry benefits of incorporating genomics and scientific approaches into their business operations through collaboration with science partners. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://newfood.events/the-food-genomics-summit/ |
| Description | Panel Discussion - The Death of Plastics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | M. Gilmour took part in a panel discussion on "the death of plastics", discussing the effect that the push for low plastic in packaging will have on food safety. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://newfood.events/the-food-safety-conference-2022/ |
| Description | Parliamentary reception |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Ian Charles and other representatives of Quadram Institute Bioscience (QIB) participated in the Parliamentary Reception (hosted by George Freeman MP) held to mark the launch of the QIB Science Strategy. It was an opportunity to discuss the strategic goals of the institute and its impact with those who will benefit. It was also an opportunity to discuss the research areas with policy makers. |
| Year(s) Of Engagement Activity | 2018 |
| Description | PhD training week |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | As part of a 6-week training block, we developed and ran hands-on bioinformatics training focused upon mapping and variant calling in comparative genomics. Students have reported use of taught techniques in their PhDs. |
| Year(s) Of Engagement Activity | 2022,2023,2024 |
| URL | https://mmbdtp.github.io/modules/comparative-genomics/programme/ |
| Description | Presentation to the Technical Group of the Chilled Foods Association |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | The Technical Group of the Chilled Foods Association meets three times per annum and includes either either the Company Microbiologist or Technical Manager from major UK food producers. Dr. Gilmour presented the scientific approaches used by the Quadram Institute to study microbial communities and population dynamics within food production facilities and foods. From this discussion, the industry group was interested that metagenomics could be used as a "problem solving tool" to understand the populations of microbes present in production environments. For others, there was particular interest in the relation of soil and water microbiomes and how those relate to what are seen in leafy green foods. There was also some interest in the transmission of organisms like E.coli through animals towards meat products. The discussion ended with an expression of interest that the Technical Group holds a future 2021 meeting on-site at Quadram to see the technologies and meet the experts first hand and discuss collaborative opportunities (there was talking of finding funding opportunities). |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.chilledfood.org/full-members/ |
| Description | Royal Norfolk Show |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Participated in panel debate 'Understanding superbugs: a panel debate on AMR' at the Royal Norfolk Show |
| Year(s) Of Engagement Activity | 2018 |
| Description | Sci festival stand |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | We ran a stall 'How Clean Is Your Home? The Bugs We Live With' at the Norwich Science Festival |
| Year(s) Of Engagement Activity | 2018 |
| Description | Sci festival talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Public lecture 'Evolution in action, how bacteria become resistant to antibiotics' as part of Norwich Science Festival |
| Year(s) Of Engagement Activity | 2018 |
| Description | Science podcast interview about AMR paper |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Interviewed on podcast to give breakdown of scientific paper |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.youtube.com/watch?v=E7fQRwtaOgU |
| Description | Science podcast interview about genome rearrangement paper |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Interviewed on podcast to give breakdown of scientific paper |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.youtube.com/watch?v=2Muv3T4QMBw |
| Description | Science soundbites audio paper series podcast |
| 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 | Media (as a channel to the public) |
| Results and Impact | Bilal Djeghout, a post doctoral researcher in my group participated in an interview by the Science Soundbites Audio paper series, organised by QIB to reach a wide podcast audience via Youtube, audio file and other media platforms. The subject area was in genomic Campylobacter diversity within an individual patient sample suffering from campylobacteriosis. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Seminar Talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Microbes in Norwich event, for which I was an invited speaker was attended by over 200 people from across three UKRI funded institutes in Norwich as well as the University of East Anglia post-graduates. This talk resulted in further discussions through breakout and networking sessions. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Spotlight profile by Trends in Microbiology |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Invited by the journal to produce a Twitter thread highlighting myself, the research group and our activities. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://twitter.com/TrendsMicrobiol/status/1525108897400373248 |
| Description | Talk in suppport of LGBTQ+ in STEMM |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Presented as part of the Out Thinkers: Celebrating LGBTQ+ in STEMM series, intended to give a platform to LGBTQ+ scientists in Norwich to share their experiences in STEMM. Sparked lively question and discussion session afterwards, and audience members went on to attend additional diversity events being staged in the area. |
| Year(s) Of Engagement Activity | 2023 |
| Description | UK agri-food system adaptation workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Professional, multidisciplinary workshop (in-person; Bristol) to collaboratively identify research gaps and priorities related to climate change impacts on the food system. Co-hosted by the Met Office and DEFRA; invited participation as a food safety expert. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Visit to Beaver scout group |
| 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 | 21 Beaver Scouts (aged 6 and 7) in Saffron Walden learnt about microbes and swabbed kitchen surfaces onto agar, with images of what grows returned. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Wellcome/BMGF NTS CHIM Workshop invited speaker |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | Nontyphoidal Salmonellae, particularly Salmonella enterica serovars Typhimurium and Enteritidis, are a major cause of enterocolitis globally. In sub-Saharan Africa NTS are also responsible for invasive disease known as invasive NTS disease or iNTS disease: bacteraemia and/or meningitis which particularly affect young children and HIV-infected individuals and have high associated case fatality rates (1,2). Effective treatment of iNTS disease is hampered by the lack of a pathognomonic clinical presentation, need for blood culturing to make a diagnosis and increasing levels of antimicrobial resistance. For these reasons, development of a vaccine against iNTS disease could have a major global public health impact. New candidate vaccines against iNTS disease have recently entered or are about to enter first-in-human trials, alone or in combination with licensed typhoid conjugate vaccine, making this workshop particularly timely. A controlled human infection model (CHIM) could have a role in the pathway to vaccine registration for healthy and special populations, Objectives of the Meeting 1. Understand possible roles for an NTS CHIM 2. Gauge utility of an NTS CHIM for vaccine development 3. Discuss different approaches to NTS CHIM development 4. Prime Wellcome's call for Expressions of Interest for NTS CHIM development |
| Year(s) Of Engagement Activity | 2021 |
| Description | Women of the Future 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | This event was led by JIC. It ran 23rd - 27th November 2020 and the two QIB films were accessible to schools who registered on the JIC page. After the event all the films were made freely accessible. I provided a short film interview covering their role and journey into science and what research at the QIB I conduct. It was aimed at 15/16 year old girls initially. Film clips were further tweeted to a larger audience via Twitter on International STEM Women's Day. |
| Year(s) Of Engagement Activity | 2020 |