Microbial Survival in the Food Chain

Lead Research Organisation: Quadram Institute Bioscience
Department Name: Contracts

Abstract

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.

Publications

10 25 50

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Chattaway M (2021) Salmonella nomenclature in the genomic era: a time for change in Scientific Reports

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De Oliveira Martins L (2022) Tatajuba: exploring the distribution of homopolymer tracts. in NAR genomics and bioinformatics

 
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 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, we have established a model to study this in the laboratory. Our biofilm evolution work has demonstrated that development of increased biomass by a bacterial biofilm is not necessarily protective of 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 physiology and impacts on AMR. The first part of this work is now published with further manuscripts in revision. We have also studied how a range of food chain relevant conditions (temperature, pH, preservatives) impact evolution of Salmonella biofilms and have documented collateral resistances and sensitivities which emerge under stress. The method has also been shared with HEI partners and training given to extend into campylobacter from salmonella and e. coli. We are already using this model in collaboration with two industrial partners in iCASE PhD projects. We are linking laboratory results with real world epidemiological data about genotypes selected - we have compared loci under selection in S. Typhi in the laboratory and isolates from our collaborations in endemic regions. We have also recently expanded work into Pseudomonads and have shown how biofilms formed by organisms from this group can take up DNA from their environment and use twitching motility to colonise new surfaces. Our work understanding the biology of biofilms is achieving the original objectives of the project. We are currently establishing mixed community models of biofilms to understand how consortia differ in their responses to stress compared to monospecies.

2. Functional genomics.
We have published our first articles describing an improved method to study the role of all genes in a bacteria in stress survival (TraDIS-Xpress). This relies on making large libraries of 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 others (acinetobacter, pseudomonas, bilophila) which has allowed cross-fertilisation of the technology into other projects and applications including microbiome work. We have also laid the foundations for using TraDIS in Listeria and staphylococci. We have designed and synthesised a novel shuttle vector that will enable TraDIS and TraDIS Xpress studies using a mariner transposon and multiple promoter options to optimise Xpress measurements of counter-directional transcriptional events. We have also developed and are optimising the conditions needed to transform a wide range of Listeria with these vector constructs, including studying the competence of this microbe that is otherwise recalcitrant to the uptake of DNA. Saturating transposon mutagenesis experiments are now planned for 2021.

We have used our technology developments to secure industry funding and partnerships to access this technology and presented it at academic and industrial conferences. We have submitted patent applications with more in preparation. We have also completed market research with a view to launching a spin out company. Finally we have applied this technology to cells in biofilms (linking two of our major themes together) and into defining virulence determinants in animal models. This work is achieving the original objectives of the project. We have also developed single cell sequencing methods to track evolution of AMR within populations of Salmonella at unprecedented detail in a collaboration with the Earlham Institute and have a paper in revision on this subject.

3. Campylobacter regulation.
We have studied the role of two novel campylobacter genes in control of important cellular processes including survival on surfaces and to oxidative shocks in a range of strains - this is informing why some strains are better adapted to survive in the food chain that others. We have also made transposon mutant libraries in camylobacter strains to further understand which genes are needed for survival in food chain relevant conditions. Finally we have defined metabolic requirements for campylobacter in different growth conditions which, with the genomic information has allowed genome scale metabolic models to be refined and we have now published our first work in this area. These models will also allow us to understand how changes in gene content favour survival of some strains rather than others. This work is achieving the original objectives of the project.
Exploitation Route Understanding how biofilms evolve will help inform eradication and control strategies and inform risk of development of AMR. Understanding how campylobacter and Salmonall 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. The TraDIS-Xpress platform can be used to discover targets or optimise bacterial strains for 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 impacts beyond the traditional academic route in a number of ways. We have provided expert advice to the UK government for its review on AMR strategy, and to parliamentarians re AMR as well as advising the WHO/FAO about multiple issues including the impact of disinfection in the food chain on AMR. One of our GLs has been appointed to the Advisory Committee for the Microbial Safety of Food (ACMSF).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. We have engaged with Industry and have multiple new projects working from the level of iCASE partnerships, joint funding from Innovate UK and significant contract funding as well as meetings to share advice. These activities relate to our expertise in genomics and biofilms being used to help industry develop new antimicrobial products, reduce antibiotic use in animal husbandry and ensure project safety. We have continued to engage with the public with showcases of our research and how it relates to peoples every day lives being made at major science festivals as well as delivering webinars to a global audience and providing expert commentary for numerous pieces in the media and advice to documentary makers. We have also protected technological innovations and have filed three patents to secure IP around some of our work with novel oligosaccharides and functional genomics. These pieces of IP will allow exploitation of out new methods with market research suggesting there is significant interest in our bacterial functional genomics work in multiple sectors.
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 Contribution to call for evidence - A new UK research funding agency
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL https://committees.parliament.uk/call-for-evidence/119/a-new-uk-research-funding-agency/
 
Description EU Report (Refresh) on the valorisation of putrescible waste
Geographic Reach Europe 
Policy Influence Type Participation in a 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 Gave evidence to a government 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 Feedback to WHO Guidance document draft for microbiological risk assessment
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
 
Description Health and Social Care Committee
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
 
Description POSTnote on AMR
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
URL https://researchbriefings.parliament.uk/ResearchBriefing/Summary/POST-PN-0595
 
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 advisory committee
URL https://reform.uk/events/role-big-data-transforming-nhs-practical-steps-forward
 
Description UK Research and Development Roadmap Survey
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/9543...
 
Description Written response to Governments 5 year AMR plan
Geographic Reach National 
Policy Influence Type Gave evidence to a government 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 £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
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 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 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 01/2022 
End 12/2024
 
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 06/2018 
End 06/2019
 
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 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 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 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 - 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 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 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 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 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 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 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 LIMITED 
Description A new spin out company that derived from ArcVax was formed on 20/10/2020. The company won a competitive accelerator award and currently has labs at Babraham Research Park, Cambs and focuses on using novel glycoengineering technology for the development of glycoconjugate vaccines with a particular emphasis on animal vaccines 
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.
 
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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- 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 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 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 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 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