Epidemiology and Evolution of Pathogens in the Food Chain

Lead Research Organisation: Quadram Institute Bioscience
Department Name: Contracts

Abstract

We will survey of genotypic diversity of Salmonella and E. coli in the food chain to gain new insights into pathogen biology and evolution and exploit genome sequences in risk assessment. Two parallel projects will be employed to deliver this objective, a structured epidemiological investigation for the comparison of Salmonella and E. coli from domestic and imported food, and an intensive batch enrichment approach aimed at the isolation of as greater diversity of Salmonella from pork and poultry food at retail. Samples from the structured epidemiological set will undergo enrichment and culture for Salmonella and E. coli. The AMR phenotype of isolates will be determined and DNA extracted for WGS on the Illumina platform. We will determine bacterial population structure and investigate phylogenetic signals and AMR genes in isolates from imported and domestic food. Using the diversity sample set, we will investigate the population structure of isolates from the pork and poultry by whole genome sequencing (WGS) and phylogenetic reconstruction. We will make comparisons with all Salmonella genomes in public databases using the BBSRC-funded Enterobase (http://enterobase.warwick.ac.uk) and with S. Typhimurium genomes collected from ten European countries by the Compare Consortium (http://www.compare-europe.eu) in collaboration with APHA, a consortium member. We will also develop and validate methods to detect and characterise pathogens and AMR genes in food without the need for culture by optimising protocols for metagenomic long-read nanopore sequencing.

We will characterise microbial populations of three sentinel bacteria (Campylobacter, E. coli, Salmonella) found in animals and in the environment across multiple farms in the Wye Valley to develop a comprehensive framework for source attribution of E. coli recovered from animals, the farm and the wider environment and assay survival and gene expression in relevant environments. A subset of 160 isolates will be subjected to long-read sequencing to investigate mobile elements relevant to virulence and AMR. We will determine the population structures and core/pan genome of Campylobacter, Salmonella and E. coli from linked environments. On a subset of environmental isolates attributed to animals, we will assay survival and gene expression in relevant environments, examining changes in gene expression via RNA-Seq.

We will use state-of-the-art bacterial GWAS to evaluate L. monocytogenes genetic variation in food and clinical isolates. Furthermore, we will investigate the phylogenetic distribution of putative essential genes for survival in the food chain identified in functional genomics experiments. Identify AMR genes/mutations and mobile genetic elements within L. monocytogenes genomes and evaluate temporal trends. We will use Oxford nanopore long-read sequencing, building on the techniques developed by O’Grady, to obtain finished L. monocytogenes genomes directly from food and identify to the sub-species level.

Publications

10 25 50
 
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 In a pilot study of the diversity of Salmonella in food, we identified S. Typhimurium as the dominant serotype. We have therefore carried out an analysis of the diversity of this serotype in animals and human infections using a representative collection of isolates from Public Health England and Animal and Plant Health Agency.

We have explored the genetic relationship of a collection of isolates that represent a large part of the diversity of S. Typhimurium, using whole genome sequencing. We found that S. Typhimurium evolved to form two major groups that differ in their distribution in livestock and wild avian species. The livestock-associated group contained isolates commonly affecting human health and were often drug resistant, while the wild avian-associated group was rarely associated with drug resistance and less frequently associated with human infection. We report distinct evolutionary processes acting on subgroups of S. Typhimurium including loss of information content of genomes, and gain and loss of genes predicted to affect functions such as antimicrobial resistance and disease potential. This study provides a framework in which to understand the epidemiology of Salmonella and improve assessment of its risk to animal and human health.
Exploitation Route Our initial analysis has identified signatures and biomarkers of risk to food safety for Salmonella Typhimurium. This information will be useful to stakeholders with an interest in surveillance and policy decisions aimed at decreasing the chances of Salmonella entering the food chain and ensuring public health.
Sectors Agriculture, Food and Drink,Healthcare

 
Description Activities from this theme have mainly provided impact in evidence for policy development to the UK government, Food Standards Agency (FSA), the European Food standards Agency (EFSA), and UKRI. We have provided expert evidence to EFSA on the use of NGS to monitor antimicrobial resistance, the use of 'omics in risk assessment, to the UK government on antimicrobial resistance and Health and Social Care committee, and the FSA through frequent update meetings. We have also participated in an advisory committee on China-UK AMR workshop.
First Year Of Impact 2019
Sector Agriculture, Food and Drink,Healthcare,Government, Democracy and Justice
 
Description CRITICAL ASSESSMENT OF THE USE OF NGS FOR THE MONITORING OF AMR ACROSS DIFFERENT ECOLOGICAL COMPARTMENTS
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
URL https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6039958/
 
Description China-UK AMR workshop 2019 run by UKRI, Department of Health and Chinese partners - Beijing China, Dec 2019
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
 
Description EFSA Scientific Colloquium 24 -'omics in risk assessment: state of the art and next steps
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
URL https://www.efsa.europa.eu/en/supporting/pub/en-1512
 
Description Founding member and chair of the Public Health Alliance for Genomic Epidemiology Validation and QC working group
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
 
Description Founding member of the Public Health Alliance for Genomic Epidemiology Infrastructures working group
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
 
Description Health and Social Care Committee
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
 
Description Hosting PHE students
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Influenced training of practitioners or researchers
Impact Have hosted multiple students working with Public Health England at my institute for training in bioinformatics.
 
Description Member of the Genomics Partnership Wales IT Working Group
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact The IT working group has overseen the development of strategy for the implementation of the IT infrastructure to support genomics in healthcare in Wales. This has underpinned the development of clinical services based on genomics for the whole of Wales. In the pathogen area this has seen over 8,000 patient samples analysed using the infrastructure developed within the IT group.
 
Description Membership of Pathogen Genomics Operational Committee
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact This work has seen the development of 4 clinical services based on next generation sequencing. This has enabled the analysis of over 8,000 patient samples using NGS approaches, underpinned by software and infrastructure developed through UKRI funded research to Cardiff University. The systems that have been built have resulted in improvements in the speed of diagnoses/characterisation of pathogens, drops in cost of testing and increased generation of clinically actionable information from the tests undertaken.
 
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 The use of NGS to monitor antimicrobial resostance - European Commission Joint Research Centre (JRC)
Geographic Reach Europe 
Policy Influence Type Participation in a advisory committee
 
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 09/2020 
End 09/2024
 
Description Development of Key Technologies for Real-Time Diagnosis, Surveillance and Intervention of Resistant-Bacterial Infections Based on Nanopore Sequencing
Amount £730,000 (GBP)
Funding ID 104991 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 05/2019 
End 04/2022
 
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 07/2018 
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 04/2021
 
Description Genomic Diversity of Salmonella enterica in Zimbabwe
Amount £9,500 (GBP)
Organisation Quadram Institute Bioscience 
Sector Academic/University
Country United Kingdom
Start 09/2019 
 
Description MRC iCASE programme
Amount £400,000 (GBP)
Funding ID MR/R015937/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 10/2018 
End 03/2022
 
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 08/2018 
End 02/2020
 
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 SP3: Scalable Software for Pathogen Reads to Clinical Results using Next Generation Sequencing
Amount £1,000,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2020 
End 02/2022
 
Title Saponin based host DNA depletion 
Description We developed a rapid and highly efficient method for removing host DNA (eg human, chicken, salmon etc) from samples when analysing the microbial content of a sample by metagenomics. This method was published in Nature Biotechnology in 2019 and is being used by multiple labs in multiple sectors (food, vererinary, human clinical). Organisations I am aware that are using our methods include: Public Health England, Harvard, University of Cambridge, University of Liverpool, University of Oxford, University of Birmingham, University of Bergen, Statens Serum Institute, Quadram Institute Bioscience (outside of my group), Guy's and St Thomas' Hospital, DSTL. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? Yes  
Impact This tool led to a major collaboration with Simcere Diagnostics in China and has led to follow on funding from Innovate UK. It has now also led to a new patent application (see patent section) and several collaborative scientific papers. 
 
Title Rapid lineage calling 
Description Our metagenomics data from respiratory samples and our understanding of diagnostics and AMR resistance and susceptibility prediction was influential in the development and optimisation of the RASE tool developed in collaboration with Harvard and published in Nature Microbiology in 2020.This tool is capable of determining whether selected pathogens are resistance or susceptible to antibiotics using metagenomics data within 5 minutes of testing. 
Type Of Material Data analysis technique 
Year Produced 2019 
Provided To Others? Yes  
Impact Several laboratories globally are starting to use the approach including University of Oxford and University of Bergen 
URL https://github.com/c2-d2/rase
 
Description Applying clinical metagenomics for the diagnosis of pneumonia 
Organisation University of Pittsburgh
Department Department of Medicine
Country United States 
Sector Academic/University 
PI Contribution I transferred out methods for performing clinical metagenomics on respiratory samples to my collaborator at Pittsburgh Medical School (Georgios Kitsios). He is now applying these methods to patient samples in Pittsburgh and achieving excellent results.
Collaborator Contribution Georgios Kitsios is now applying our respiratory metagenomics methods in Pittsburgh, currently in a research context, to diagnose hospital acquired and ventillator associated pneumonia. We have submitted an conference abstract together on his study and a journal publication will follow later this year.
Impact Metagenomic DNA sequencing of respiratory microbial communities for detection of etiologic pathogens of pneumonia in mechanically-ventilated adult patients - American Thoracic Society abstract
Start Year 2018
 
Description Bioinformatic tool development for the rapid analysis of clinical metagenomics data 
Organisation Harvard University
Department Harvard T.H. Chan School of Public Health
Country United States 
Sector Academic/University 
PI Contribution We transferred out respiratory clinical metagenomics data to Harvard (William Hanage) for bioinformatic tool development and analysis. Nobody else in the world had nanopore respiratory metagenomics data.
Collaborator Contribution Bill Hanage and colleagues developed a bioinformatic tool to rapidly genotype respiratory pathogens. He tested this on bacterial isolated, which worked well. Then he heard we had respiratory metagenomes and he applied his tools on our data. It was then possible to predict antimicrobial resistance/susceptability directly from metagenomics data within 5 mins.
Impact Lineage calling can identify antibiotic resistant clones within minutes - BioXriv preprint currently under review in Nature Biotechnology.
Start Year 2018
 
Description Collaboration with Public Health Wales related to pipeline development and C. difficile tracking/typing 
Organisation Public Health Wales NHS Trust
Country United Kingdom 
Sector Public 
PI Contribution The research team is contributing: - Expertise in software development and software outputs generated by this research activity to aid the development of pathogen processing pipelines that will be used in clinical service use. - Training for interpretation of software results - Resources for the analysis and interpretation of samples isolated from food sources, linking this to clinical data
Collaborator Contribution Public Health Wales have developed a set of clinical services built on an HPC infrastructure to examine C. difficile, and is building services for examining antimicrobial resistant pathogens. As part of this collaboration, PHW have shared existing software they have developed, and are providing access to the genomic sequence data for over 1,000 samples that they have sequenced, as well as support in clinical interpretation and specialist knowledge around anaerobic bacteria.
Impact The outputs from the collaboration to date are still internal, and are currently under development but are scheduled to include; A large linked dataset of C. difficile from clinical, environmental and food sources Software for performing QC on sequence data A pipeline for performing relatedness analysis for food and clinical samples for a range of species
Start Year 2018
 
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 Oxford Nanopore Technologies collaboration 
Organisation Oxford Nanopore Technologies
Country United Kingdom 
Sector Private 
PI Contribution We are working closely with ONT to develop clinical metagenomics applications in diseases such as UTIs, pneumonia and meningitis.
Collaborator Contribution ONT have co-funded a PhD student in my lab, are an iCASE partner and have provided financial and in-kind contributions to a number of my research projects. They have hosted one PhD student and will host another next year at ONT for 3 months where they have been trained in bioinformatics and library preparation techniques.
Impact 1. ASHTON, P. M., NAIR, S., DALLMAN, T., RUBINO, S., RABSCH, W., MWAIGWISYA, S., WAIN, J. & O'GRADY, J. 2015. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol, 33, 296-300. 2. BRINDA, K., CALLENDRELLO, A., COWLEY, L., CHARALAMPOUS, T., LEE, R. S., MACFADDEN, D. R., KUCHEROV, G., O'GRADY, J., BAYM, M. & HANAGE, W. P. 2018. Lineage calling can identify antibiotic resistant clones within minutes. bioRxiv. 3. CHARALAMPOUS, T., RICHARDSON, H., KAY, G. L., BALDAN, R., JEANES, C., RAE, D., GRUNDY, S., TURNER, D. J., WAIN, J., LEGGETT, R. M., LIVERMORE, D. M. & O'GRADY, J. 2018. Rapid Diagnosis of Lower Respiratory Infection using Nanopore-based Clinical Metagenomics. bioRxiv, 387548. 4. IP, C. L. C., LOOSE, M., TYSON, J. R., DE CESARE, M., BROWN, B. L., JAIN, M., LEGGETT, R. M., ECCLES, D. A., ZALUNIN, V., URBAN, J. M., PIAZZA, P., BOWDEN, R. J., PATEN, B., MWAIGWISYA, S., BATTY, E. M., SIMPSON, J. T., SNUTCH, T. P., BIRNEY, E., BUCK, D., GOODWIN, S., JANSEN, H. J., O'GRADY, J., OLSEN, H. E., MIN, I. O. N. A. & REFERENCE, C. 2015. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Res, 4, 1075. 5. JAIN, M., KOREN, S., MIGA, K. H., QUICK, J., RAND, A. C., SASANI, T. A., TYSON, J. R., BEGGS, A. D., DILTHEY, A. T., FIDDES, I. T., MALLA, S., MARRIOTT, H., NIETO, T., O'GRADY, J., OLSEN, H. E., PEDERSEN, B. S., RHIE, A., RICHARDSON, H., QUINLAN, A. R., SNUTCH, T. P., TEE, L., PATEN, B., PHILLIPPY, A. M., SIMPSON, J. T., LOMAN, N. J. & LOOSE, M. 2018. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol, 36, 338-345. 6. JAIN, M., TYSON, J. R., LOOSE, M., IP, C. L. C., ECCLES, D. A., O'GRADY, J., MALLA, S., LEGGETT, R. M., WALLERMAN, O., JANSEN, H. J., ZALUNIN, V., BIRNEY, E., BROWN, B. L., SNUTCH, T. P., OLSEN, H. E., MIN, I. O. N. A. & REFERENCE, C. 2017. MinION Analysis and Reference Consortium: Phase 2 data release and analysis of R9.0 chemistry. F1000Res, 6, 760. 7. SCHMIDT, K., MWAIGWISYA, S., CROSSMAN, L. C., DOUMITH, M., MUNROE, D., PIRES, C., KHAN, A. M., WOODFORD, N., SAUNDERS, N. J., WAIN, J., O'GRADY, J. & LIVERMORE, D. M. 2017. Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing. J Antimicrob Chemother, 72, 104-114.
Start Year 2014
 
Description Simcere collaboration 
Organisation Simcere Diagnostics
Country China 
Sector Private 
PI Contribution We have transferred methods to Simcere and will continue to work with them as part of a new grant (Innovate UK UK-China AMR grant) to develop these methods for clinical implementation.
Collaborator Contribution Simcere are further developing our methods to clinical standards for future implementation.
Impact Follow on funding - an Innovate UK grant
Start Year 2018
 
Title Rapid metagenomics based diagnosis of nosocomial pneumonia 
Description We have developed a rapid (6hr) metagenomics sequencing method for diagnosis of nosocomial pneumonia. This method is currently being evaluated in comparison with PCR tests in the INHALE trial (NIHR, £2.5M). 
Type Diagnostic Tool - Non-Imaging
Current Stage Of Development Early clinical assessment
Year Development Stage Completed 2018
Development Status Under active development/distribution
Clinical Trial? Yes
UKCRN/ISCTN Identifier NIHR funded trial: RP-PG-0514-20018 INHALE: Potential of Molecular Diagnostics for Hospital-Acquired and Ventilator-Associated Pneumonia in UK Critical Care
Impact This method has generated a lot of interest and is being used by a lot researchers around the world. The ones that I am aware of, as I am directly collaborating with them, are: Pittsburgh Medical School, University of Bergen, PHE, University of Oxford, University of Cambridge, Harvard and one large Chinese multinational company. 
URL https://www.biorxiv.org/content/10.1101/387548v1
 
Title Simcere respiratory metagenomics products 
Description Simcere Diagnostics, a division of Simcere Pharmaceuticals (top 100 Chinese pharma company with >5000 employees), have developed a nanopore sequencing based respiratory metagenomics test in collaboration with O'Grady (and incorporates O'Grady's host depletion technology). This test is being used in multiple hospitals across China. This collaboration is the basis of an Impact Case for REF 2021. 
Type Diagnostic Tool - Non-Imaging
Current Stage Of Development Early clinical assessment
Year Development Stage Completed 2019
Development Status Under active development/distribution
Impact Development of this product led to further funding from Innovate UK (UK-China AMR grant >£1million between UK and Chinese partners). It has also led to clinical evaluation study on >200 patients - the paper on this study was submitted in March 2020. Impact Case for REF 2021. 
 
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
 
Description AMR workshop Canada 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact "Towards a Human and Animal Health Risk Assessment for Foodborne and Environmental Antimicrobial Resistance", International Expert Workshop, 3-7 March 2019. The workshop comprised 40 international experts on AMR; projected outcomes include a publication.
Year(s) Of Engagement Activity 2019
 
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 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 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 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 Genomics Partnership Wales meeting with Bahraini delegation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Introducing pathogen genomics to a delegation from Bahrain who are working to plan for setting up a genomics programme
Year(s) Of Engagement Activity 2019
 
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 Food production site visit 
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 Visit to a ready to eat food production site to discuss bacterial pathogens in the food processing environment and interaction with bacterial communities.
Year(s) Of Engagement Activity 2017
 
Description Gave an Eijkman Lecture at Infection and Immunity, Utrecht University, Utrecht, The Netherlands, Dec 6, 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Gave a presentation entitled "Applications and complications: Using genomics to understand bacterial transmission and antimicrobial resistance"
Year(s) Of Engagement Activity 2019
 
Description Impact showcase talk at Supercomputing, Denver 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact This talk introduced how the application of HPC/Cloud computing is being used to derive insight from genomics to track and treat pathogens. The venue for the talk was the Supercomputing conference, one of the largest conferences for computer science in the world, with many of the audience being from industry and other areas. Further engagement with industry followed the talk.
Year(s) Of Engagement Activity 2019
 
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 speaker at Microbes in Norwich event 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact I was an invited speaker at the 2019 Microbes in Norwich symposium, giving a talk entitled "Bugs, drugs and evolution: Genomic epidemiology of drug-resistant infections"
Year(s) Of Engagement Activity 2019
 
Description Invited speaker at the Evolution and Infection Symposium, Amsterdam, The Netherlands, Oct 4, 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invited speaker to the Evolution and Infection Symposium in Amsterdam, speaking on "Antimicrobial resistance and the food chain"
Year(s) Of Engagement Activity 2019
 
Description Invited speaker to University of Cambridge Department of Veterinary Medicine Seminar series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other audiences
Results and Impact Presentation to faculty, staff and students at the Department of Veterinary Medicine at the University of Cambridge on the genomic epidemiology of bacterial antimicrobial resistance across the One Health spectrum
Year(s) Of Engagement Activity 2020
 
Description Invited speaker to University of Liverpool 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Other audiences
Results and Impact I was an invited speaker to the University of Liverpool's Institute of Integrative Biology's Genomes, Systems and Therapeutic Targeting Seminar Series, with a title entitled "Seeking sources and reservoirs of Salmonella using whole genome sequencing"
Year(s) Of Engagement Activity 2018
 
Description Invited speaker to afternoon symposium, Department of Veterinary Medicine, 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 Presentation was "Mining (meta)genomics for meaningful microbial matters: pathogen and AMR transmission across the One Health spectrum" delivered at an afternoon symposium
Year(s) Of Engagement Activity 2020
 
Description Invited speaker to give a seminar at the Norwegian Veterinary Institute, Oslo, Norway 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Presentation on "Whole genome sequencing and metagenomics to understand bacterial transmission and antimicrobial resistance" on 24 February 2020
Year(s) Of Engagement Activity 2020
 
Description London International Youth Science Forum 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact I spent the day with the participants involved with this forum, which involves 500 students aged 16-21 from 70 different countries. I gave a lecture entitled 'Antimicrobial resistance - an evolving and international problem' to 40-50 of the participants, and then discussed key areas of debate around this issue.
Year(s) Of Engagement Activity 2018
URL https://www.liysf.org.uk/
 
Description PANDORA project MinION workshops 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Approx 40 PhD students and postdoctoral scientists from Europe and Africa attended 2 workshops on MinION sequencing (approx 20 on each occasion) which we taught on (Alp Aydin, PhD student O'Grady group and O'Grady) and helped organise for the PANDORA -ID network at UCL in London (The Pan-African Network For Rapid Research, Response, Relief and Preparedness for Infectious Disease Epidemics (PANDORA-ID-NET) is a €10 million grant funded by the European and Developing Countries Clinical trials Partnership).
Year(s) Of Engagement Activity 2019,2020
URL https://www.pandora-id.net/news
 
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 Participation at meeting to establish the Public Health Alliance for Genomic Epidemiology 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I participated in work to establish an international organisation to facilitate the development of standards for the application of genomics to epidemiology and public health. This work particularly involved engagement with researchers from Africa and the US CDC.
Year(s) Of Engagement Activity 2019
 
Description Participation in the SMBE workshop on Pathogen Transmission 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I participated in the SMBE workshop on Pathogen Transmission, which involved engagement with public health professionals, epidemiologists, basic scientists and other bioinformaticians. The engagement activity included presenting a talk, and engaging with colleagues, which have since resulted in at least one international grant applicataion.
Year(s) Of Engagement Activity 2018
 
Description Presentation to Welsh Assembly Comittee 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact This talk introduced pathogen genomics, and how it is enabled to a Welsh Assembly Committee, stimulating increased interest in this subject area and informing the committee on the uses of computational resources for the processing of pathogen genomic data.
Year(s) Of Engagement Activity 2019
 
Description Presenting a talk at the Clostpath 2019 conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented a talk summarising the results of collaborative work between Public Health Wales, Cardiff University and QIB in the area of whole genome sequencing and analysis of C. difficile in a clinical setting. The talk was presented at the main international conference for researchers working in the area, and was very well received. Outputs from the talk have included engagement with Chinese CDC, ECDC and infection control and public health surveillance in the Netherlands. Plans are already in progress to develop new projects building off of this work.
Year(s) Of Engagement Activity 2019
 
Description Press release on respiratory metagenomics Nature paper 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact We wrote and shared a press relaese on our Nature Biotechnology paper published in June 2019. It was covered by several print and online media outlets, leading to a high Altmetric score (260).
Year(s) Of Engagement Activity 2019
URL https://quadram.ac.uk/new-rapid-test-lower-respiratory-infections/
 
Description Providing content to be displayed at 'Food Matters Live' Industry Network Meeting 
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 Provided written content to be displayed, alongside images, during the Food Matters Live industry network meeting (please see below for exact content). The content focused on the transmission of pathogens through the food chain and highlighted the work being undertaken as part of this theme.

"By walking across different livestock farming sites and testing the mud samples on their boots, scientists from the Quadram Institute are looking at the transmission routes of harmful bacteria into the food chain. Knowing exactly at what point these pathogens enter the food chain, and how they evolve, spread, survive and compete with each other, will help in the development of strategies for more targeted interventions to reduce the burden of foodborne illness."
Year(s) Of Engagement Activity 2018
 
Description Ran a workshop at a Pathogen Transmission Conference. 
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 Ran a workshop during the Pathogen Transmission Conference, with a focus on audience participation.
Year(s) Of Engagement Activity 2018
 
Description Royal Norfolk Show - AMR research tent and Superbugs panel 
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 Demonstrating MinION naopore sequencing to school kids and the general public and explaining how we use it for the detection on pathogens and antimicrobial resistance. Also on a discussion panel re superbugs and how to control them. Both activities led to multiple questions on the nanopore technology and how we can use this British technology to control superbugs and fight AMR.
Year(s) Of Engagement Activity 2018
URL https://royalnorfolkshow.rnaa.org.uk/discovery-zone/
 
Description Science Museum Lates - Superbugs 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Interactive presentation on the rapid diagnosis of infection and antimicrobial resistance using metagenomics performed multiple times over the evening. 50-100 people were present for each presentation. Several people asked questions afterwards about the technology and the importance of diagnostics in the fight against AMR.
Year(s) Of Engagement Activity 2018
URL https://www.sciencemuseum.org.uk/see-and-do/lates
 
Description Seminar speaker at the Doherty Institute, University of Melbourne 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact I gave a seminar at the Doherty Institute, University of Melbourne entitled "Adventures in Salmonella sequencing: genomic epidemiological investigations of outbreaks and antimicrobial resistance"
Year(s) Of Engagement Activity 2018
 
Description Talk at NHS meeting on pathogen genomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A talk introducing bioinformatics for the analysis of pathogen genomic sequences in healthcare
Year(s) Of Engagement Activity 2019
 
Description UK AMR Funders Forum workshop 
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 I was an invited participant in this workshop, where the objective was to consider the evidence on antimicrobial workshop from a human, animal, agricultural/ food, and environmental perspective to identify research gaps and opportunities, and to help inform and better achieve policy objectives. The outcomes of the workshop informed the refresh of the UK AMR strategy and how it can be best delivered.
Year(s) Of Engagement Activity 2018
 
Description Workshop on WGS in healthcare 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I spoke at, and engaged with a workshop organised at RIVM in the Netherlands to introduce the pathogen genomics work that is going on in Wales. The engagement provoked detailed discussions following the event, with both researchers and with clinical staff.
Year(s) Of Engagement Activity 2020