Microbes and Food Safety: Microbial threats from foods in established and evolving food systems
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
To identify where and when microbial threats emerge in traditional and novel foods through an improved understanding of their genotypic variation metabolic potential and interactions within microbial communities.
Planned Impact
unavailable
Publications
Simmonds P
(2024)
Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2024).
in Archives of virology
Sidorczuk K
(2024)
adhesiomeR: a tool for Escherichia coli adhesin classification and analysis
in BMC Genomics
Bloomfield SJ
(2024)
Genomic characterization of Pseudomonas spp. on food: implications for spoilage, antimicrobial resistance and human infection.
in BMC microbiology
Wojtowicz EE
(2024)
Low protein diet protects the liver from Salmonella Typhimurium-mediated injury by modulating the mTOR/autophagy axis in macrophages.
in Communications biology
Dziegiel AH
(2024)
High Campylobacter diversity in retail chicken: epidemiologically important strains may be missed with current sampling methods.
in Epidemiology and infection
Pye HV
(2024)
Phage diversity in One Health.
in Essays in biochemistry
Pye HV
(2023)
Strain and serovar variants of Salmonella enterica exhibit diverse tolerance to food chain-related stress.
in Food microbiology
| Description | Expert Advice to Food Standards Scotland |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | Expert Advice to UK Government (FSA) |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | Expert Advice to UK Government (FSA) |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | The ACMSF committee members all have a part in influencing the FSA on using scientific evidence and expert advice on matters pertaining to foodborne pathogens. This in turn influences regulatory bodies and works towards effective solutions for societal and public health challenges. The influence also has impact on effectiveness of public service delivery where applicable to topics raised to the ACMSF members |
| Description | Invited member of the PATH-SAFE Consortium Data Platform Development Effort Community Input Advisory Group |
| Geographic Reach | Europe |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.food.gov.uk/our-work/path-safe-programme-national-foodborne-disease-genomic-data-platfor... |
| Description | BBSRC ICURe Explore Programme |
| Amount | £35,000 (GBP) |
| Organisation | United Kingdom Research and Innovation |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 06/2024 |
| Description | Exploring variation within Salmonella Dublin using sequencing and multi-model phenotyping to define markers of virulence and zoonosis |
| Amount | £974,479 (GBP) |
| Funding ID | BB/Z516673/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2025 |
| End | 01/2028 |
| Description | Klebsiella, phages and the capsule: what's going on? |
| Amount | £115,000 (GBP) |
| Funding ID | BB/T008717/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2023 |
| End | 09/2027 |
| Description | MEtaGenome-informed Antimicrobial resistance Surveillance: Harnessing long-read sequencing for an analytical, indicator and risk assessment framework |
| Amount | £366,426 (GBP) |
| Funding ID | MR/Y034457/1 |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 01/2027 |
| Title | Listeria - benchmarking panel of international isolates |
| Description | A benchmarking panel of significant Listeria strains created by and contributed from the Public Health Agency of Canada, Health Canada, Canadian Food Inspection Agency and Quadram Institute. Strains represent key public health events and natural biological variants. |
| Type Of Material | Biological samples |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | A key enabling panel for studies within the UK - Canada international partnership |
| Title | Use of hybrid assembly to characterise Campylobacter genomes |
| Description | This bioinformatic technique was used for approx 800 genomes from my research collection of Campylobacter genomes in support of genomic characterisation |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | This dataset is the base for further method development to understand population diversity of Campylobacter using novel techniques |
| Description | Bioinformatic pipelines for Campylobacter population structure |
| Organisation | Utrecht University |
| Department | Institute for Risk Assessment Sciences |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | This partnership is a shared interest in the population structure and strain level difference in Campylobacter. We have contributed >1,000 genomes for shared analysis and testing of novel bioinformatic pipeline approaches. |
| Collaborator Contribution | Our Risk Assessment Institute, Utrecht University |
| Impact | Outcomes thus far have been the appointment of a Master's student (Utrecht University) to the project and monthly progress meetings |
| Start Year | 2022 |
| Description | Collaboration with Huvepharma |
| Organisation | Huvepharma |
| Country | Bulgaria |
| Sector | Private |
| PI Contribution | Attracted funding for a CASE studentship to work with Huvepharma. My research group is providing expertise in molecular biology, pathogen genomics, gut metagenomics and phage biology to work with Huvepharma to develop technologies and materials to develop potential products for the use as antimicrobials and probiotics in livestock feed. |
| Collaborator Contribution | Huvepharma provide expertise in developing products and their commercialisation for use in the feed industry. |
| Impact | Successfully attracted funding for a studentship to develop antimicrobials |
| Start Year | 2023 |
| Description | Collaboration with professor Amit Rai India |
| Organisation | National Agri-Food Biotechnology Institute |
| Country | India |
| Sector | Public |
| PI Contribution | We hosted the visit of prof Amit Rai to QIB and In March 20204 Arjan Narbad visited NABI-DTP institute and gave a presentation and discussed further collaboration. |
| Collaborator Contribution | Prof Rai visited QIB in February 2024 and this resulted in further planned collaboration grant applications to extend the link between QIB and NABI-DBT institute. Joint experimental work is planned. |
| Impact | Further short term funding to undertake collaboration experimental work via staff exchange from NABI to QIB. |
| Start Year | 2024 |
| Description | Microevolution of Salmonella enterica serovar Typhimurium - molecular basis of emerging threats to human health |
| Organisation | UK Health Security Agency |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Collaboration with UKHSA where together we add value to routine surveillance data aimed at understanding what drives the emergence of food borne bacterial pathogens. This information can be used to inform policy, practice and interventions aimed at decreasing the burden of food born infections. We provide expertise in bacterial genomics. |
| Collaborator Contribution | UKHSA provide expertise in surveillance and epidemiology |
| Impact | Poster and oral presentation of research plans and analysis |
| Start Year | 2024 |
| 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 |
| Title | BACTERIOPHAGE COMPOSITIONS |
| Description | A method of identifying and/or isolating one or more bacteriophages that display lytic activity against at least one target bacterial genus, species, or strain. The method includes the creation of a transposon mutant library using at least one bacterial strain from said genus or species and identifying the genes involved in resistance and/or susceptibility by exposing said library to at least one or more bacteriophages. |
| IP Reference | WO2025008620 |
| Protection | Patent / Patent application |
| Year Protection Granted | 2025 |
| Licensed | No |
| Title | Metaprokka |
| Description | A fork of "prokka" focused on improving annotation results when analysing phage genomes (or metagenomes including virome) |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Open Source License? | Yes |
| Impact | A publication (https://pmc.ncbi.nlm.nih.gov/articles/PMC11210395/) where the impact of using appropriate genetic codes for gene prediction in phages was analysed. Metaprokka implements the methods and allows others to apply it to their datasets. |
| URL | https://bioconda.github.io/recipes/metaprokka/README.html |
| Description | Activity stand - Be a Pathogen Detective |
| 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 | An interactive activity where children had the chance to experience the process of pathogen isolation from a patient, followed by pathogen identification and reporting, in a child friendly manner. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Attendance and presentation of research at Salmonella Biology and Pathogenesis Gordon Research Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dissemination of research findings and discussion on latest research activities in the global Salmonella research field. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Discussion with a leading producer of raw pet food |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Discussion with a leading producer of raw pet food to implement phage antimicrobials to improve the safety of product. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Discussion with representative from the British Retail Consortium |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Discussion with representative from the British Retail Consortium to identify potential implementation of phage antimicrobials to combat bacterial pathogens in the food chain |
| Year(s) Of Engagement Activity | 2024 |
| Description | Festival of Genomics and Biodata |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Talk at the Festival of Genomics and Biodata in London |
| Year(s) Of Engagement Activity | 2025 |
| Description | Food Safety Research Network Community meeting |
| 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 | Participation in the Food Safety Research Network Community meeting in Birmingham in February 2024 to network to exchange knowledge on approaches to improve food safety and disseminate our activities in the use of phage as antimicrobials and the impact of copper on Salmonella in pigs. Potential applications and needs of industry were established. Contacts for further discussion were identified. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Hosted 1-week visit of scientists from the Public Health Agency of Canada's Advanced Genomics Unit |
| 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 | Support project planning and strategic connections on shared interests in genomics, bioinformatics, and metagenomics |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited seminar presentation to Cefas |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Presentation to the Centre for Environment, Fisheries and Aquaculture Science on genomic epidemiology approaches applied to food safety |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited webinar speaker to PATH-SAFE |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Invited speaker to UK government-funded PATH-SAFE programme (Pathogen Surveillance in Agriculture, Food and Environment) webinar series on the genomic epidemiology of foodborne organisms |
| Year(s) Of Engagement Activity | 2023 |
| Description | Knowledge exchange with UKHSA enteric pathogen surveillance team |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Meeting to share analysis of surveillance data that adds value to UKHSA core activities to improve public health |
| Year(s) Of Engagement Activity | 2025 |
| Description | Listeria project planning discussions with UKHSA |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | January 2024 visit of Quadram's Listeria group (staff and students) to UKHSA Colindale to exchange knowledge and plan for conjoint projects on Listeria genomics, Metagenomics, food microbiology |
| Year(s) Of Engagement Activity | 2024 |
| Description | Poster talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | This engagement was at the Microbiology Society Annual meeting where a poster on the characterisation of Campylobacter, the most prevalent foodborne bacterial pathogen in the UK, using metagenomic approaches. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation at plasmid workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Invited presentation to plasmid workshop to discuss research on AMR and plasmids |
| Year(s) Of Engagement Activity | 2023 |
| Description | Project planning with global food producer |
| 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 | Site visit to Quadram and project planning regarding investigation of food spoilage using microbiology, genomics and metagenomics |
| Year(s) Of Engagement Activity | 2024 |
| Description | Seminar presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | The hybrid Seminar event, hosted by George Mason University Science and Technology Campus included approx 55 participants across higher education staff from senior management, academics, post graduate and undergraduate students, post doctoral staff and researchers. The topic of discussion was the application of metagenomics in understanding complex transmission dynamics of zoonotic pathogens. This was followed by round table discussions with students and early career researchers. |
| Year(s) Of Engagement Activity | 2024 |
| Description | The NIHR Health Protection Research Unit in Genomics and Enabling Data Conference 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The NIHR Health Protection Research Unit in Genomics and Enabling Data Conference 2024 |
| Year(s) Of Engagement Activity | 2024 |
| Description | UKHSA-QIB "Afternoon of Campy" Seminar Talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The day long seminar and facility visit was attended by QIB researchers and UKHSA staff. I presented on Campylobacter trends and characterisation methodology research as well as conducted meetings with gastroenterics reference laboratory staff at UKHSA. |
| Year(s) Of Engagement Activity | 2024 |