Microbial ecology and metagenomics of a foodborne pathogen
Lead Research Organisation:
University of East Anglia
Department Name: Postgraduate Research Service
Abstract
Campylobacter is the commonest bacterial cause of diarrhoeal disease in the UK, where is it most often associated with the consumption of poultry, and amongst the top five causes of diarrhoeal disease in low and middle-income countries, where transmission routes are unclear. The detection of Campylobacter is challenging as it is difficult to grow in the laboratory, suggesting an important role of the microbial communities in which Campylobacter thrives - in laboratory conditions it is grown as a pure culture. Metagenome, culture independent, sequencing of samples where Campylobacter is found, offers an approach which can be used to examine the interaction between Campylobacter and the total microbial diversity of a sample.
This multidisciplinary project will examine the microbial communities associated with both the presence and absence of Campylobacter on chicken. This may suggest novel mechanisms to reduce the survival of Campylobacter in the food chain. This project will include both wet lab and dry lab components; culturing for the diversity of Campylobacter, exploring competitive exclusion of Campylobacter, and whole genome and metagenome sequencing and analysis.
This multidisciplinary project will examine the microbial communities associated with both the presence and absence of Campylobacter on chicken. This may suggest novel mechanisms to reduce the survival of Campylobacter in the food chain. This project will include both wet lab and dry lab components; culturing for the diversity of Campylobacter, exploring competitive exclusion of Campylobacter, and whole genome and metagenome sequencing and analysis.
Organisations
People |
ORCID iD |
Publications
Dziegiel A
(2025)
Microbial ecology and metagenomics of a foodborne pathogen
Dziegiel AH
(2024)
High Campylobacter diversity in retail chicken: epidemiologically important strains may be missed with current sampling methods.
in Epidemiology and infection
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/T008717/1 | 30/09/2020 | 29/09/2028 | |||
| 2445272 | Studentship | BB/T008717/1 | 30/09/2020 | 29/09/2024 |
| Description | This project has uncovered diversity of Campylobacter on individual retail chicken samples that has been previously under-studied and highlighted the effect of isolation method on recovery, which may affect outbreak investigations. The project also explored whether or not direct sequencing of whole samples with metagenomics can be used for pathogen detection and characterisation with a major focus on Campylobacter. Detection and characterisation of Campylobacter from retail chicken metagenomes can be difficult, though exploration of metagenomics-based detection of Salmonella in clinical cases suggests that this may be dependent on the specific pathogen of interest, its abundance and diversity. While detection and characterisation is more likely in clinical samples, metagenomics-based pathogen typing methods require further improvement (such as enriching for the pathogen) for accurate detection. |
| Exploitation Route | Findings from this project may be of interest to policymakers and public health professionals, due to their relevance for pathogen detection method development and potential implications on Campylobacter outbreak tracking. |
| Sectors | Agriculture Food and Drink |
| Description | EU Reference Laboratory for Campylobacter Annual Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited presentation at the EU Reference Laboratory for Campylobacter Annual Workshop. The director of the EU Reference Laboratory for Campylobacter got in touch to ask for a presentation following our publication on Campylobacter diversity on retail chicken. They were interested in the work given their discussions of the current ISO standard and sequencing application in the context of outbreak detection. The presentation fuelled interesting questions and discussion for the NRL network. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Engagement with Government - UKHSA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | The knowledge exchange of this meeting has informed the UKHSA on Campylobacter trends and diversity in food and human samples, along with metagenomic approaches to clinical specimens. This has influenced the research and validation UKHSA are considering in these areas. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Engagement with Industry - KraftHeinz |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | This was a group discussion with the global Microbiology lead at KraftHeinz. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Engagement with Industry Cranswick Foods) - discussion session |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | This was an opportunity to discuss potential collaborations with Industry and share research findings that may be beneficial in food production. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Engagement with Visiting Scientists from Canada's National Microbiology Laboratory |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Scientists from Canada's National Microbiology Laboratory visited the institute, listened to talks and engaged in discussions about food safety monitoring. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Engagement with project collaborators |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Knowledge exchange of Quadram Institute research highlights and Norfolk and Norwich University Hospital/Eastern Pathology Alliance lab updates |
| Year(s) Of Engagement Activity | 2023 |
| Description | MeatingPod interview |
| 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 | Industry/Business |
| Results and Impact | We were approached by an editor of MeatingPlace magazine to appear on their MeatingPod podcast to discuss our work on Campylobacter diversity on retail chicken. The podcast aims to engage with the meat processing industry and professionals on matters including food safety. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Medical Research Foundation National PhD Training Programme in AMR Research 6th Annual Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | This was a talk and poster presented at a conference organised by the Medical Research Foundation National PhD Training Programme in AMR Research, which was a great opportunity to share research outputs and network with other early career researchers working in the field |
| Year(s) Of Engagement Activity | 2023 |
| Description | Norwich science festival 2021 |
| 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 | The activity involved hosting an activity table with a game aimed at children and their parents to learn about microbiology and evolution. This was a one-day event at the Forum in Norwich, part of the Norwich Science Festival. The feedback from participants indicated interest and eagerness to learn more about the subject area. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Quadram Institute Student Science Showcase |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | This was a presentation at the Institute Student Science Showcase, organised to share research outputs from students to the wider institute research community. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Visit to Quadram Institute and policy roundtable with Food Standards Agency Chief Scientific Adviser Prof Robin May |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Prof Robin May visited the institute and researchers involved in food safety research gave presentations about their work. This was followed by discussions about the implications of the findings. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Year 10 science camp |
| 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 activity involved a virtual workshop for Year 10 students in order to inspire and inform about careers in science. As part of the activity, PhD students did a presentation about their work and journey into science. This was followed by a Q&A session, and the feedback indicated that the students were more informed and more likely to pursue a career in science. |
| Year(s) Of Engagement Activity | 2021 |