Microbial Communities in the Food Chain
Lead Research Organisation:
Quadram Institute Bioscience
Department Name: Contracts
Abstract
We will explore the chicken gut microbiome using culture-based and sequence-based approaches. We will document the microbial ecology of Salmonella and E. coli in the food chain to prime novel ecological and synthetic biology strategies for preventing the spread of pathogens and AMR.
Organisations
Publications
Baker DJ
(2021)
CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes.
in Genome medicine
Chewapreecha C
(2019)
Genetic variation associated with infection and the environment in the accidental pathogen .
in Communications biology
Foster-Nyarko E
(2020)
Gambian poultry isolates from hyperendemic group of AMR Escherichia coli strains in sub-Saharan Africa
in Access Microbiology
Foster-Nyarko E
(2020)
Genomic diversity of Escherichia coli isolates from healthy children in rural Gambia
Foster-Nyarko E
(2021)
Genomic diversity of from healthy children in rural Gambia.
in PeerJ
Foster-Nyarko E
(2020)
Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
in Microbial Genomics
Gilroy R
(2020)
A Genomic Blueprint of the Chicken Gut Microbiome
| Description | Novel bacterial species identified in the chicken gut Display of useful enzymes on the bacterial flagellum |
| Exploitation Route | Identification of novel species in the chicken gut will inform all future studies on this microbiome; might allow identification of novel probiotics Smart probiotics could perhaps be developed incorporating enhanced flagellar display |
| Sectors | Agriculture, Food and Drink,Pharmaceuticals and Medical Biotechnology |
| 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 | 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 | 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 | Characterisation of large flagellins |
| Organisation | Imperial College London |
| Department | Imperial College Business School |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Laboratory and bioinformatics work on large flagellins |
| Collaborator Contribution | Laboratory and bioinformatics work on large flagellins |
| Impact | http://pubmed.org/30462661,29258714 |
| Start Year | 2018 |
| Description | Chicken gut metagenome |
| Organisation | London School of Hygiene and Tropical Medicine (LSHTM) |
| Department | Department of Pathogen Molecular Biology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have agreed to perform metagenomic sequencing of chicken samples |
| Collaborator Contribution | They have agreed to supply the chciken samples |
| Impact | None yet. |
| Start Year | 2018 |
| Description | Chicken gut microbiome investigations |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have performed metagenome sequencing on chicken faecal samples |
| Collaborator Contribution | Roberto La Ragione and his team have provided us with chicken faecal samples |
| Impact | Generation of metagenome sequences and metagenome-assembled genomes from chicken faeces |
| Start Year | 2019 |
| Description | Chicken gut microbiome investigations |
| Organisation | University of Surrey |
| Department | School of Veterinary Medicine |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have performed metagenome sequencing on chicken faecal samples |
| Collaborator Contribution | Roberto La Ragione and his team have provided us with chicken faecal samples |
| Impact | Generation of metagenome sequences and metagenome-assembled genomes from chicken faeces |
| Start Year | 2019 |
| Description | Gambian Chicken metagenomics |
| Organisation | London School of Hygiene and Tropical Medicine (LSHTM) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Metagenomic sequencing of chicken and guinea fowl caecal samples |
| Collaborator Contribution | Harvesting and supply of relevant samples. |
| Impact | No publication outputs so far, but sequences have been generated |
| Start Year | 2017 |
| 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 | 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 | 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 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 | MRC-CLIMB workshop in The Gambia, 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A CLIMB delegation ran a bioinformatics workshop in The Gambia, in collaboration with the MRC Unit in Fajara (The Gambia), that hosted the course. One day (Jan.22) was dedicated to set up the course (computer performance test, virtual machine, workshop simulation), then 21 students attended the three-day workshop (January 23-25) and were introduced to bioinformatics, cloud computing, Illumina and Nanopore sequencing, microbial genomics and metagenomics, phylogenesis and phylogenetic trees. Aims of the course were defined with Gambian tutors, and the activities were planned accordingly. The success of the workshop is well documented in a survey filled by participants at the end of the course: quality of presentations, assistance during the workshop, relevance for their research were reported to be very good or excellent. The MRC-CLIMB Unit in The Gambia is interested in making it an annual appointment. |
| Year(s) Of Engagement Activity | 2018 |
| 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 | 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 |