Microbial Survival in the Food Chain

Lead Research Organisation: Institute of Food Research
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
 
Description 1. Biofilm evolution.
Our biofilm evolution work has demonstrated that development of increased biomass by a bacterial biofilm is not necessarily protective of antimcrobial stress and that biofilms are highly sensitive to exposure to low concentrations of antimicrobials which exert a strong evolutionary pressure to select resistance. This alters current understanding of biofilm physiology and impacts on AMR. This work is currently being prepared for submission for publication
Exploitation Route Understanding how biofilms evolve will help inform eradication and control strategies and inform risk of development of AMR.
Sectors Agriculture, Food and Drink,Energy,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Appointed WHO/FAO expert advisor about foodborne antimicrobial resistance
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
 
Description EU Report (Refresh) on the valorisation of putrescible waste
Geographic Reach Europe 
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 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 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 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 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 MRC DART iCASE Sship
Amount £100,028 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 10/2018 
End 09/2021
 
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 08/2018 
End 02/2020
 
Description Testing poultry vaccines
Amount £54,000 (GBP)
Organisation Bioproperties Ltd 
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 
 
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 
 
Description Collaboration with Amira Roess - Department of Global Health, George Washington University, USA. 
Organisation Australian National University (ANU)
Department Department of Global Health
PI Contribution This collaboration led to a successful joint funding application to the Gates Foundation. John Wain from QIB, is a co-investigator on the grant. The QIB team will be building infrastructure within Bangladesh for nanopore sequencing and metagenomics.
Collaborator Contribution This collaboration led to a successful joint funding application to the Gates Foundation. Amira Roess, from GWU, is a principle investigator on the grant.
Impact This collaboration led to a successful grant application to the Gates Foundation. The application was led by Amira Roess (GWU), with partners at QIB (John Wain as the QIB co-investigator and Alison Mather, Justin O'Grady and Andrew Page, as named investigators). The grant title is: A longitudinal, source attribution study of Campylobacter emergence and transmission in rural Bangladesh to inform intervention development.
Start Year 2018
 
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 Grant proposals in preparation for Gates Grand Challenge call 23.
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 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 Nestle iCASE 
Organisation Nestlé Research Center
Department Nestle PTC York
Country Switzerland 
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 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 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 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
 
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 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 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 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 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 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 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 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 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 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 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