Investigating mechanisms of antimicrobial resistance in food-borne pathogens and developing methods for the study of evolution in biofilms

Lead Research Organisation: Institute of Food Research
Department Name: Contracts

Abstract

Background. Antimicrobial resistance (AMR) is a threat to human and animal health, widely recognised as one of the most important challenges facing society today. Extensive evidence has shown that AMR pathogens are present and can be selected for in the food chain and that this has detrimental impacts on animal and human health. Biofilm formation is a major mechanism of persistence and contamination throughout the food chain. However, our understanding of the genetic basis for biofilm formation, evolution and stress survival under food chain relevant conditions is limited.

Objectives
• To develop a tractable laboratory model to study adaptation in biofilms under food chain relevant stresses
• To investigate the evolution of resistance to relevant antibiotics in biofilms

Task 1 Adapting a biofilm model to study evolution under stress. We will adapt the ‘bead’ model of biofilm evolution (described by Poltak and Cooper), this model has the advantage of including all the phases of biofilm formation (dissemination, colonisation and maturation) and allows multiple variables to be tested. We will introduce the application of antimicrobial stress to the model and develop protocols for recovery and characterisation of resistant mutants as they emerge within the biofilm.

Task 2 Investigating adaptations to life in a biofilm. We will investigate adaptations to AMR in biofilms by exposing representative Salmonella biofilms to prolonged sub-lethal exposure to antimicrobials found in the food chain. We will use the bead-based model that we will optimise in task 1. Biofilms will be iteratively exposed to antibiotics, recovered, stored and characterised for ability to form a biofilm and AMR. Genome sequencing will identify the genetic basis for adaptation under stress. Candidate genes identified will be characterised using standard molecular techniques.

Outcomes. A greater appreciation of the biology of biofilm formation and mechanisms of biofilm adaptation under stress.

Publications

10 25 50
 
Description We have developed a biofilm based evolution model to study how bacteria attached to surfaces (as in the real world) respond to drug exposure. This has shown novel routes to resistance in this context and will allow us to study how bacteria evolve in more realistic ways
Exploitation Route The model is highly likely to be used by others - we have an iCASE studentship with P&G already to exploit this
Sectors Agriculture, Food and Drink,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
 
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 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 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
 
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 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 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