Investigating mechanisms of antimicrobial resistance in food-borne pathogens and developing methods for the study of evolution in biofilms
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
Department Name: UNLISTED
Abstract
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Technical Summary
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.
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.
Planned Impact
unavailable
People |
ORCID iD |
| Mark Webber (Principal Investigator) |
Publications
Chang MX
(2021)
Contribution of Different Mechanisms to Ciprofloxacin Resistance in Salmonella spp.
in Frontiers in microbiology
Darby E
(2022)
Molecular mechanisms of antibiotic resistance revisited
in Nature Reviews Microbiology
Guest K
(2022)
Responses of Salmonella biofilms to oxidizing biocides: Evidence of spatial clustering.
in Environmental microbiology
Holden ER
(2023)
Genome-wide analysis of genes involved in efflux function and regulation within Escherichia coli and Salmonella enterica serovar Typhimurium.
in Microbiology (Reading, England)
Holden ER
(2022)
Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli.
in Microbial genomics
Kettles RA
(2019)
The Escherichia coli MarA protein regulates the ycgZ-ymgABC operon to inhibit biofilm formation.
in Molecular microbiology
Ogbolu DO
(2020)
Opening Pandora's box: High-level resistance to antibiotics of last resort in Gram-negative bacteria from Nigeria.
in Journal of global antimicrobial resistance
Page AJ
(2020)
AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments.
in PLoS computational biology
| Description | The major aim of this award was to develop and apply a model to study bacterial evolution in context of biofilms. We have successfully developed, tested and validated a biofilm based evolution model to study how bacteria attached to surfaces (as in the real world) respond to drug exposure. This model was used to show there are novel routes to antimicrobial resistance when bacteria are in the biofilm context (rather than in liquid as mainly studied in the history of microbiology), and this allows us to study how bacteria evolve in more realistic ways. We found that biofilms do rapidly evolve antibiotic resistance but some of the mechanisms were novel and had other costs to the cells ability to do other things - this may be important in understanding how antibiotic resistance occurs in the real world. |
| Exploitation Route | The model is already being used by others - we have an iCASE studentship with P&G already to exploit this and have delivered training to collaborating groups from Cambridge University and the London School of Hygiene and Tropical Medicine to transfer the technology. |
| Sectors | Agriculture Food and Drink Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| Description | Our research was highlighted as evidence of a knowledge gap in study of biofilm evolution, and as a method to address this by the European Food Safety Authority in a scientific opinion piece to inform research priorities to guide policy |
| First Year Of Impact | 2021 |
| Sector | Healthcare |
| Impact Types | Policy & public services |
| Description | Appointed WHO/FAO expert advisor about foodborne antimicrobial resistance |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Description | Evidence for EU EFSA opinion piece |
| Geographic Reach | Europe |
| Policy Influence Type | Citation in systematic reviews |
| URL | https://efsa.onlinelibrary.wiley.com/doi/full/10.2903/j.efsa.2021.6651 |
| Description | Evidence for UK AMR review |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | BBSRC DTP Studentship (mixed community evolution in biofilms) |
| Amount | £96,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2020 |
| End | 09/2024 |
| Description | IAA |
| Amount | £10,000 (GBP) |
| Funding ID | BB/S506679/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 03/2022 |
| 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 Hosted training events for collaborating groups to allow transfer of the technology |
| 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 |
| Title | Responses of Salmonella biofilms to stress |
| Description | A series of biofilm evolution experiments have been completed where Salmonella biofilms were exposed to various stress conditions including pH, salt, temperature, preservatives and antibiotics. Mutants were phenotyped and sequenced after exposure to allow analysis of impact of stress on phenotype and genotype |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | We have had numerous requests to learn about the model system leading to new collaborations |
| Title | TraDIS biofilm formation datasets |
| Description | A series of experiments were completed to identify the genes needed for Salmonella and E. coli to form biofilms over time and to identify similarities and differences between the species |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Novel genes have been the basis for successful applications for follow on PhD student funding |
| 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 | Biofilms, the good the bad and the ugly. A Webinar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A global webinar was delivered explaining why biofilms are important, why they are antimicrobial resistant and a perspective on possible treatment options. Invited by GARDP - a WHO initiative for development of new antimicrobials |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://revive.gardp.org/biofilms-what-are-they-and-why-do-we-care/ |
| Description | Contribution to exhibition 'I'm a Scientist'. 2023 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Contributed material for an exhibition about diverse nature of scientists displayed at Norwich Science Festival |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://norwichsciencefestival.co.uk/ |
| Description | Discussion with waitrose and suppliers |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | A series of meetings were held with Waitrose and technical managers interested in food safety from their key suppliers. Discussions about our skills and interests and how these relate to their issues were held and potential future collaborative projects identified. The events increased awareness of our abilities for industry and of industries needs and current challenges for us |
| Year(s) Of Engagement Activity | 2019 |
| 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 | Invited Speaker at Microbiology Society Focussed meeting (Microbiome and mucosa associated infectious disease, Dublin 2022) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk given about research to microbiome focussed meeting covering aspects of work with Salmonella, E. coli and Staphylococcus |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://microbiologysociety.org/event/society-events-and-meetings/gut-microbiome-and-mucosa-associat... |
| 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 |