Selection for antibiotic resistance in complex microbial communities

Lead Research Organisation: University of Exeter
Department Name: University of Exeter Medical School

Abstract

It is becoming increasingly clear that the natural environment plays an important role in the evolution and dissemination of antibiotic resistance. This studentship will determine the mechanistic basis and significance of gene flow that underlies the abundance of antimicrobial resistance genes in bacteria inhabiting polluted natural environments such as downstream of waste water treatment plants (WWTPs). It is unclear whether increased prevalence of antibiotic resistant organisms associated with WWTPs is due to constant emissions of resistant organisms or whether bacteria such as multi-drug resistant E. coli persist and/or acquire resistance genes by horizontal gene transfer (HGT) in aquatic sediments under selection by environmental pollutants including antibiotic residues. This project will study selection for resistance in complex communities utilising mesocosm studies interrogated using culture and culture independent methods. The latter will include real-time PCR for enumeration of key marker genes and next generation sequencing (NGS) to determine the effects of single antibiotics, mixtures of different classes of antibiotic and field samples of polluted effluents on relative abundance of all known resistance genes. This knowledge will be used to support environmental policy development and environmental risk management.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/N504026/1 01/10/2015 30/09/2019
1641426 Studentship BB/N504026/1 01/10/2015 30/09/2019 Isobel Catherine Stanton
 
Description ? Invited to meeting in South America (Argentina or Uruguay in June 2018) to advise the Interagency Coordination Group on Antimicrobial Resistance (IACG) co-chaired by the UN Deputy Secretary-General and the Director General of the World Health Organization.
Geographic Reach Multiple continents/international 
Policy Influence Type Gave evidence to a government review
 
Description Co-authored a box in Chief Medical Officers annual report
Geographic Reach National 
Policy Influence Type Citation in other policy documents
URL https://www.gov.uk/government/publications/chief-medical-officer-annual-report-2017-health-impacts-o...
 
Description Invited by Lee Slater (Senior Policy Advisor on AMR in the environment at Defra) to sit on a panel of academic experts in a series of workshops between the US, UK, China and India on antimicrobial resistance and antibiotic pollution in the environment. It's being co-ordinated by the UK Science and Innovation Network and the USA Centers for Disease Control and Prevention.
Geographic Reach Multiple continents/international 
Policy Influence Type Gave evidence to a government review
 
Description Invited to speak to Defra Antimicrobial Resistance Coordination (DARC) Group Autumn 2017 on AMR in the environment.
Geographic Reach Multiple continents/international 
Policy Influence Type Participation in a advisory committee
Impact Talk to Defra and veterinary medicines directorate about antibiotics in the environment
 
Description Invited to speak to Defra Hazardous Substances Advisory committee about AMR in the environment
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
Description Report for United Nations Env Programme
Geographic Reach Multiple continents/international 
Policy Influence Type Gave evidence to a government review
Impact Report was published alongside UNEA commitment to tackle AMR form an environment and human health perspective
 
Description Strategies for Addressing Antimicrobial Resistance - Future challenges for UK policy
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description Mapping the evidence for the risks of human exposure and transmission of AMR in the natural environment
Amount £80,590 (GBP)
Funding ID NE/S015965/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2019 
End 09/2019
 
Description Microbiology Society Annual Conference Grant
Amount £300 (GBP)
Organisation Microbiology Society 
Sector Learned Society
Country Unknown
Start 04/2017 
End 04/2017
 
Description Microbiology Society Travel Grant
Amount £254 (GBP)
Organisation Microbiology Society 
Sector Learned Society
Country Unknown
Start 10/2018 
End 10/2018
 
Description The environmental dimension of antimicrobial resistance: informing policy, regulation and practice.
Amount £72,525 (GBP)
Funding ID NE/S006257/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2019 
End 12/2020
 
Description Towards Developing an International Environmental AMR Surveilance Strategy
Amount £44,356 (GBP)
Funding ID MR/S037713/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 01/2019 
End 12/2019
 
Description Travel Grant
Amount £150 (GBP)
Organisation British Society for Antimicrobial Chemotherapy 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2017 
End 12/2018
 
Description ? Attended a Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) workshop in Gothenburg 
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 Attended a Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) workshop in Gothenburg in September 2017 to explore and identify critical research needs that relate to the environmental dimensions of AMR, both in the longer term for providing input to an updated JPIAMR Strategic Research Agenda, but also in the shorter term to provide guidance for specific calls.
Year(s) Of Engagement Activity 2017
URL https://www.jpiamr.eu/wp-content/uploads/2017/11/Report-_JPIAMR-workshop-on-Environmental-dimensions...
 
Description ? Gaze WH. The environmental aspects of antibiotic resistance. Learned Societies AMR meeting. June 25th, 2015 London. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Antimicrobial resistance: environments,evolution and transmission Networking workshops for researchers
Year(s) Of Engagement Activity 2015
URL https://www.responsibleantibioticuse.org/#xl_xr_page_index
 
Description ? Invited by MRC to work with Viadynamics to develop an AMR framework to map out research challenges and ways in which we are addressing those challenges. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Advise RCUK policy on research priorities on AMR
Year(s) Of Engagement Activity 2017
 
Description ? Invited to EA meeting on AMR in waste water to plan EA programme of investigation. March 2017 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Help inform water industry AMR research programme
Year(s) Of Engagement Activity 2017
 
Description ? NERC Planet Earth article "Have we opened the floodgates on antimicrobial resistance?" Winter 2016/17. 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact ?Article for Planet earth detailing role of flooding and climate change on environmental transmission of Amr
Year(s) Of Engagement Activity 2017
 
Description BSAC conference 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Annual workshop for the British Society for Antimicrobial Chemotherapy. Poster presentation. Discussion with other delegates.
Year(s) Of Engagement Activity 2016
 
Description BSAC conference 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Annual workshop for the British Society for Antimicrobial Chemotherapy. Poster presentation. Discussion with other delegates.
Year(s) Of Engagement Activity 2017
 
Description EDAR conference 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact International conference for the Environmental Dimension of Antibiotic Resistance. Poster presentation. Discussion with other delegates.
Year(s) Of Engagement Activity 2017
 
Description ISME16 - Montreal 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact International conference for the International Society of Microbial Ecology. Poster presentation. Discussion with other delegates.
Year(s) Of Engagement Activity 2016
 
Description Microbiology Society Annual Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Annual conference for the Microbiology Society. Poster presentation. Discussion with other delegates.
Year(s) Of Engagement Activity 2017
 
Description NERC KE Fellowship working with EA, Defra, Water and pharmaceutical industries 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact This is in its early stages but it has already resulted in a JPIAMR (MRC) funded network on environmental AMR surveillance which has resulted in engagement with gov stakeholders and national / international partners
Year(s) Of Engagement Activity 2019
 
Description Public Outreach Event - Eden Project. BSAC & Public Health England 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Attended Eden Project to engage both children and parents visiting during half term on the issues of antimicrobial resistance and spread of disease. Children were involved in activities to show the importance of hand washing, the spread of germs when sneezing and basic demonstrations of how antibiotic resistance begins and spreads. Parents were spoken to about antimicrobial resistance and sparked discussions about not using them for viral infections/colds/flu etc and the importance of vaccines. Parents were also encouraged to sign up to become Antibiotic Guardians (Public Health England's Scheme).
Year(s) Of Engagement Activity 2016
URL http://antibioticguardian.com/keep-antibiotics-working/
 
Description SETAC conference 2016 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact International conference for the Society of Environmental Toxicology and Chemistry. Poster presentation. Discussion with other delegates.
Year(s) Of Engagement Activity 2016
 
Description SETAC conference 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact International conference for the Society of Environmental Toxicology and Chemistry. Flash talk and Poster presentation. Discussion with other delegates.
Year(s) Of Engagement Activity 2017
 
Description Speaking at House of Commons UKRI AMR research strategy refresh 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Speaking at House of Commons UKRI AMR research strategy refresh focusing on existing UKRI funded work in the area of AMR and the environment
Year(s) Of Engagement Activity 2019