Using next generation sequencing to reveal human impact on aquatic reservoirs of antibiotic resistant bacteria at the catchment scale

Lead Research Organisation: UNIVERSITY OF EXETER
Department Name: University of Exeter Medical School

Abstract

The threat of antibiotic resistance has been compared to that posed by climate change and global terrorism by the Chief medical Officer Dame Sally Davies. Bacterial resistance to antibiotics has existed for hundreds of millions of years, as it evolved to combat antibiotics produced by bacteria and fungi. Resistance is conferred either by mutation or by uptake of DNA from other bacteria which may not even be closely related. This horizontal resistance gene transfer is one of the most important issues facing the fight against infection in the clinic. Novel resistance genes that are taken up by clinical pathogens originate in environmental bacteria, and once in human pathogens or even harmless commensal bacteria, will be selected for by clinical use of antibiotics. However, little is known about the conditions under or locations in which these genes are mobilised into human associated bacteria, or what the human exposure routes for transmission of these resistance genes are. Increasing evidence suggests that the use of antibiotics in agriculture contributes to the increase in resistance seen in the clinic, however much less research has focused on evolution of resistance in farm animals than in humans so less evidence is available. Even less is known regarding reservoirs of resistant bacteria in the natural environment, particularly locations heavily polluted by human or animal waste.

11 billion litres of waste water are discharged into UK rivers every day; critically much of this treatment does not significantly reduce numbers of resistant bacteria. Millions of tons of animal faecal wastes are spread to agricultural land every year, providing additional inputs of resistant organisms into the wider environment. Our previous work has shown that the use of a marker gene, which is predictive of levels of antibiotic resistance genes in sediments, varies by up to 1000 times between clean and dirty sediments. Our data also shows that waste water treatment plants are responsible for the majority of this effect (about 50%), and 30% is associated with diffuse pollution from land adjacent to the river. Other data generated by the consortium suggests that there are real human exposure risks to these environmental reservoirs of resistant organisms, with several million exposure events occurring each year in England and Wales through recreational use of coastal waters alone.

This project will, for the first time, use cutting edge high through put DNA sequencing technologies and computational analyses to increase our understanding of the human activities that drive increased levels of antibiotic resistant bacteria across the River Thames catchment. Abundance and identity of over 3000 different resistance genes will be determined at 40 sampling sites, in triplicate at three time points over one year, to capture impacts of seasonality and flow. We will also measure a range of antibiotic residues, metals and nutrients. We will use graphical information system data on waste water treatment plant type, size and location and land use throughout the catchment. Together this data will be used to produce a model which will reveal the main drivers of resistance gene abundance and diversity at the catchment scale. We will also identify novel molecular markers associated with different sources of pollution that can be used as source tracking targets. We aim to analyse the effects of specific mitigation strategies that are able to reduce levels of resistant bacteria, this will enable estimates of reduction in resistance levels that can inform policy and regulatory targets.

A translational tool will be developed for surveillance of the most important marker genes identified from the DNA sequence analyses and modelling work. This will be an affordable test that will help identify key factors for human health risk assessment.

Planned Impact

In addition to researchers, regulators and government bodies described previously, the wider stakeholders who will benefit will include the water industry, farmers, shellfish producers / harvesters and parts of the tourism sector who are involved with recreational freshwater and coastal water use. They will gain insights into potential hazards, and mitigation strategies for reducing exposure to AMR bacteria.

Antimicrobial resistance (AMR) has been highlighted by Dame Sally Davies (Chief Medical Officer), and crucially the government's 5 year AMR strategy highlights the need for a "One Health" approach including consideration of the agricultural and natural environments.

"Antimicrobial resistance is a global problem and we all need to take responsibility. I have already been speaking with the World Health Organization, the G8 and with countries across the world to make sure we're all working together and I am pleased to see that steps are being taken in the UK to help us take the fight to resistant bacteria".

"After her report in 2013, AMR was put on the government's national risk register of civil emergencies - which provides guidance on potential threats such as terrorist attacks, pandemic flu and major flooding".

In the long term the outputs of the proposed research are extremely important to society as it is crucial that we gain fundamental insights into evolution and dissemination of AMR, not only in the clinic, but in the wider environment. As discussed later in this proposal, there is increasing evidence that pollution introduces clinically significant AMR bacteria into river catchments where there is a real human exposure risk, particularly in receiving coastal waters. In addition, a widely agreed research priority is to investigate the potential for environmental antibiotic residues to select for AMR in polluted natural environments such as rivers.

We will work with project partners in the UK (LGC) and abroad (Austrian Institute of Technology) to develop surveillance tools for the most important resistance markers we will identify during the proposed research. We will also work with UK based Advanced Anaerobics Ltd to evaluate the impacts of treatment of animal waste on AMR dissemination.

Our project outputs will be available to academic and private sector researchers to study the ecology of AMR in a key UK catchment. This will consist of a Thames catchment metagenomic sequence database, plus a database of metadata at each sample site and time point plus replicate sediment samples from each sample site and time point stored at -80 degrees C. The significance of this resource should not be underestimated as it will facilitate a wide range of in silico analyses and future research projects that can make use of our state of the art project outputs.

AMR has huge costs to society both economically and from a human health perspective. Our research will provide critical data on AMR, allowing mitigation of transmission of AMR bacteria and fundamental research on drivers of resistance in the environment and in the clinic. The latter will stem from our work on selection for resistance at low antibiotic concentrations which are present in the environment and also in the human body.

We anticipate that we will generate data that will inform government policy, and that of key regulators, within the lifetime of the grant. This will impact human health if steps are put in place to reduce environmental dissemination, selection and human exposure.

Publications

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Murray AK (2019) Comparing the selective and co-selective effects of different antimicrobials in bacterial communities. in International journal of antimicrobial agents

 
Description Antibiotic resistance genes are widespread in aquatic sediment microbial communities and prevalence of genes is higher than expected. Associations between urbanisation and AMR and association with waste water treatment plant effluent point sources of pollution. Confirmation that anthropogenic pollution and waste management practices influence dissemination of AMR at the landscape scale.

We are in final stages of manuscript preparation and we see clear associations between SOME AMR genes and water treatment plants, human bacterial pollution and urban/suburban land usage. The picture is complex but it is clear that human activity has significant impacts on the magnitude of AMR prevalence and the type of AMR genes that are present in the environment.
Exploitation Route All data will be presented to Defra, EA, water company and pharmaceutical industry representatives at our Programme Integration Grant in Spring 2018. We are already advising Defra, the EA and Water Industry and I am talking to the UN, WHO and European Environment agency.

Knowledge gained and data generated continues to inform government policy through my KE Fellowship with Defra and the EA.
Sectors Agriculture

Food and Drink

Environment

Healthcare

Government

Democracy and Justice

Pharmaceuticals and Medical Biotechnology

 
Description I have used the experience of designing this study and conducting sediment sampling in the Thames catchment to advise Pis of two Canadian government funded projects on AMR. Attended an Environment Agency meeting to discuss AMR in the environment (9th March 2016) Gave talk to Defra SEVENTEENTH MEETING OF THE HAZARDOUS SUBSTANCES ADVISORY COMMITTEE (HSAC) on risks associated with antibiotic residues in the environment Awarded NERC KE Fellowship with EA/Defra/water and pharma industries to related findings to regulators/policymakers and industry 2020 This project has continued to inform advice to gov, EA and the water and pharma industries through my NERC KE Fellowship and has informed the govs approach to tackling AMR in the environment. 2021 Experience from this project contributed to advice to government which has helped inform the PATH-SAFE AMR surveillance programme currently being undertaken by the FSA, UKHSA and EA.
First Year Of Impact 2021
Sector Agriculture, Food and Drink,Environment,Healthcare,Government, Democracy and Justice,Pharmaceuticals and Medical Biotechnology
Impact Types Societal

Policy & public services

 
Description ? Participated in Epi-Net meeting Dec 3rd 2021.
Geographic Reach Europe 
Policy Influence Type Membership of a guideline committee
Impact Will determine future AMR surveillance policy and practice on Europe
 
Description ? Second consultative meeting in preparation of the report on the environment and health impacts of pesticides and fertilizers (UNEP, WHO, FAO). Geneva, UNEP. 2019.
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
Impact I sit on the WHO/FAO working group on pesticides and fertilizers where the risks of AMR and environment are being discussed in relation to manure based fertilizers and biosolids amendments to agricultural land.
 
Description Acknowledgement in O'Neill Report on ANTIMICROBIALS IN AGRICULTURE AND THE ENVIRONMENT: REDUCING UNNECESSARY USE AND WASTE
Geographic Reach Multiple continents/international 
Policy Influence Type Citation in other policy documents
 
Description Advised European Bank for Reconstruction and Development on AMR
Geographic Reach Europe 
Policy Influence Type Contribution to new or improved professional practice
Impact Advised European Bank for Reconstruction and Development on AMR
 
Description Advising Deloitte on evaluation of the UK gov AMR surevillance programme PATH-SAFE
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
Impact Informing national policy
 
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 Consulting for DG Sante on AMR policy
Geographic Reach Europe 
Policy Influence Type Contribution to a national consultation/review
Impact Informing EU policy
 
Description Gave evidence to Defra on AMR and ENvironment
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
 
Description Held KE meeting at the University of Exeter attended by ES, Defra, Welsh and NI devolved governments, water industry, clinicians etc
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Description Invited by British Society of Antimicrobial Chemotherapy to contribute to discussion around new AMR National Action Plan. One of a small number of academics to be invited.
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description Invited to participate in Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC) Genomic Surveillance of Antimicrobial Resistance working group workshop lead by Professor Kate Baker, Dr Elita Jauneikaite, Professor Sharon Peacock and Professor Nicholas Feasey.
Geographic Reach Europe 
Policy Influence Type Participation in a guidance/advisory committee
Impact NA
 
Description Member of UK AMR NAP Stakeholder group
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
Impact iNFORMING NATIONAL HEALTH POLICY
 
Description Second consultative meeting in preparation of the report on the environment and health impacts of pesticides and fertilizers (UNEP, WHO, FAO).
Geographic Reach Multiple continents/international 
Policy Influence Type Membership of a guideline committee
 
Description Three papers cited in the Download the JPIAMR Strategic Research and Innovation Agenda on Antimicrobial Resistance 2019
Geographic Reach Multiple continents/international 
Policy Influence Type Citation in other policy documents
URL https://www.jpiamr.eu/wp-content/uploads/2019/05/JPIAMR_SRIA_final.pdf
 
Description UNEP Frontiers 2017 report only one of two cited papers/reports on AMR and the environment in Interagency Coordination Group on AMR Final report presented to the UN Secretary general
Geographic Reach Multiple continents/international 
Policy Influence Type Citation in other policy documents
Impact This is arguably the most important document on AMR produced by the WHO/FAO/OIE and scientific experts in recent years as it will shape the global response to AMR by the UN/WHO.
URL https://www.who.int/antimicrobial-resistance/interagency-coordination-group/en/
 
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 09/2020
 
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 12/2021
 
Description Towards Developing an International Environmental AMR Surveilance Strategy
Amount £44,356 (GBP)
Funding ID MR/S037713/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 01/2019 
End 12/2020
 
Description We are currently involved in five AMR PATH-SAFE contracts in collaboration with UKCEH on three contracts and WSP on one contract
Amount £200,000 (GBP)
Organisation Environment Agency 
Sector Public
Country United Kingdom
Start 08/2022 
End 03/2023
 
Description Advgisory group member for Eden Project Wellcome Invisible Worlds exhibition 
Organisation The Eden Project
Country United Kingdom 
Sector Private 
PI Contribution Advisory group to Invisible Worlds (£1 million Wellcome funded exhibition that includes microbiology)
Collaborator Contribution Advisory group to Invisible Worlds (£1 million Wellcome funded exhibition that includes microbiology)
Impact The Eden Project will be hosting the Programme Integration Grant (NERC Environmental Microbiology and Human Health) final meeting and we will develop a display of the NERC programme data
Start Year 2017
 
Description Supervising EA staff member for postgraduate degree on environmental AMR surveillacne 
Organisation Environment Agency
Country United Kingdom 
Sector Public 
PI Contribution We have supervised the EA staff member who works on the UKHSA?FSA/EA PATH-SAFE AMR surveillance programme
Collaborator Contribution Research student
Impact Will inform EA AMR surevillance strategy
Start Year 2022
 
Description Working with UKCEH on PATH-SAFE projects 
Organisation UK Centre for Ecology & Hydrology
Country United Kingdom 
Sector Public 
PI Contribution We have jointly bid and are delivering three contracts on AMR for the Environment Agency through PATH-SAFE
Collaborator Contribution Joint delivery of three contracts
Impact Three reports which may lead to publications
Start Year 2022
 
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. Co-selection for AMR by quaternary ammonium compounds. Royal Academy of Science. Stockholm. March 2016. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Talk at the Royal Academy of Science in Stockholm on AMR in the environment
Year(s) Of Engagement Activity 2016
 
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 ? Gaze WH. The environmental aspects of antibiotic resistance. Learned Societies AMR scoping meeting. Society for Applied Microbiology symposium on AMR, Royal Society of medicine. December 2015. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk to diverse audience on AMR in the environment
Year(s) Of Engagement Activity 2015
 
Description ? Gaze, W.H. Selection for, dissemination of and exposure to antibiotic resistant bacteria in the natural environment. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact 4th International Conference on Responsible Use of Antibiotics in Animals, The Hague, September 2016.
Year(s) Of Engagement Activity 2016
URL https://www.responsibleantibioticuse.org/#xl_xr_page_index
 
Description ? Gaze, W.H. Taking action to improve healthcare by addressing the links with environment chemistry. Scotland (NHS), 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Talk to NHS Scotland on AMR in the environment
Year(s) Of Engagement Activity 2016
 
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 ? Presented to the APPG on Antibiotics with report generated requestruing AMR be included in the new Environment Bill 
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 Myself, Aimee Murray and Isobel Stanton gave evidence to the APPG on Antibiotics, highlighting the importance of the environmental dimension of AMR. We presented evidence that should inform the environment bill which is currently at amendment stage.
Year(s) Of Engagement Activity 2020
 
Description Contributed to Aviva Investors report on AMR, biodiversity loss and climate change 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation of report at Aviva Investors, London
Year(s) Of Engagement Activity 2022
URL https://www.avivainvestors.com/en-gb/views/aiq-investment-thinking/2022/11/antimicrobial-resistance/
 
Description Filming for BBC4 program on AMR 
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 Filmed with freelance program makers for a Michael Mosley BBC4 documentary on AMR
Year(s) Of Engagement Activity 2017
 
Description GW4/BristolBridge: Systems approaches to AMR in Different Environments (16 Mar 2017) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Presented outline of grant to researchers working on AMR in the environment
Year(s) Of Engagement Activity 2017
 
Description HCWH webinar with myself and Dame Sally Davies, I hr to journalists and other specialists eg. WHO. 
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 Policymakers/politicians
Results and Impact Webinar with myself and Dame Sally Davies answering questions from policy makers and media around AMR
Year(s) Of Engagement Activity 2019
 
Description Invited speaker UK:Russia AMR roundtable, Nov 23rd organised by BSAC. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact ~30 AMR specialists from the UK and Russia discussing potential collaborations, coordinated by the British Society for Antimicrobial Chemotherapy.
Year(s) Of Engagement Activity 2021
 
Description Invited to speak at Bolivian conference on AMR attended by the minister of health. Santa Cruz, June 2019. 
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 I had previously been invited to travel to Bolivia and speak to the AMR Action plan committee hosted by the British Embassy in La Paz, this was a follow up presentation to a similar group including the Minister of Health.
Year(s) Of Engagement Activity 2019
 
Description Keynote speaker at the Environmental Dimension of Antibiotic Resistance conference in Hong Kong in June 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was an international conference attended by academics and representatives from Wellcome, WHO and UNEP. I presented the theoretical framework which underpins this project grant and it was well received with both Wellcome and WHO requesting a copy of my presentation.
Year(s) Of Engagement Activity 2019
 
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 Presentation at the Environmental Dimension of AMR meeting in Hong Kong 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Presentation from EDAR5 (basis for UK:Argentina grant detailing conceptual framework for Environmental AMR) requested by Tim Jinks (Head of Infection at Wellcome) and David Sutherland (WHO Technical Officer One Health Tripartite Coordination Group for Asia and the Pacific). "I'd be very grateful if you could send your presentation. It will be treated in confidence but will help with my briefing to WHO and FAO (duly acknowledged) and modifications to my risk framework".
Year(s) Of Engagement Activity 2019
 
Description Quadripartitie one health priority research agenda for antimicrobial resistance 
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 Contributed towards the report, sitting on a panel of experts who contributed to teh report
Year(s) Of Engagement Activity 2023
URL https://www.who.int/publications/i/item/9789240075924
 
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
 
Description Wrote opinion piece on One Health and AMR for the Microbiology Society 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Wrote opinion piece on One Health and AMR for the Microbiology Society
Year(s) Of Engagement Activity 2020
URL https://microbiologysociety.org/static/c7d8d35c-6936-4d8d-af7576c5d28b2722/Antimicrobial-Resistance-...
 
Description Youtube film with Steve Mould and the Eden Project 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact As part of the program integration grant we commissioned 3 films through the Eden project, employing Steve Mould who has a science Youtube channel
Year(s) Of Engagement Activity 2019
URL https://www.youtube.com/watch?v=GzCLp1KBf4Q