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.
 
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 practcies influence dissemination of AMR at the landscape scale.
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.
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
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Environment,Healthcare,Government, Democracy and Justice,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Policy & public services

 
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 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 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 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 Advgisory group member for Eden Project Wellcome Invisible Worlds exhibition 
Organisation The Eden Project
Country United Kingdom 
Sector Charity/Non Profit 
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 ? 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 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 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 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