Quantifying Spatial AMR Patterns across Urban and Rural Landscapes

Lead Research Organisation: University of Strathclyde
Department Name: Civil and Environmental Engineering

Abstract

Antimicrobial resistance is increasing in nature and threatens the effectiveness of our drug therapies and infection control. However, it remains difficult to distinguish what originates from human activities or what is natural. Therefore, we must extend the scale and depth monitoring efforts to better understand what is driving the increases in resistance traits.

This project will use two collections of previously characterised soils to compare and contrast distributions of AR genes under widely varying conditions, ranging from urban, agriculture, legacy mining, and pristine rural environments. The project will utilise DNA extractions and new genetic technology to quantify over 230 AR genes in the samples. Soil inventories provide us well-characterised soils and the wealth of information that describes both the soils and the impacts at source locations.

The project will generate an astonishing 120,000 AR-related data points (400 locations x 300 genes), each with extended background information on environmental conditions-creating among the largest geographic representation of AR gene distribution across landscapes ever created; sufficiently detailed to make cross-cutting observations of landscape effects on acquired vs innate AR levels. With advanced multi-parametric statistics, we will relate specific environmental conditions and factors with observed AR genes levels in soils to identify risk factors associated resistance development and impacts on human and agricultural health.

Planned Impact

"Pump prime" funding will be used to enhance and strengthen research collaborations between University of Strathclyde, Newcastle University, James Hutton Institute and the Chinese Academy of Sciences. It is also an opportunity to broaden current investigations into a holistic view of landscape-related contributions to AMR (antimicrobial resistance) in the environment. This will allow us to better understand the distributions of AMR traits, their potential sources and/or factors that affect their abundances, and contribute to geographical assessment of health risks.

The investigating team has an excellent track record of working for, and engaging with media, environmental health agencies, and the general public. To help relate results to potential health risks, we have engaged with Eleanor Anderson (Health Protection Scotland) and Prof Matt Wright (Health Protection Research Unit at Newcastle) to help interpret results in respects to public health and maximise the impact/dissemination of the information. The inclusion of these representatives will not only create opportunities to share results to those beneficiaries, but (more importantly) will allow us to keep abreast of local and regional issues and how to best carry out the research to maximise impact. Knowledge exchange is important, and meetings will be held every six months to facilitate these interactions.
Research staff and students working on this project will benefit by interacting within a multidisciplinary research team, but also through engagement with other organisations. They will gain insight not only into the technical aspects of the research, but also into the regulatory context of the work, enhancing their future employability in academia.

Publications

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Pagaling E (2023) Antibiotic resistance patterns in soils across the Scottish landscape in Communications Earth & Environment

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Pagaling E (2023) Antibiotic resistance patterns in soils across the Scottish landscape in Communications Earth & Environment

 
Description 1.) In a survey of DNA extracted from soils collected in Northeast England: antimicrobial gene abundances in soils from industrially contaminated land exceed (1-2 orders of magnitude greater) than abundances from pristine lands and agriculture.
2.) Antimicrobial resistance gene abundances across the Scottish landscape have been mapped, possibly representing the first ever surveillance database across a national scale. We find that AMR gene abundances often correlate with pollution levels in soils (either metals or persistent organic pollutants).
Exploitation Route Publication and discussions with AR Surveillance strategy meetings.
Data are being archived at EIDC and JHI
Sectors Agriculture, Food and Drink,Environment,Leisure Activities, including Sports, Recreation and Tourism

 
Description Results from this study have contributed to WHO/UN publication to influence public perception and policy: Implementation circular/rapid advice/letter to e.g. Ministry of Health - Technical brief on water, sanitation, hygiene and wastewater management to prevent infections and reduce the spread of antimicrobial resistance. Published by World Health Organization, Food and Agriculture Organization of the United Nations, and World Organisation for Animal Health [D Graham co-author] (2020)
First Year Of Impact 2020
Sector Agriculture, Food and Drink,Environment
Impact Types Policy & public services

 
Description Technical brief on water, sanitation, hygiene and wastewater management to prevent infections and reduce the spread of antimicrobial resistance. Published by World Health Organization, Food and Agriculture Organization of the United Nations, and World Organisation for Animal Health [D Graham co-author]
Geographic Reach Multiple continents/international 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
Impact This document defines the six Action Areas that need to be addressed to reduce global AMR, especially in LMICs via full WaSH implementation. The Technical Brief has been translated into six languages so far and is underpinning One Health solutions to AMR around the world.
URL https://www.who.int/publications/i/item/9789240006416
 
Description Antimicrobial Resistance in the Real World Integration Programme
Amount £107,777 (GBP)
Funding ID NE/N019474/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 02/2018 
End 12/2020
 
Description GCRF Water Security and Sustainable Development Award
Amount £17,100,000 (GBP)
Funding ID ES/S008179/1 
Organisation Economic and Social Research Council 
Sector Public
Country United Kingdom
Start 02/2019 
End 02/2024
 
Description Impact Acceleration Award
Amount £31,000 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 07/2019
 
Description Research proposals 2017
Amount £38,800 (GBP)
Organisation UK-India Education and Research Initiative (UKIERI) 
Sector Academic/University
Country United Kingdom
Start 03/2018 
End 03/2020
 
Title Antibiotic resistance genes found in soils across the entire Scottish landscape (2007-10) 
Description The dataset collates the relative concentration of nearly 300 antimicrobial resistance (AMR) genes found in soil locations across Scotland. Soils were obtained from the National Soils Inventory of Scotland (NSIS2), from which the total community DNA were extracted and provided to assess AMR gene content. Sampling of the NSIS2 was conducted between 2007-2010 at 183 soil locations representing intersections of a 20km grid across all of Scotland. For each sample, nearly 300 AMR genes were assessed representing major antibiotic classes, and included many resistance traits: aminoglycosides, beta-lactams, FCA (fluoroquinolone, quinolone, chloramphenicol, florfenicol and amphenicol resistance genes), MLSB (macrolide, lincosamide, streptogramin B), tetracycline, vancomycin, sulphonamide, efflux pumps and integron genes. The data represent relative gene abundance, i.e., the amount of genes per "total bacteria" 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact n/a 
URL https://catalogue.ceh.ac.uk/documents/d3498e93-4ac5-4eab-bc1a-eb2328771d24
 
Title Community antimicrobial resistance genes and concentrations of polycyclic aromatic hydrocarbons and metals in NE England soils (2016) 
Description The dataset collates the relative concentration of nearly 300 antimicrobial resistance (AMR) genes, and concentrations of polycyclic aromatic compounds (PAH) and potentially toxic elements (PTE; e.g., "metals") found in soils across northeastern England during a sampling expedition in June 2016 by researchers at Newcastle University. Top soils (15cm depths; "A" horizon) were obtained from 24 rural and urban locations around Newcastle upon Tyne, representing a spectrum of landscape conditions relative to anticipated PTE contamination. There are three files related to different types of data collected: antimicrobial resistance genes, metal concentrations and PAH concentrations. The high-throughput analysis of nearly 300 AMR genes include many resistance traits representing major antibiotic classes: aminoglycosides, beta lactams, FCA (fluoroquinolone, quinolone, chloramphenicol, florfenicol and amphenicol resistance genes), MLSB (macrolide, lincosamide, streptogramin B), tetracycline, vancomycin, sulphonamide, and efflux pumps. PAH data represent the US Environmental Protection Agency priority polycyclic aromatic hydrocarbons as one of the measures of pollution impact. The other measure of impact is based on levels of twelve PTE represented by "total" and "two bio-available" concentrations, based on three extraction methods. Elements included aluminium, arsenic, beryllium, cadmium, chromium, copper, iron, lead, mercury, nickel, phosphorus, and zinc. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
 
Description Chinese Academy of Sciences - Xiamen, China 
Organisation Chinese Academy of Sciences
Department Institute of Urban Environment
Country China 
Sector Academic/University 
PI Contribution Collection and provision of environmental samples to generate geographic atlas of resistome data.
Collaborator Contribution The Chinese Academy of Sciences has generated the methodology for high-throughput, quantitative analysis of genetic samples for antibiotic resistance genes. They are provide instrumental analyses and expertise.
Impact Resistome data - multiparametric (300 genes/sample) output of antibiotic resistance genes.
Start Year 2016
 
Description James Hutton Institute 
Organisation James Hutton Institute
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Resistomic analysis of environmental samples
Collaborator Contribution Provision of soils/extracted DNA from the National Soil inventory.
Impact In the process of generating geographic atlas of environmental antibiotic-resistance genes in Scottish soils.
Start Year 2016
 
Description Newcastle University 
Organisation Newcastle University
Department Business School
Country United Kingdom 
Sector Academic/University 
PI Contribution Collaboratively examining antibiotic resistance traits in the environment in Scotland and northernEngland. Efforts include collection and sharing of samples, genetic analysis of key genetic traits, interpretation and analysis of data, and manuscript generation.
Collaborator Contribution Collaboratively examining antibiotic resistance traits in the environment in Scotland and northern England. Efforts include collection and sharing of samples, geochemical analysis of soils, interpretation and analysis of data, and manuscript generation.
Impact Data and analysis of environmental samples.
Start Year 2016
 
Description 'Superbug gene' found in one of the most remote places on earth 
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 Public/other audiences
Results and Impact Newcastle University Press Release. 28 January 2019. This release matched the storyline presented in the 29 January 2019, Antibiotic resistant 'superbug' genes found in the High Arctic, piece in The Conversation.
Year(s) Of Engagement Activity 2019
URL https://www.ncl.ac.uk/press/articles/archive/2019/01/arcticbugs/
 
Description Adviser and co-author of new WASH guidance from the World Health Organisation relative to AMR - David Graham 
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 As a result of working with the US CDC, Graham was invited to advise and co-write WASH guidance. The guidance document is currently in revision (as of 02/19) with a planned publication date of 05/19. Our role was to write sections on the value of incremental sanitation improvements to reduce AMR and infectious disease. Our work was informed by all our prejects that relate environmental AMR and contaminated soils and water.
Year(s) Of Engagement Activity 2018,2019
 
Description Annual Graham Group Newsletter 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Annual Graham Research Group newsletter available online and set as a pdf to interested parties. It highlight the group's research efforts and compliments the group's research blog. It provides a condensed version for our funders, research partners, university colleagues, alumni, and students as well as friends and family.
Year(s) Of Engagement Activity 2020,2021
URL https://blogs.ncl.ac.uk/grahamr/?page_id=31
 
Description Antibiotic resistant 'superbug' genes found in the High Arctic 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The article, presented in a layman terms, revealed the discovery of antibiotic-resistant genes in the High Artic and presented an explanation of how this finding has huge implications for global antibiotic resistance spread.
Year(s) Of Engagement Activity 2019
URL https://theconversation.com/antibiotic-resistant-superbug-genes-found-in-the-high-arctic-110636
 
Description Antimicrobial Resistance Cross Council Initiative Challenges and Opportunities 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Antimicrobial resistance in the UK workshop
Year(s) Of Engagement Activity 2017
 
Description Antimicrobial resistance in the environment of emerging countries [Amelie Ott] 
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 Other audiences
Results and Impact Stop-motion film entry for the Institute for Social Science Post Graduate Researcher Impact Award 2019. Awarded third place. It was posted on YouTube for 18 months but has since been made private by the creator Amelie Ott.
Year(s) Of Engagement Activity 2019
 
Description Antimicrobial resistance in the real world meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact NERC sponsored AR in real world meeting. Talks of further collaborations and joint-efforts for thereafter.
Year(s) Of Engagement Activity 2017
 
Description Antimicrobial resistance in the real world meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Annual meeting with other AMR-related project holders.
Year(s) Of Engagement Activity 2019
 
Description Brocher Fondation, Geneva, Switzerland: War: the beginning and end of antibiotics? 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact I was invited to discuss the environmental role in the development of drug-resistance, for example in Acinetobacter baumanni -- an emerging superbug in areas of conflict/war. Attended by a multi-disciplinary team of microbiologists, chemists, anthropologist, medical epidemiologist, surgeons/physicians from >12 countries, this discussion led to the formation of a major EC-H2020 project bid, joint publications, and further engagement and cross-disciplinary discussions on the subject.

The environmental role on human health and drug-resistance development was highlighted, and became more accepted as a strong contributor to the problem.
Year(s) Of Engagement Activity 2018
URL https://www.brocher.ch/en/events/321/war-the-beginning-and-end-of-antibiotics/
 
Description CARS - research network meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact CARS (Control of Antimicrobial Resistance in Scotland) working group / expert panel meeting to discuss research needs for the surveillance of antibiotic resistance in the environment. Attended by members representing Health Protection Scotland (hosts), Scottish Water, Scottish Environment Protection Agency, local councils, and academic researchers. Discussions about research needs, possible research alignments, support mechanisms needed, and reporting recommendations to the Scottish government of research needs related to antimicrobial resistance surveillance.
Year(s) Of Engagement Activity 2017
 
Description Calls for action now to prevent next global pandemic 
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 Public/other audiences
Results and Impact Newcastle University Press Office. 12 June 2020. Accouchement the accompany the Conversation piece that call for greater international co-operation to bring about improved water, sanitation and health provision as a way to prevent the next global pandemic
Year(s) Of Engagement Activity 2020
URL https://www.ncl.ac.uk/press/articles/latest/2020/06/amractionnowtopreventnextpandemic/
 
Description Expert panel and co-writer of whitepaper sponsored by the Sackler Instuitute for Nutrition and New York Academy of Science - David Graham 
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 Graham is working as co-author and expert advisor in developing an integrated One Health strategy for reducing antimicrobial resistance in the animal food production industry. Initial meetings are occurring now (March 2018 to March 2019) with the goal of an international launch for proposed strategies in New York in April 2019.

Launch announcement can be found at https://www.nyas.org/events/2019/antibiotics-in-animal-agriculture-what-you-need-to-know/.
Year(s) Of Engagement Activity 2018,2019
URL https://www.nyas.org/events/2019/antibiotics-in-animal-agriculture-what-you-need-to-know/
 
Description GrahAMR Research Group Blog 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact The GrahAM Research Group blog highlights the work of the Graham research team, focusing primarily on work surrounding antimicrobial resistance (AMR), taking a collaborative and multidisciplinary approach to global health and well-being. The team of researchers, led by Newcastle University Prof David W Graham, utilises a holistic 'One Health Approach', and contributes to several of the UN's Sustainable Development Goals (SDGs).

Our research provides guidance to various international organisations, including the World Health Organisation, and bridges sustainable development, engineering, health, and sociotechnical mitigation options for reducing global AMR.

The main topics we explore are

the transmission, fate and impact of antibiotic resistance genes in the environment resulting from human activity;
energy minimization in water, wastewater and solid waste management systems;
the microbiology and ecology of greenhouse gas suppression and production in geochemical settings, especially in Polar regions; and
water and environmental quality in the developing and emerging world.
Year(s) Of Engagement Activity 2020,2021
URL https://blogs.ncl.ac.uk/grahamr/
 
Description Lecture tour of environmental and medical institutions in Israel - David Graham 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Provided a series of lectures at different organisations in Israel, including the Rambon Healthcare Center, the Technion University, The Hebrew University (in Rehovot), and at the Ben Gurian Desert Institute, all on AMR mitigation, especially blocking environmental pathways of spread. Audiences ranged from students to healthcare professionals to academics across disciplines. These have led to collaborative work on AMR spread, initially in Ethiopia. More impact would have been seen if the UK had not ceased their funding to the JPIAMR scheme.
Year(s) Of Engagement Activity 2019
 
Description Newcastle University Find Antibiotic Resistant Genes in Arctic 
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 Short film made available on the Newcastle University YouTube Channel. 28 January 2019. The content dovetails with the Antibiotic resistant 'superbug' genes found in the High Arctic in The Conversation and the 'Superbug gene' found in one of the most remote places on earth, Newcastle University Press Release on 28 January 2019.
Year(s) Of Engagement Activity 2019
URL https://www.youtube.com/watch?v=eDiIDkb4pDg
 
Description Presentation: training day on integrated pollution prevention and conrtrol 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Training day on Integrated Pollution Prevention and Control for delegates from the Hebei Provincial Government, China, organised by Sino-Bridge International
Year(s) Of Engagement Activity 2017
URL https://pure.strath.ac.uk/admin/editor/dk/atira/pure/api/shared/model/activity/editor/attendanceedit...
 
Description Scientists around the world are already fighting the next pandemic 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Graham DW and Collignon P (9 June 2020 • 06:00 am) The Conversation.
Year(s) Of Engagement Activity 2020
URL https://theconversation.com/scientists-around-the-world-are-already-fighting-the-next-pandemic-11524...
 
Description Training Workshop on Mitigating antimicrobial Resistance (AMR) in the water cycle: Analytical methodologies and improving water quality - David Graham/David Werner 
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 We organised and led this workshop in association with four universities in Ethiopia, two universities in Israel, and members of the FAO and WHO. The goal was explain AMR in comparatively simple terms, and then promote new work in Ethiopia that bridges government, NGOs and academic groups in the country. It is also taught research methods.
Year(s) Of Engagement Activity 2019
 
Description UK-China AMR workshop (Shanghai, China) 
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 Grant shaping workshop for the development of institutional-level collaborations.
Year(s) Of Engagement Activity 2017
 
Description University visit and guest lecture: Rajamangala University of Technology-Krungthep, Bangkok, Thailand 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact Visiting lecture to Rajamangala University of Technology-Krungthep, as part of the Environmental Impact Assessment series. Much of the lecture focused on the NERC project that related AMR to Scottish landscape, and discussed how environmental conditions in Thailand could contribute to the prevalence of AMR. This fostered further discussions on the value of AMR contributing factors in Environmental Impact Assessments, a new curriculum for the university in Thailand.
Year(s) Of Engagement Activity 2020
 
Description Workshop on Pharmaceuticals in the Environment: Risks in low and middle income countries (Nairobi, Kenya) - David Graham 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact This was a think tank organised by AstraZeneca to discuss the impact of pharmaceutical pollutants in the environment in developing countries. It included experts from around the world, but also included representatives from NGOs, government agencies. The product of the workshop is a call for action, which is aimed at industry and governments around the world.
Year(s) Of Engagement Activity 2019