Occurrence and horizontal gene transfer of carbapenemase and ESBL genes in soil microbiomes

Lead Research Organisation: University of Southampton
Department Name: School of Biological Sciences

Abstract

This project aims to understand the potential of environmental reservoirs and transmission of AMR in members of autochthonous soil microbiomes and between transient allochthonous human and animal pathogens entering the environment, for example from faecal agricultural wastes or domesticated or wild animal and bird faecal ingress. It also seeks to understand if horizontal gene transfer occurs successfully between potential pathogens in the various soil microbiomes and complex matrices encompassing clay, loam and sandy soils. The work will utilize modern molecular biology and genomics to screen microbiome populations and defined third generation ESBL and fourth generation carbapenemase E. coli and Klebsiella pneumoniae donor strains, with an E. coli sensitive strain as the recipient.

The University of Southampton team comprises an established scientific group with expertise in survival of faecal pathogens in soil and water, and HGT of ESBL and carbapenemase resistance genes between different species, in collaboration with an Early Career Researcher with expertise in soil microbiology and processes, and stable isotope probing (SIP) to understand community viability, metabolic turnover and gene acquisition. Previous work for UKWIR and Defra/FSA has developed grassed soil microcosms of clay, loam and sandy soils and demonstrated survival of zoonotic pathogens therein for several weeks following faecal waste irrigation. These pathogens were subsequently released from the complex soil matrices using a novel, gentle pulsification procedure followed by membrane filtration and quantitative resuscitation on appropriate selective agar media.

This proposal will help identify the specific environmental drivers of the HGT and beta lactamase selection processes, including implications for both anthropogenic (animal husbandry, human wastewater disposal) and non-anthropogenic (wild animal and bird faecal ingress) drivers. The work will also include identifying the implications for pathogens of clinical and/or veterinary importance such Klebsiella pneumonia and E. coli. The research will be able to help inform AMR policy and management strategies, and will form the basis of a subsequent large research proposal to address these policies and strategies more fully.

The approaches and methodologies to be developed in this proposal could be translated to other environments, antibacterials or other bacterial communities of interest to the AMR funding bodies.

Planned Impact

The project will investigate the potential of environmental reservoirs and transmission of AMR in members of authochthonous soil microbiomes and between transient allochthonous human and animal pathogens entering the environment, for example from human wastewater, faecal agricultural wastes or domesticated or wild animal and bird faecal ingress. It also seeks to understand if horizontal gene transfer occurs successfully between potential pathogens in the various soil microbiomes and complex matrices encompassing clay, loam and sandy soils.

Thus, the project provides a major opportunity for UK PLC, firstly through improved management of agricultural land to avoid infection of grazing animals from faecally contaminated land, potentially reducing their health status and a source of food poisoning, but also protect humans from handling or consuming crops grown on the land. Thus industry will benefit from improved animal health and providing high quality, safe food to the public. Secondly, benefits to the wider industry from this research in terms of reduced chemical use when faecal wastes are managed properly.

Immediate beneficiaries will include all fresh produce suppliers and retail outlets in the UK and internationally. The producers will better comply with international sanitary standards for the sale of fresh produce and protect their workers from exposure to AMR pathogens; the retailers will benefit from improved customer confidence and sales. The consumer will benefit since it is critical to establish the safest means of animal husbandry and fresh produce production from the farm to the fork to protect the public health, improve their diet, and maintain consumer confidence following the regular reports of food-borne disease outbreaks. Thus, directly impacting on the nation's health, wealth and culture.

Publications

10 25 50
 
Description Carbapenems are rapidly inactivated in agricultural soil. In addition to members of the Proteobacteria, including Stenotrophomonas, poorly characterised members of the phylum Acidobacteria have been identified as important members of the soil resistome in the presence of carbapenems
Exploitation Route This will inform agencies concerned with persistence of antibiotics in soil affecting ecosystems and potential uptake by plants and growing crops
Sectors Agriculture, Food and Drink,Environment,Pharmaceuticals and Medical Biotechnology

 
Description Presentations on the project have been made to the China-UK Joint Workshop on Antimicrobial Resistance in the Environment, Jiaxing, Zhejiang Province, China and the Antimicrobial Resistance Workshop in the Food Chain (Title: Food Retailers, Supply Chains and the Anti-microbial Resistance Challenge) hosted by Food Standards Agency, London. Presentations and interactions with school children were also given at John Keble School in Hursley, Hampshire and Winchester Science Centre, a hands-on, interactive, science and technology centre located in Morn Hill, just outside the city of Winchester in Hampshire.
First Year Of Impact 2017
Sector Aerospace, Defence and Marine,Agriculture, Food and Drink,Chemicals,Education,Energy,Environment,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Retail
Impact Types Cultural,Societal,Economic

 
Description AMR in the Real World Integration Programme
Amount £88,000 (GBP)
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2018 
End 12/2020
 
Description Global Partnerships Award 2017-18
Amount £5,000 (GBP)
Organisation University of Southampton 
Sector Academic/University
Country United Kingdom
Start 03/2018 
End 07/2018
 
Description 2nd Global Soil Biodiversity Conference, Nanjing, China. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Give a talk: Multi-drug resistant bacteria in British agricultural soil
Year(s) Of Engagement Activity 2017
 
Description AMR In the Real World Meeting - Bristol June 7, 2017 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Study participants or study members
Results and Impact An NERC showcase meeting on the Antimicrobial Resistance in the Real World Initiative. It was attended by representatives from the research council and other funders, relevant stakeholders and representatives from each funded project. Presentations were made from key stakeholders and the consortium leads, followed by a discussion with NERC to encourage further collaboration between PI's on different projects. The outcome was that NERC provided funds for integration of the different projects and additional meetings are planned.
Year(s) Of Engagement Activity 2017
 
Description International Workshop 
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 A China-UK Joint Workshop on Antimicrobial Resistance in the Environment was held last week to discuss common issues and research interests. Centre for Ecology & Hydrology scientists were among more than 70 experts who attended the workshop in Jiaxing, Zhejiang Province (31 October - 2 November 2016). Antimicrobial resistance, especially resistance to antibiotics, is recognised as a growing global problem. The workshop was hosted by Jiaxing Municipal People's Government, Institute of Urban Environment (Chinese Academy of Sciences) and Centre for Ecology & Hydrology, part of the Natural Environment Research Council, UK. It was sponsored by Jiaxing Science and Technology Bureau, Jiaxing Agricultural Sciences Research Institute and Zhejiang Huateng Animal Husbandry Co Ltd.

Gareth Taylor, Science & Innovation Consul from the British Consulate General Shanghai, introduced current research progress and details of the Newton Fund's support on AMR research. He said he expected the scientific exchange and collaboration could be deepened between both sides. The workshop focused on issues of relevance to environmental regulators. Chemical drivers of AMR in the environment and how these might differ between the UK and China, AMR pathways in the environment, impacts and risk assessment of AMR in the environment, knowledge gaps and mitigation of AMR in the environment were all discussed. The perspectives captured during the workshop will form the basis of publications and future collaborations.
Year(s) Of Engagement Activity 2016
URL http://www.ceh.ac.uk/news-and-media/news/china-uk-scientists-attend-joint-workshop-antimicrobial-res...
 
Description Invited talk at Zhejiang University, China 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Give a talk: Application of stable-isotope labelling techniques for the detection of bacteria using plant-derived carbon and pathogens in agricultural soils
Year(s) Of Engagement Activity 2017
 
Description NAMRIP's 'You the doctor' AMR Exhibit (Winchester Science Centre) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Marcela Hernandez participated in the antimicrobial resistance (AMR) exhibit on February 17th, 2017. Children enjoyed the game and interested in the concept of keeping patients alive until 2050. They asked many questions about bacteria and viruses and the importance of a right treatment. Some children wanted to go further and experiment up to level 4 which means treating patients against bacteria, virus, fungi and parasitic infection (e.g. malaria). Adults were also very interested in discussing the importance of a correct treatment and prevention methods, and also the significance of washing hands in disease prevention.
Year(s) Of Engagement Activity 2017
URL http://www.southampton.ac.uk/namrip/news/2017/02/winchester-science-centre.page
 
Description Research Councils UK (RCUK), Newton Fund - UK-China Antimicrobial Resistance (AMR) Centre Partnerships Initiative for a participation in a workshop in Shanghai, China 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact During the workshop, we worked in groups to identify synergies and work out the areas of antimicrobial resistance (AMR) research where China and the UK are particularly strong. There were 5 such breakout sessions and each time the scientists joined different groups. Through these intense discussions the scientists identified the challenges and gaps in AMR research between China and UK, as well as synergies and were able to develop ideas about how to work together to greater advantage. Finally we joined groups according to our disciplines in order to design possible structures to reflect what a Centre Partnership might look like.
Year(s) Of Engagement Activity 2017
 
Description Visit to John Keble Church of England primary school (Winchester) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact On Wednesday February 8th, Marcela Hernandez and Marc Dumont visited the school during their science week. We brought a microscope from the University of Southampton and spent a morning showing the children protozoa swimming in pond water. The children found it fascinating and asked many thoughtful questions. The teachers were also enthusiastic about our visit. The children were very interested about bacteria and their forms and colours, also about human immune system and how we can protect ourselves from infection by handwashing.
Year(s) Of Engagement Activity 2017
 
Description Workshop (university of Southampton) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact On 30th January 2017, Marcela Hernandez gave a talk entitled "Stable isotope probing with 18O-water to investigate antimicrobial resistant bacteria in natural environments" at the Antimicrobial Resistance - Theme 3 Workshop - Understanding real world interactions at the Southampton University. The workshop was organised by the NAMRIP (Network for Antimicrobial Resistance and Infection Prevention) group and the talk was presented to scientific members of the NAMRIP where we described the project and preliminary results about the effect of the antibiotic meropenem on acidic soils from the Chilworth experimental site of the University of Southampton. We received valuable input from the audience, which will help us with some fine details of our experimental design.
Year(s) Of Engagement Activity 2017
 
Description Workshop at the Food Standards Agency, London. 
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 On November 25th, 2016, Bill Keevil and Marc Dumont participated in a workshop at the FSA on antimicrobial resistance in the food chain (Title: Food Retailers, Supply Chains and the Anti-microbial Resistance Challenge). This was a unique workshop including representatives from various UK bodies, including government, food producers, livestock veterinarians, food retailers and scientists. Marc Dumont gave a talk on the evolution of antibiotic resistance and the potential AMR risks related to the soil environment as related to this NERC project. This led to an active panel discussion on the risks of resistance in soil and the routes of entry of both pathogens and AMR compounds. There was input from various members, including veterinarians discussing doses of antibiotics administered to livestock and the impact on concentrations of the antibiotics entering the environment. Professor Tim Leighton FREng FRS (University of Southampton) is proposing that the contents of the meeting be published in a special issue in the journal 'Multidisciplinary dispatches on Anti-Microbial Resistance, Infection Prevention and Vaccination', therefore there is potential that the output could reach a global audience.
Year(s) Of Engagement Activity 2016