Determination of the dynamics of antimicrobial resistance genes in the human and animal gut microbiome.

Lead Research Organisation: University of Cambridge
Department Name: Veterinary Medicine

Abstract

This research aims to develop a much deeper understanding of how antimicrobial resistance (AMR) resistance genes survive and spread within people and animals and to develop an understanding of how we might change the way we use antibiotics to reduce the amount and spread of AMR. AMR does not operate in an ecological vacuum and to understand the process properly, we need to obtain a much clearer appreciation of the underlying bacterial population and community dynamics of bacteria possessing AMR genes.

The aims of this research are to measure the numbers and AMR genes in bacteria found in patients, farm animals and the environment and the way they change over time (the dynamic changes), and in response to the use of antibiotics with a particular emphasis on the clinical outcomes in cases of human and animal disease. The research will use state-of-the-art DNA sequencing technology and analytical techniques to look at mixed populations of bacteria on samples of bacteria obtained from experiments performed in the laboratory and samples taken from hospitals and farms. Many of the bacteria in the gut are impossible or very difficult to grow in the laboratory and are considered to be 'unculturable'. Previous research has ignored these.

The overarching hypothesis to be tested is that the unculturable microbiome provides a reservoir of AMR genes that may both receive and donate AMR genes, in particular when the microbiome is under antimicrobial selective pressure.

The specific objectives are:

1. To establish the accuracy and reproducibility of two novel DNA sequencing methods that enable the DNA from individual bacterial species containing AMR genes to be identified from within faecal microbiome samples.

2. To use these novel genomic techniques in experimental conditions (in mice and pigs) to investigate AMR gene transfer from E. coli expressing Extended Spectrum Beta-Lactamase (ESBL) and Salmonella enterica serovar Typhimurium with fluoroquinolone resistance within the gut microbiome both following the treatment with antibiotics that are effective and when an antibiotic is used to which the bacteria are resistant.

3. To perform studies of the gut bacteria over time in farmed pigs and humans receiving antibiotics for treatment of clinical disease.

4. To develop mathematical models that capture the flux of AMR genes in bacterial populations to identify factors that lead to the build-up or transmission of resistance.

Technical Summary

Research on Antimicrobial resistance (AMR) in host people and animals has focused on pathogenic bacterial species which are readily cultured in the laboratory. Recent advances in chromosome conformation methodology such as enable the metagenomic DNA sequencing of complex microbiomes with the assembly of genomic data from individual constituent bacterial species. Using these techniques it is possible to track the fate of AMR genes when they move between species of bacteria, or move between separate lineages of the same species. The aim of the proposed research is to define the nature and frequency of transfer of antimicrobial resistance (AMR) genes between pathogenic and commensal bacteria within their hosts under varying selection pressures.
The proposed research consists of 6 work packages (WP) with the following objectives:
WP1. To establish the accuracy and reproducibility of two novel metagenome sequencing methodologies that enable the individual genomic backgrounds of bacteria containing AMR genes to be identified from within faecal microbiome samples.
WP2 & WP3. To use these novel genomic techniques in experimental conditions (in mice and pigs) to investigate horizontal AMR gene transfer from E. coli expressing Extended Spectrum Beta-Lactamase (ESBL) and Salmonella enterica serovar Typhimurium with plasmid-mediated fluoroquinolone resistance within the gut microbiome both following the therapeutic use of antimicrobials that lead to bacterial cure, and following the use of antimicrobials to which these strains are resistant.
WP4 & WP5. To perform longitudinal studies of the gut microbiome in farmed pigs and humans receiving antibiotics for treatment of clinical disease to test the external validity of observations made from experimental animal infections.
WP6. To develop mathematical models that capture the flux of AMR genes in bacterial populations to identify key parameters in the build-up or transmission of resistance.

Planned Impact

Increasing frequency of antimicrobial resistance (AMR) resistance genes in bacterial pathogens is a major problem in human and animal medicine. This research will provide important information about the impact of antimicrobial drug use in populations of bacteria found in agricultural and hospital environments. This knowledge is essential for the development of strategies concerning the responsible use of antimicrobial drug in both veterinary and human medicine. Animal agriculture and particularly farmed species such as pigs, poultry and dairy cows currently have a high dependence on blanket treatments of antibiotics in the face of infectious disease. Changes in these practices would have profound effects on the economics of food production and rational decisions need to be based on high quality evidence from appropriately conducted scientific studies. The results from this research would have impacts in the welfare of farm animals at the individual and group level; at the farm level; and for the whole industry. It would enable informed discussion to precede the adoption of industry-wide strategies to reduce levels and further induction of AMR arising from agricultural use of antibiotics. The dynamics of AMR gene flux in both animals and people will enable public and animal health policies to be developed that maximise the clinical effectiveness of narrow spectrum antimicrobial treatments, and help inform decisions on the most judicious use of broader spectrum antibiotics and those of greater importance to human health.

The proposed research will provide the groundwork to inform future antimicrobial stewardship in animal and human health. It is an ambitious and fundamental study of the way antimicrobial resistance (AMR) genes behave in the context of a host's microbiome.

One of the outcomes of the research is the generation of data about the previously unknown species of bacteria that contribute to human and animal microbiota. The application and further development of novel metagenomic sequencing techniques will identify the considerable proportion of the gut microbiome that is 'unculturable'. The proposed research will generate genome data from these occult species of bacteria that will not only be of value in the study of AMR but also provide data that will improve our understanding of the microbiology of the gut in healthy and diseased individuals.

Publications

10 25 50
 
Description Alborado Research Fund award
Amount £37,182 (GBP)
Organisation University of Cambridge 
Department Alborada Research Fund
Sector Academic/University
Country United Kingdom
Start 07/2016 
End 06/2017
 
Description Does AMR in livestock contribute to AMR in people in NE India? An interdisciplinary study.
Amount £1,358,389 (GBP)
Funding ID ES/S000186/1 
Organisation Economic and Social Research Council 
Sector Public
Country United Kingdom
Start 07/2018 
End 06/2021
 
Description UK-China AMR Partnership Initiative
Amount £783,728 (GBP)
Funding ID MR/P007201/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 07/2016 
End 06/2019
 
Description Roslin institute 
Organisation University of Edinburgh
Department The Roslin Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution We have been implementing Hi-C metagenomics methodology and designed experimental and survey work using this technique.
Collaborator Contribution Mark Stevens is our co-PI at the Roslin Institute where experimental work will be performed as part of this collaboration.
Impact None to date
Start Year 2016
 
Description Invited conference talk: 2018 August 25, International Symposium on Staphylococci and Staphylococcal Infections, "Susceptibility to a combination of penicillins and beta-lactamase inhibitors in MRSA" Copenhagen, Denmark 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Presentation to a research conference. Considerable discussion with other researchers after the talk developing future collaborations
Year(s) Of Engagement Activity 2018
 
Description Invited talk 2017 December 10, ithree institute, Research Seminar, University of Technology Sydney, Australia. "A comparison of antimicrobial resistance on high- and low- antibiotic use farms using Hi-C metagenomics". 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Research talk given at leading research institute in Australia. Generated a lot of interest in the methodology we have developed over the course of this project.
Year(s) Of Engagement Activity 2017
 
Description Public lecture entitled Confronting the Microbial Menace in Our Food'. Professor Mark Stevens 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact The inaugural lecture of Professor Mark Stevens was held on 30 October 2017 on his BBSRC-funded research to identify bacterial and host factors influencing the ability of Salmonella, Campylobacter and E. coli to colonise farm animals and cause disease. It was attended by children from local schools, members of the public, students at The Roslin Institute and wider University of Edinburgh and posted online.
Year(s) Of Engagement Activity 2017,2018
URL https://media.ed.ac.uk/media/Inaugural+lectureA+Confronting+the+microbial+menace+in+our+food/1_x5k5e...
 
Description Research seminar at Roslin Institute 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact 2016 Apr 12, Research Seminar "The mecC story - a new MRSA equally at home in animals and people." Roslin Institute, Edinburgh
Year(s) Of Engagement Activity 2016
 
Description Seminar at Gates Scholars Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact 2016 June 16, Gates Scholars Biennial Conference "Are we in an Antibiotic-free Era?", St John's College, Cambridge
Year(s) Of Engagement Activity 2016
 
Description Seminar at Glasgow University 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact 2016 Oct 19, Research seminar, University of Glasgow. "Using chromosome conformation sequencing to look at the dynamics of transmission of antimicrobial resistance genes"
Year(s) Of Engagement Activity 2016
 
Description Seminar at Imperial College, University of London 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact 2016 Sept 22, Antimicrobial Research Collaborative Conference, Imperial College. Keynote lecture: "Using chromosome conformation metagenomics to look at movement of AMR genes in complex bacterial populations"
Year(s) Of Engagement Activity 2016