NEC05836 The environmental REsistome: confluence of Human and Animal Biota in antibiotic resistance spread (REHAB)

Lead Research Organisation: NERC Centre for Ecology and Hydrology
Department Name: Science Programme Office


We do not fully understand how important types (species) of bacteria and packages of genetic material (genes) coding for antibiotic resistance move between humans, animals and the environment, or where, how and why antibiotic resistance emerges. This study aims to look in detail at the genetic level at bacteria in farm animals, human/animal sewage, sewage treatment works and rivers, to work out the complex network of transmission of important antibiotic-resistant bacteria and antibiotic resistance genes. We will use this information to work out how best to slow down the spread of antibiotic resistance between humans, livestock and the environment.

Infections are one of the most common causes of ill-health in human and animal medicine, and are caused by a range of different micro-organisms, including viruses and bacteria. Amongst bacteria, there are some species, or types, of bacteria, which can live harmlessly in human and animal intestines, sewage, and rivers, but can also cause disease in humans and animals if they get into the wrong body space, such as the bloodstream or urine. Examples of these bacteria include E. coli, and other similar organisms, which belong to a family of bacteria called "Enterobacteriaceae".

It has generally been possible to treat infections caused by bacteria using several classes of medicines, known as antibiotics. Different antibiotics kill bacteria in different ways: for example, they can switch off critical chemical processes that the bacteria need to survive, or they can break down the outer shell of the bacteria. In response to the use of antibiotics, bacteria have changed over time, finding ways to alter their structure so that antibiotics no longer have a target to act on, or by producing substances that break down the antibiotic before it has a chance to kill the bacteria. These changes to the bacteria's genetic code, so that they are no longer killed by an antibiotic, create antibiotic resistance. Bacteria can also acquire packages of genes that cause antibiotic resistance from other surrounding bacteria. This is known as horizontal gene transfer. Through these mechanisms, members of the Enterobacteriaceae family of bacteria have developed antibiotic resistance to a number of different antibiotics over a short period of time. In some cases we are no longer able to treat these infections with the antibiotics we have available.

Studying antibiotic resistance and horizontal gene transfer in bacteria found in humans, animals and the environment is difficult because we cannot directly see how bacteria and their genetic material move between them. However, new "Next Generation Sequencing" (NGS) technologies allow scientists to look in great detail at the genetic code of large numbers of bacteria. Comparing this information across bacteria which have been living in the different parts of the environment (e.g. sewage treatment works, rivers) and in human and animal sewage allows us to see how bacteria have evolved to become resistant to antibiotics, and how resistance genes have been shared between them.

This study will use NGS technologies to look at the genetic code of large numbers of Enterobacteriaceae bacteria found in humans, animals (pigs, sheep and poultry), sewage (pre-, during and post-treatment), and rivers. These different groups/areas will be sampled in different seasons of one calendar year to determine how antibiotic resistance genes move around between these locations and over time, and what factors might influence this movement. We will also be investigating whether various chemicals and nutrients in the water may be affecting how quickly horizontal gene transfer occurs. Understanding this is essential to work out how we might intervene more effectively to slow the spread of antibiotic resistance genes and bacteria, and keep our antibiotic medicines useful.

Planned Impact


Antimicrobial resistance (AMR) is a major threat to the treatment of infections in humans and animals, and a particular problem in a family of bacteria known as the Enterobacteriaceae. These organisms can cause a wide range of infectious syndromes, but are also able to asymptomatically colonise the gastrointestinal tracts of humans and animals, and wider environmental reservoirs such as sewage and rivers. They are particularly effective at sharing resistance genes using mobile genetic elements (e.g. plasmids). At present there are limited data to explain how resistance genes spread amongst Enterobacteriaceae, and where this is most likely to occur (humans, animals, the environment); as a result, it is difficult to design appropriate interventions.

This study represents the first detailed analysis of resistance genes, resistance gene vectors and important strains of Enterobacteriaceae harbouring them, sampled across humans, animals, sewage and rivers, and evaluated at multiple time points. The concept has been developed by a collaborative, multi-disciplinary team of researchers, with a view to providing valuable outputs to a similarly broad range of research users/stakeholders. As a result, information generated by the study will be of benefit to:

1. Human and animal public health agencies, in developing public health policy and designing strategic interventions to combat AMR across scientific disciplines
2. Healthcare providers, in managing hospital waste and potentially using it as a resource to monitor the degree of AMR present within hospital institutions, and identifying potential wider sources contributing to AMR in disease-causing strains of Enterobacteriaceae
3. Water and wastewater service providers, who will be assisted in designing any necessary interventions to limit the spread of AMR elements through effluent, sewage treatment works and water systems
4. Farmers, who will gain insight into how AMR might be spreading to, within and from their animal herds/flocks, and will be given support in considering interventions which may limit this spread
5. Environmental agencies, who will be able to use the information and methods from this study to assess whether current policy regarding sludge use on arable land and effluent discharge into rivers restricts the spread of AMR elements in the environment
6. The general public, who stand to gain from the detailed knowledge of resistance gene transmission networks generated by this study, which can then be used as a platform for appropriate, targeted interventions to limit further AMR spread and evolution
7. Academic users and scientific researchers, who will have the largest collection of fully sequenced Enterobacteriaceae strains and plasmids, well-characterised environmental metagenomic datasets, and tools for genomic and metagenomic analysis, made available to them

Overall, the data and insights generated from this study will enable a wide range of user groups to participate in designing strategic interventions to combat AMR in Enterobacteriaceae regionally, nationally and internationally. In addition to producing early results that will have an impact on guiding approaches to appropriately tackling AMR in Enterobacteriaceae regionally and nationally, we aim to establish a series of sampling frames and analytical methods relevant to the implementation of long-term, on-going surveillance, that can eventually be used as a model system for successful global monitoring of the spread of AMR genes, plasmids and strains.


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Title Library of samples 
Description A library of samples collected from farms (environmental and biological), rivers and sewage treatment works for use potentially in future funded research projects. 
Type Of Material Biological samples 
Provided To Others? No  
Impact No impact yet. 
Title Bioinformatic pipeline for the analysis of AMR genes in metagenomic data 
Description A bioinformatic pipeline (ResPipe) designed for the accurate assignment and counting of genes that are classified as expressing antimicrobial resistance phenotypes. The pipleine is containerised and made available via Nextflow. 
Type Of Material Data analysis technique 
Year Produced 2018 
Provided To Others? No  
Impact Respipe is currently being used in-house during optimisation and testing phases, but will be made publically available to the research community when this is complete. 
Title Database/Collection of data 
Description Database generated to allow metadata to be recorded related to samples collected from farms, rivers and sewage treatment works. 
Type Of Material Database/Collection of data 
Provided To Others? No  
Impact No impact to date 
Description PacBio sequencing 
Organisation Icahn School of Medicine at Mount Sinai
Country United States 
Sector Academic/University 
PI Contribution Investigation of plasmid structure
Collaborator Contribution Sequencing and analysis. Member of REHAB Steering Committee
Impact None yet
Start Year 2016
Description Thames Water Collaboration 
Organisation Thames Water Utilities Limited
Country United Kingdom 
Sector Private 
PI Contribution Access to results of AMR in Sewage Treatment Works
Collaborator Contribution Provide access and Health and safety training for Sewage Treatment Works. Member of the REHAB Steering Committee
Impact None as yet
Start Year 2016
Description University of Oxford 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Provide project management, and wet lab support including DNA extractions of the samples. Sewage treatment work site identification, sample collection. Development of bioinformatic tools.
Collaborator Contribution Project management, and wet lab support including DNA extractions and metagenomic sequencing of the samples. Provide collaborative link with Mount Sinai for PacBio long read sequencing. Development of bioinformatics pipelines and tools.
Impact None yet
Start Year 2016
Description University of Reading 
Organisation University of Reading
Country United Kingdom 
Sector Academic/University 
PI Contribution Provision of data and ideas for the development of a bioinformatic pipeline for the analysis of antimicrobial resistance in metagenomics data.
Collaborator Contribution Programming of bioinformatic pipeline (ResPipe), testing and data analysis.
Impact No outcomes yet
Start Year 2018
Description collaboration with APHA 
Organisation Animal and Plant Health Agency
Country United Kingdom 
Sector Public 
PI Contribution Provide project management, and wet lab support including DNA extractions and metagenomic sequencing of the samples.
Collaborator Contribution Collection of samples from a variety of farms in the Oxfordshire area, including environmental farm samples for potential future studies. providing wetlab support and intellectual know how. Member of REHAB Steering Committee
Impact A library of pooled faecal samples, individual bacterial isolates and metagenomes from pig, sheep and cattle farms.
Start Year 2016