The environmental REsistome: confluence of Human and Animal Biota in antibiotic resistance spread (REHAB)
Lead Research Organisation:
University of Oxford
Department Name: Experimental Medicine
Abstract
OVERALL STUDY AIM
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.
STUDY BACKGROUND AND AIMS IN MORE DETAIL
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.
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.
STUDY BACKGROUND AND AIMS IN MORE DETAIL
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
IMPACT SUMMARY
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.
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.
Organisations
- University of Oxford (Lead Research Organisation)
- Animal and Plant Health Agency (Collaboration)
- Thames Water Utilities Limited (Collaboration)
- PUBLIC HEALTH ENGLAND (Collaboration)
- National Institute for Public Health and Environment (RIVM) (Collaboration)
- UK CENTRE FOR ECOLOGY & HYDROLOGY (Collaboration)
- Icahn School of Medicine at Mount Sinai (Collaboration)
- National Centre for Infectious Diseases (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- Public Health England (Project Partner)
Publications
Bush SJ
(2020)
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism-calling pipelines.
in GigaScience
De Maio N
(2019)
Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes.
in Microbial genomics
Gweon HS
(2019)
The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples.
in Environmental microbiome
Matlock W
(2021)
Flanker: a tool for comparative genomics of gene flanking regions
Matlock W
(2021)
Genomic network analysis of environmental and livestock F-type plasmid populations.
in The ISME journal
Shaw LP
(2021)
Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.
in Science advances
Smith RP
(2023)
A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone.
in Frontiers in microbiology
Description | Antimicrobial (AMR) genes found in E.coli circulating in wastewater and farms resulting in resistance to certain antibiotics are dominated by the niche (waste water and farms) and local geography rather than the seasons throughout the year. The number of different AMR genes is high, and are constantly changing, and this information is important to ensure local strategies are put in place to control the emergence and spread of AMR. Evidence is suggesting that there is sharing of plasmids between the new sample and those in isolates causing bloodstream infection. |
Exploitation Route | Our analyses are feeding into key aims of the latest National Action Plan on antimicrobial resistance which aims to understand the transmission of AMR through the environment. |
Sectors | Agriculture Food and Drink Environment Healthcare |
Description | Our analyses have fed into policy documents including the ERAMMP process in Wales. We were using some of the findings to support an educational program on AMR for children and caregivers in community. |
First Year Of Impact | 2021 |
Sector | Agriculture, Food and Drink,Education,Environment,Healthcare |
Impact Types | Cultural Policy & public services |
Description | Review of Welsh Government Report on AMR |
Geographic Reach | Local/Municipal/Regional |
Policy Influence Type | Contribution to a national consultation/review |
URL | https://erammp.wales/sites/default/files/2022-11/55%20ERAMMP%20Report-55%20AMR%20v1.0_en.pdf |
Description | : MRF AMR DPhil Studentship: Genomics and Metagenomics of Animal, Environmental and Human Samples to Understand Resistance Gene Transmission Amongst Enterobacteriaceae in Oxfordshire |
Amount | £66,210 (GBP) |
Organisation | Medical Research Council (MRC) |
Department | Medical Research Foundation |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2019 |
End | 09/2023 |
Description | DPhil in Clinical Medicine (4 yr)/Medical Research Foundation National PhD Training Programme in Antimicrobial Resistance Research (AMR) scholarship 07/10/2018 |
Amount | £129,400 (GBP) |
Funding ID | MRF NDM-OX/KC |
Organisation | University of Oxford |
Sector | Academic/University |
Country | United Kingdom |
Start | 09/2018 |
End | 10/2022 |
Description | HPRU HAI and AMR |
Amount | £5,761,932 (GBP) |
Funding ID | NIHR200915 |
Organisation | National Institute for Health Research |
Sector | Public |
Country | United Kingdom |
Start | 03/2020 |
End | 03/2025 |
Description | One Health interventions to prevent or reduce the development and transmission of AMR: Phage-Stop-AMR |
Amount | € 1,403,467 (EUR) |
Funding ID | MR/W031248/1 |
Organisation | JPIAMR Virtual Research Institute |
Sector | Academic/University |
Start | 03/2022 |
End | 03/2025 |
Description | Oxford Martin Programme on Antibiotic resistance |
Amount | £907,210 (GBP) |
Organisation | University of Oxford |
Sector | Academic/University |
Country | United Kingdom |
Start | 09/2020 |
End | 10/2023 |
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 |
Title | Pipeline developed to analyse long read sequences |
Description | A workflow has been developed to fully circularise long read whole genome sequences to identify species and predict antimicrobial resistance |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | None yet. |
Title | Pipeline to analyse metagenomic whole genome sequences |
Description | A pipeline to elucidate bacterial species within WGS data containing multiple bacteria, working towards resistance prediction |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | Pipeline has been made available to collaborator at University of Virginia and has been used by other researchers within the group |
Title | Closed plasmid sequences |
Description | Complete closed plasmid sequences genererated using long and short read sequences |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | No |
Impact | None yet |
Title | Complete bacterial assemblies for 'Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK' |
Description | Complete bacterial assemblies from the journal article 'Matlock, William, et al. "Enterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK." Elife 12 (2023): e85302.' 'assemblies.zip' contains assemblies for n=1,458 isolates with circularised chromosomes and n=3,697 circularised plasmids. If you use this data please cite the journal article and the Zenodo DOI. |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/7948129 |
Title | Environmental metagenome data |
Description | Environmental metagenome raw data |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | No |
Impact | None yet |
Title | Farm Metagenome data |
Description | Farm metagenome sequence data |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | No |
Impact | None yet |
Title | Illumina sequence data from farms and STW |
Description | Genomic sequence data from farms and STW for four key species of Enterobacteriaceae. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | No |
Impact | None yet |
Title | MOESM3 of The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples |
Description | Additional file 3: Table S1. Metagenomic data. Each sample was sequenced in replicate across four lanes (2 × 4 = 8 files per sample), combining to give the ~ 200 million reads per sample used in the study. The number of reads mapping to T. thermophilus from each sample is also given. Provided as Excel spreadsheet. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM3_of_The_impact_of_sequencing_depth_on_the_inferre... |
Title | MOESM3 of The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples |
Description | Additional file 3: Table S1. Metagenomic data. Each sample was sequenced in replicate across four lanes (2 × 4 = 8 files per sample), combining to give the ~ 200 million reads per sample used in the study. The number of reads mapping to T. thermophilus from each sample is also given. Provided as Excel spreadsheet. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM3_of_The_impact_of_sequencing_depth_on_the_inferre... |
Title | MOESM4 of The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples |
Description | Additional file 4: Table S2. Hybrid sequencing details for cultured isolates. Statistics are shown for both short reads (Illumina) and long reads (PacBio) sequenced from the same DNA extracts. Provided as Excel spreadsheet. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM4_of_The_impact_of_sequencing_depth_on_the_inferre... |
Title | MOESM4 of The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples |
Description | Additional file 4: Table S2. Hybrid sequencing details for cultured isolates. Statistics are shown for both short reads (Illumina) and long reads (PacBio) sequenced from the same DNA extracts. Provided as Excel spreadsheet. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM4_of_The_impact_of_sequencing_depth_on_the_inferre... |
Title | MOESM5 of The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples |
Description | Additional file 5: Table S3. Details of mapping metagenomic reads to isolate hybrid assemblies. Each sample is shown on a different sheet. Provided as Excel spreadsheet. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM5_of_The_impact_of_sequencing_depth_on_the_inferre... |
Title | MOESM5 of The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples |
Description | Additional file 5: Table S3. Details of mapping metagenomic reads to isolate hybrid assemblies. Each sample is shown on a different sheet. Provided as Excel spreadsheet. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM5_of_The_impact_of_sequencing_depth_on_the_inferre... |
Title | MOESM6 of The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples |
Description | Additional file 6: Table S4. PERMANOVA results based on Bray-Curtis dissimilarities for sample replicates. Analyses are shown in relation to sample replicates and sequencing lanes for both (a) CARD AMR abundance data, (b) Centrifuge taxonomic abundance data. Provided as Excel spreadsheet. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM6_of_The_impact_of_sequencing_depth_on_the_inferre... |
Title | MOESM6 of The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples |
Description | Additional file 6: Table S4. PERMANOVA results based on Bray-Curtis dissimilarities for sample replicates. Analyses are shown in relation to sample replicates and sequencing lanes for both (a) CARD AMR abundance data, (b) Centrifuge taxonomic abundance data. Provided as Excel spreadsheet. |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
URL | https://springernature.figshare.com/articles/MOESM6_of_The_impact_of_sequencing_depth_on_the_inferre... |
Title | Metadata database |
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 |
Title | Model to allow automated circularisation of plasmid sequences obtained from long read sequence platforms |
Description | Adapting existing open access software to allow circularisation of plasmids which have been generated from long read sequence platforms such as PacBio |
Type Of Material | Data analysis technique |
Provided To Others? | No |
Impact | No impact |
Title | Nanopore sequence data |
Description | Raw long read sequence data from farms and STW for four key species of Enterobacteriaceae. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | No |
Impact | None yet |
Title | Sewage Treatment Works Samples |
Description | Sample (date, location, physicochemical parameters) data for sampling from Oxfordshire Sewage Treatment Works and their surrounding environment. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | No |
Impact | None yet |
Title | Supporting data for "Genomic diversity affects the accuracy of bacterial SNP calling pipelines" |
Description | Accurately identifying SNPs from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained.
This study evaluates the performance of 209 SNP calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally-sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia and Klebsiella. We evaluated the performance of 209 SNP calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic, bacteria such as Escherichia coli, but less dominant for clonal species such as Mycobacterium tuberculosis. The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often employed the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup or Strelka. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | Yes |
URL | http://gigadb.org/dataset/100694 |
Description | Collaboration with CEH |
Organisation | UK Centre for Ecology & Hydrology |
Country | United Kingdom |
Sector | Public |
PI Contribution | Provide 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 |
Collaborator Contribution | Identify relevant sample collection sites from sewage treatment work and rivers in Oxfordshire, arrange access to STW and collect the samples. Provide support with metagenomic analyses and intellectual input for the project |
Impact | identification of suitable STW and rivers. |
Start Year | 2016 |
Description | Collaboration with National Centre for Infectious Diseases, Singapore |
Organisation | National Centre for Infectious Diseases |
Country | Singapore |
Sector | Hospitals |
PI Contribution | Use of plasmid sequence analysis methods developed in REHAb to AMR plasmid data analysis on a collection of CPE plasmids in Singapore. |
Collaborator Contribution | Sharing of data and metadata |
Impact | No outputs yet - data analysis underway. |
Start Year | 2022 |
Description | Collaboration with RIVM (Dutch public health agency) |
Organisation | National Institute for Public Health and Environment (RIVM) |
Country | Netherlands |
Sector | Academic/University |
PI Contribution | Using plasmid sequence classification methods developed as part of REHAB to analyse a collection of carbapenemase-producing plasmids from the Netherlands. |
Collaborator Contribution | Supply of the sequencing data and metadata. |
Impact | ECCMID presentation (2023) Public health - improvement of drug resistance plasmid surveillance workflows in the Netherlands |
Start Year | 2022 |
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 the CRyPTIC General Assembly. Member of REHAB Steering Committee |
Impact | Two publications |
Start Year | 2014 |
Description | Phage research - Dr Alfred Fillol-Salom |
Organisation | Imperial College London |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Provision of REHAb isolates. |
Collaborator Contribution | Analysis of REHAB isolates. |
Impact | No outputs yet. |
Start Year | 2022 |
Description | Phage-PCI hybrid research - Dr Jose Penates |
Organisation | Imperial College London |
Department | MRC Centre for Molecular Bacteriology and Infection |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Contribution of REHAB isolates. |
Collaborator Contribution | Analysis of REHAB isolates. |
Impact | No outputs yet. |
Start Year | 2022 |
Description | Public Health England (PHE) |
Organisation | Public Health England |
Country | United Kingdom |
Sector | Public |
PI Contribution | Access to sequencing data and research results. |
Collaborator Contribution | Access to S. aureus, Norovirus, C. difficile and TB samples and related epidemiological data. Staff to collect the samples and data and to ship this to Oxford and the Wellcome Trust Sanger Institute for sequencing. As well as intellectual input into the research. Member of REHAB Steering Committee |
Impact | Successful translation of next generation sequencing into public health microbiology |
Start Year | 2009 |
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 |
Impact | None as yet |
Start Year | 2016 |
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. Provide collaborative link with Mount Sinai for PacBio long read sequencing |
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. |
Impact | A library of pooled faecal samples and individual bacterial isolates from pig, sheep and cattle farms. |
Start Year | 2016 |
Description | Bacterial world - Oxford Natural History Museum |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Showcasing Bash the Bug and encouraging particpation. |
Year(s) Of Engagement Activity | 2018,2019 |
URL | http://www.oum.ox.ac.uk/bacterialworld/ |
Description | Late Night: 'Uncultured' a talk - Natural History Museum |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | a talk delving into the private lives of bacteria and discover how these tiny organisms run the world tocelebrate the opening of Bacterial World exhibition. |
Year(s) Of Engagement Activity | 2018 |
Description | Microscope on Modernising Medical Microbiology |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | Join scientists as they show us how the Modernising Medical Microbiology group is using DNA to forensically track the spread of infection, detect antibiotic resistance in tuberculosis more quickly and discover the genes responsible for making bacteria dangerous. |
Year(s) Of Engagement Activity | 2019 |
Description | Royal Society Summer Science Exhibtion |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Public/other audiences |
Results and Impact | A Stall at Summer Science Exhibition showcasing the work undertaken under CRyPTIC and encouraging participation in Bash the Bug Community project. 1,000,000 reads from Bash the Bug were acheived in 2018. |
Year(s) Of Engagement Activity | 2018 |
Description | Science exhibition at school |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | KS2 Science exhibition for local school |
Year(s) Of Engagement Activity | 2019 |
Description | Set up patient panels |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | We circulated an advert inviting members of the public to join patient panels to inform all aspects of the groups' work. Over 100 individuals responded, and we held two open meetings where different aspects of the work were presented. Following this smaller groups have been set up to review and advise on different projects. Members of the public have really valued the opportunity to get involved. |
Year(s) Of Engagement Activity | 2014,2016 |
Description | Showcase UK AMR research |
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 | Showcase UK AMR research relative to UK Government's 5-year action plan and 20-year vision for antimicrobial resistance (AMR). |
Year(s) Of Engagement Activity | 2020 |