The rates and routes of transmission of multidrug resistant Klebsiella clones and genes into the clinic from environmental sources.
Lead Research Organisation:
University of Bath
Department Name: Biology and Biochemistry
Abstract
Recent years have seen a dramatic global increase of strains of bacteria that pose a high risk in health care settings due to broad resistance to a wide range of antibiotics.
Our research project will concentrate on Klebsiella pneumoniae (Klebsiella), a leading cause of multidrug resistant hospital-acquired infections globally, particularly among neonates, the elderly and immunosuppressed patients, with reported mortality rates upwards of 50%. It is also responsible for an increasing burden due to community-acquired invasive infections, which can lead to pyogenic liver abscess, pneumonia, and meningitis. In addition to causing disease, Klebsiella is an ecological generalist and can be carried asymptomatically in the intestinal tract, skin, nose, and throat of healthy individuals, and can thrive in a range of arthropod, bird or plant hosts (including crops and trees) and environmental niches such as water and soil. It can also cause invasive disease in several animal species, and it is a common cause of mastitis in dairy herds.
In order to control the spread of Klebsiella through targeted surveillance and intervention policies it is necessary to identify the sources of emergent community and health-care associated infection from the interlinked and varied niches encompassing "the environment". Environmental prevalence data provides a critical baseline, but is not always sufficient to inform on public health policy. For instance, the observation that gulls frequently harbour Klebsiella is, by itself, insufficient to guide policy on managing gull populations, as direct transmission to humans remains very difficult to demonstrate. However, if, say, water were to be identified as a major Klebsiella reservoir with frequent transmission to and from the clinic, this might in turn impact on waste water treatment procedures. Similarly, if cockroaches are found to be associated with Klebsiella this should lead to increased pest control both in hospitals and in the community.
To address this, we will take samples in order to identify Klebsiella from multiple clinical, community, agricultural, veterinary and environmental settings. Then we will use a novel approach based on whole genome sequencing to provide a much more efficient means to understand ecological adaptation, the distribution of resistance and virulence genes in the bacteria, and to identify key environmental settings from which these Klebsiella bacterial clones emerge. This approach will involve sequencing multiple colonies of bacteria simultaneously in order to detect a wider sample of genes present within a given sample. We will build a comprehensive, data-driven, model of adaptation, diversification, gene flow and transmission dynamics between all relevant ecological and clinical compartments. This will then pave the way for the development of targeted disease management strategies.
Our research project will concentrate on Klebsiella pneumoniae (Klebsiella), a leading cause of multidrug resistant hospital-acquired infections globally, particularly among neonates, the elderly and immunosuppressed patients, with reported mortality rates upwards of 50%. It is also responsible for an increasing burden due to community-acquired invasive infections, which can lead to pyogenic liver abscess, pneumonia, and meningitis. In addition to causing disease, Klebsiella is an ecological generalist and can be carried asymptomatically in the intestinal tract, skin, nose, and throat of healthy individuals, and can thrive in a range of arthropod, bird or plant hosts (including crops and trees) and environmental niches such as water and soil. It can also cause invasive disease in several animal species, and it is a common cause of mastitis in dairy herds.
In order to control the spread of Klebsiella through targeted surveillance and intervention policies it is necessary to identify the sources of emergent community and health-care associated infection from the interlinked and varied niches encompassing "the environment". Environmental prevalence data provides a critical baseline, but is not always sufficient to inform on public health policy. For instance, the observation that gulls frequently harbour Klebsiella is, by itself, insufficient to guide policy on managing gull populations, as direct transmission to humans remains very difficult to demonstrate. However, if, say, water were to be identified as a major Klebsiella reservoir with frequent transmission to and from the clinic, this might in turn impact on waste water treatment procedures. Similarly, if cockroaches are found to be associated with Klebsiella this should lead to increased pest control both in hospitals and in the community.
To address this, we will take samples in order to identify Klebsiella from multiple clinical, community, agricultural, veterinary and environmental settings. Then we will use a novel approach based on whole genome sequencing to provide a much more efficient means to understand ecological adaptation, the distribution of resistance and virulence genes in the bacteria, and to identify key environmental settings from which these Klebsiella bacterial clones emerge. This approach will involve sequencing multiple colonies of bacteria simultaneously in order to detect a wider sample of genes present within a given sample. We will build a comprehensive, data-driven, model of adaptation, diversification, gene flow and transmission dynamics between all relevant ecological and clinical compartments. This will then pave the way for the development of targeted disease management strategies.
Technical Summary
Klebsiella pneumoniae (Kp) is a leading cause of multidrug resistant hospital-acquired infections globally, and is responsible for an increasing public health burden in the community. In order to control the spread of Kp through targeted surveillance and intervention policies it is necessary to identify the sources of emergent community and health-care associated infection from the interlinked and varied niches encompassing "the environment". To address this, we will sample from multiple clinical, community, agricultural, veterinary and environmental settings in and around a single town, Pavia, in Northern Italy, and supplement these data with matched samples from France and elsewhere. We will use whole genome sequencing of community (mixed-colony) samples to assay accessory gene abundance and distribution. This contrasts with the more common approach based on phylogenetic analysis of single colonies, which would be of limited utility over broad environmental scales due to the complexity of transmission chains, environmental dormancy, and high rates of recombination.
This gene-centric approach provides a much more efficient means to understand ecological adaptation, the distribution of resistance and virulence genes, and to identify key environmental reservoirs from which clinical clones emerge. A key deliverable of this project will be the establishment of a pan-genome database ('pangenomium') that will integrate with both existing Kp genome community resources established by project partners (BIGSdb-kp, and wgsa.net). We will also develop mathematical models to further explore gene flow between environmental compartments, and will use the Oxford Nanopore Minion TM platform to characterise AMR plasmids, and understand their distribution and transfer, using hybrid assemblies.
This gene-centric approach provides a much more efficient means to understand ecological adaptation, the distribution of resistance and virulence genes, and to identify key environmental reservoirs from which clinical clones emerge. A key deliverable of this project will be the establishment of a pan-genome database ('pangenomium') that will integrate with both existing Kp genome community resources established by project partners (BIGSdb-kp, and wgsa.net). We will also develop mathematical models to further explore gene flow between environmental compartments, and will use the Oxford Nanopore Minion TM platform to characterise AMR plasmids, and understand their distribution and transfer, using hybrid assemblies.
Planned Impact
Klebsiella pneumoniae (Kp) is a highly diverse pathogen that is ubiquitous in the environment. This high level of variation will seriously hinder attempts to infer transmission dynamics between different environmental niches (including animal hosts) using approaches based on SNP variation within the core genome. This is due to factors such as the complex fitness landscape of the wider environment, the high level of genomic diversity (even within single hosts), high rates of co-colonisation, environmental dormancy, recombination, complex transmission chains and the simultaneous transmission of multiple variants. These issues would lead to inevitable gaps in sampling and statistical uncertainties stemming from the chance sequencing of one colony over another for any given sample.
This project will address these difficulties by providing a novel framework for understanding transmission on the basis of the distribution of accessory genes, rather than core genome variation, and in doing so will be of direct benefit to medical microbiologists and bacterial genomicists working on Kp, as well as the broader microbial genomics community. Our approach will be to construct a database of all known genes in this species, then used mixed colony sequencing to assay the distribution of these genes across multiple ecological niches within and around a single town (Pavia, northern Italy). This will enable us to identify niche specific genes, which will then be used as markers to determine the principal routes by which Kp moves through the environment and into healthcare settings. The identification of specific environmental settings enriched with particular AMR or virulence genes will inform on community risk assessment and policy guidelines. The project will involve the development of novel statistical and bioinformatics approaches and mathematical models, and all pipelines and tools will be readily accessible to the broader community via MRC-CLIMB. The resultant database and analysis tools will provide the means for users to infer the likely environmental source of query genomes by automated mining for the presence of our niche-specific marker genes. This will provide critical knowledge for future source attribution studies of Kp infections and to prioritize interventions to limit the spread of MDR-Kp from its natural reservoirs to human carriage and infections. Our team includes the developers of both Kp-BIGsdb and wgsa.net genomic platforms, and working to common standards between these two systems will be of further broad utility to the community at large. We will also develop and utilise our hybrid assembly methods to combine long read data generated by the Oxford Nanopore Minion with short read Illumina data which can be used for the complete assembly of plasmids (Bayliss et al, Gigascience 2017). In this way we will provide critical data concerning plasmid composition and mobility; understanding the genetic bases of (in)compatibilities between resistance genes, mobile elements and host chromosomes will play a key role in mitigating their spread. In addition to shedding light on plasmid transfer and evolution in Kp, our project will also provide important methodological advances for studying accessory elements on population scales.
In sum, this project will define, at what we believe is an unprecedented scale, the distribution of Kp lineages and genes in various environments. The project will also contribute to strengthen the bioinformatics infrastructures (wgsa.net, BIGSdb-Kp) used by the global microbiology and surveillance communities to communicate on the epidemiology and population biology of Kp. These advances will prove critical in the ongoing battle to mitigate the global spread of this serious pathogen.
This project will address these difficulties by providing a novel framework for understanding transmission on the basis of the distribution of accessory genes, rather than core genome variation, and in doing so will be of direct benefit to medical microbiologists and bacterial genomicists working on Kp, as well as the broader microbial genomics community. Our approach will be to construct a database of all known genes in this species, then used mixed colony sequencing to assay the distribution of these genes across multiple ecological niches within and around a single town (Pavia, northern Italy). This will enable us to identify niche specific genes, which will then be used as markers to determine the principal routes by which Kp moves through the environment and into healthcare settings. The identification of specific environmental settings enriched with particular AMR or virulence genes will inform on community risk assessment and policy guidelines. The project will involve the development of novel statistical and bioinformatics approaches and mathematical models, and all pipelines and tools will be readily accessible to the broader community via MRC-CLIMB. The resultant database and analysis tools will provide the means for users to infer the likely environmental source of query genomes by automated mining for the presence of our niche-specific marker genes. This will provide critical knowledge for future source attribution studies of Kp infections and to prioritize interventions to limit the spread of MDR-Kp from its natural reservoirs to human carriage and infections. Our team includes the developers of both Kp-BIGsdb and wgsa.net genomic platforms, and working to common standards between these two systems will be of further broad utility to the community at large. We will also develop and utilise our hybrid assembly methods to combine long read data generated by the Oxford Nanopore Minion with short read Illumina data which can be used for the complete assembly of plasmids (Bayliss et al, Gigascience 2017). In this way we will provide critical data concerning plasmid composition and mobility; understanding the genetic bases of (in)compatibilities between resistance genes, mobile elements and host chromosomes will play a key role in mitigating their spread. In addition to shedding light on plasmid transfer and evolution in Kp, our project will also provide important methodological advances for studying accessory elements on population scales.
In sum, this project will define, at what we believe is an unprecedented scale, the distribution of Kp lineages and genes in various environments. The project will also contribute to strengthen the bioinformatics infrastructures (wgsa.net, BIGSdb-Kp) used by the global microbiology and surveillance communities to communicate on the epidemiology and population biology of Kp. These advances will prove critical in the ongoing battle to mitigate the global spread of this serious pathogen.
Organisations
- University of Bath (Lead Research Organisation)
- University of Tromso (Collaboration)
- University of Groningen (Collaboration)
- University of Plymouth (Collaboration)
- UNIVERSITY OF EXETER (Collaboration)
- Washington State University (Collaboration)
- Khalifa University (Collaboration)
- UNIVERSITY OF GLASGOW (Collaboration)
- Cardiff University (Collaboration)
- Bugando Medical Centre (Collaboration)
- Bangalore University (Collaboration)
- Pasteur Institute, Paris (Collaboration)
- Utrecht University (Collaboration)
- University of Bristol (Collaboration)
- UNIVERSITY OF SYDNEY (Collaboration)
- University of Birmingham (Project Partner)
Publications
Argimón S
(2021)
Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch.
in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Batisti Biffignandi G
(2021)
Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae.
in G3 (Bethesda, Md.)
Bayliss SC
(2017)
The use of Oxford Nanopore native barcoding for complete genome assembly.
in GigaScience
Bayliss SC
(2019)
PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria.
in GigaScience
Booton RD
(2021)
One Health drivers of antibacterial resistance: Quantifying the relative impacts of human, animal and environmental use and transmission.
in One health (Amsterdam, Netherlands)
Description | GCRF |
Amount | £1,351,083 (GBP) |
Funding ID | EP/P028403/1 |
Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
Sector | Public |
Country | United Kingdom |
Start | 04/2017 |
End | 04/2020 |
Description | One Health Drivers of Antibacterial Resistance in Thailand |
Amount | £2,919,177 (GBP) |
Funding ID | MR/S004769/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 04/2018 |
End | 04/2022 |
Description | Tools for the Epidemiology of AMR Plasmids, One-Health Transmission and Surveillance (TEAPOTS) |
Amount | £40,000 (GBP) |
Funding ID | MR/X031640/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 02/2023 |
End | 02/2024 |
Title | "Pangenomium" bioinformatics tool for deducing gene and strain abundance profiles from mixed colony short read sequencing data |
Description | A pipeline has been developed to analyse "plate sweep" data, whereby multiple colonies (in this case belonging to the Klebsiella genus) are harvested and sequenced en masse. The pipeline works by mapping these short reads to a pan-reference database containing all known genes in Klebsiella genomes (>100,000 genes). This then provides abundance profiles of each gene which can then be used to detect genes that are enriched in specific niches (using a machine-learning approach). The pipeline is also being used to define species and sub-species clusters using a combination of two recently published tools, MSweep and PopPunk. |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2019 |
Provided To Others? | No |
Impact | None yet |
Title | Improvement to MSweep bioinformatics tool |
Description | Improvement of method to determine bacterial community profiles from plate sweep data based on the published method : DOI: 10.1099/mgen.0.000075 |
Type Of Material | Improvements to research infrastructure |
Year Produced | 2019 |
Provided To Others? | No |
Impact | More accurate and efficient categorisation of short sequencing reads to species and sub-species level. Designed for use on large datasets (eg the 1000 plate sweep datasets generated in SpARK). |
Title | Genome sequence database |
Description | ~3,500 genomes of Klebsiella and Raoultella species sequenced on Illumina (short read) platform from multiple clinical and non-clinical sources in and around Pavia. ~1,000 metagenomics "plate sweeps" of Klebsiella and Raoultella species sequenced. ~1500 genomes completed on long-read (Nanopore or Pac Bio) platform-> >3000 complete plasmid sequences |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | No |
Impact | Phylogenetic and AMR analyses ongoing, Work on plasmid diversity and transmission - paper currently under review at Lancet Microbe (preprint here: https://www.biorxiv.org/content/10.1101/2024.01.05.574329v1_ |
Title | PIGGY |
Description | This bioinformatics pipeline provides a means to cluster and align intergenic region (IGR) sequences from large genome datasets. This allows the detection of IGR "switching", a process whereby a single gene is associated with different intergenic regions (hence promoters and other regulatory elements) - this has been shown to be associated with changes in gene expression. This work has been accepted for publication in Gigascience. |
Type Of Material | Data analysis technique |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | The work has received a great deal of interest form the scientific community. |
URL | http://gigadb.org/dataset/100410 |
Title | PIRATE: pipeline for exploring the pan-genome |
Description | A new bioinformatics pipeline for exploring bacterial pan-genomes using different thresholds of sequence identity to define gene homology groups. |
Type Of Material | Data analysis technique |
Provided To Others? | No |
Impact | Manuscript in preparation |
Title | Synthetic Escherichia coli mixture samples with variable coverage |
Description | This dataset contains the synthetic mixture samples and reference sequences - as well as the appropriate metadata - that were originally used in the 2021 revision of the mSWEEP manuscript. There are 87 samples in total, each containing 100bp paired-end Illumina sequencing reads from 10 different Escherichia coli strains from 10 different lineages. The number of reads is set so that the sequencing coverage of the individual strains varies between 50x and 0.10x and sums up to 100x. |
Type Of Material | Database/Collection of data |
Year Produced | 2021 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/5535712 |
Title | genome sequences E. coli and klebsiella spp |
Description | We have generated over 3500 complete genome sequences from 15 Klebsiella species form various ecological sources (clinical and non-clinical) in and around the city of Pavia, Italy. We have generated 1000 'plate sweep' datasets from these samples. we have generated almost 1000 complete hybrid assemblies from these samples by complimenting the short read data with long read data. We have generated over 1000 E. coli sequences and 700 Klebsiella sequences from Thailand. We have 500 complete hybrid assemblies (ising long read data) |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | No |
Impact | A number of emerging collaborations and invited presentations |
URL | https://pubmed.ncbi.nlm.nih.gov/36411354/ |
Title | mSWEEP v1 example dataset |
Description | Example dataset for mSWEEP (https://github.com/probic/mSWEEP) # Changelog ## 4 July 2023 - Updated the dataset for Themisto v3 and mSWEEP v2 ## 30 June 2023 - Added the toy dataset supplied with mSWEEP v1.X.X |
Type Of Material | Database/Collection of data |
Year Produced | 2023 |
Provided To Others? | Yes |
URL | https://zenodo.org/record/8101284 |
Description | Antimicrobial treatment, resistome and microbiome |
Organisation | University of Glasgow |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Expertise in diversity analysis |
Collaborator Contribution | Expertise in epidemiology of mastitis and AMR |
Impact | Funding application to BBSRC responsive mode |
Start Year | 2015 |
Description | Aquaculture and antimicrobial resistance |
Organisation | University of Plymouth |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | Expertise in diversity analysis and statistics of diversity |
Collaborator Contribution | Expertise in aquaculture and microbiome analysis |
Impact | Funding application to the BBSRC NEWTON fund for the UK-China AMR initiative. |
Start Year | 2016 |
Description | BMC |
Organisation | Bugando Medical Centre |
Country | Tanzania, United Republic of |
Sector | Hospitals |
PI Contribution | We initiated collaboration with Bugando Medical Centre in Mwanza, Tanzania. We visited BMC and met with key administrative contacts. We have since set up an MoU with BMC and involved BMC as a partner on an MRC grant application. |
Collaborator Contribution | Professor Stephen Mshana from Bugando Medical Centre participated in several workshops on AMR, hosted a visit by delegates from the University of Glasgow, facilitated the signing of an MoU and contributed to the writing of a grant proposal that is under consideration by MRC. His team will also contribute Klebsiella isolates to the MRC funded SpARK project, funded as JPI-AMR project and led by Prof. Ed Feil at the University of Bath. |
Impact | This collaboration is multi-disciplinary and involves one or more representatives of the following disciplines: anthropology, epidemiology, genomics, health economics, human geography, mathematics, medical science, microbiology, pharmacology, sociology, veterinary medicine |
Start Year | 2017 |
Description | Collaboration with Khalifa University, Abu Dhabi (with Cefas, APHA, University of Oxford) |
Organisation | Khalifa University |
Country | United Arab Emirates |
Sector | Academic/University |
PI Contribution | Providing bioinformatics and population genomics expertise |
Collaborator Contribution | Providing strain collections and genome data from multiple 'One-Health (eg clinical, veterinary, community) settings |
Impact | A 'Memorandum of Understanding' is currently being agreed by the Universities of Bath and Khalifa. This will provide the means for Khalifa to release funds, strains, data etc to Bath. This forms part of a wider collaboration involving Cefas, APHA and the University of Oxford. A workshop was held at the end of February 2023 in Abu Dhabi with various stakeholders to establish a framework for a large 'One Health' project to manage AMR in this country. EF is also a named (no-cost) collaborator on an internal KU grant on the epidemiology of meningitis. |
Start Year | 2022 |
Description | GWAPES (GW4 AMR Plasmid Epidemiology and Surveillance) |
Organisation | Cardiff University |
Department | School of Medicine |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | A network funded under the third round of the GW4 generator fund. The project focuses on managing the spread of antimicrobial resistance (AMR) by exploring how the genes spread on plasmids between different bacterial strains, different ecological settings, and different geographical regions. Members of the network represent the four GW4 Universities ; Bath, Bristol, Cardiff and Exeter Also partners Cefas (Weymouth), MicrobesNg and the centre for genomic pathogen surveillance (university of Oxford). |
Collaborator Contribution | Hybrid meetings, sharing of data and research resources. |
Impact | Further network funding (JPIAMR network TEAPOTS), and further collaboration (eg with Khalifa University in UAE). Multidiscplinary 'One-Health' (agricultural + clinical) plus modelling and experimental aspects. |
Start Year | 2022 |
Description | GWAPES (GW4 AMR Plasmid Epidemiology and Surveillance) |
Organisation | University of Bristol |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | A network funded under the third round of the GW4 generator fund. The project focuses on managing the spread of antimicrobial resistance (AMR) by exploring how the genes spread on plasmids between different bacterial strains, different ecological settings, and different geographical regions. Members of the network represent the four GW4 Universities ; Bath, Bristol, Cardiff and Exeter Also partners Cefas (Weymouth), MicrobesNg and the centre for genomic pathogen surveillance (university of Oxford). |
Collaborator Contribution | Hybrid meetings, sharing of data and research resources. |
Impact | Further network funding (JPIAMR network TEAPOTS), and further collaboration (eg with Khalifa University in UAE). Multidiscplinary 'One-Health' (agricultural + clinical) plus modelling and experimental aspects. |
Start Year | 2022 |
Description | GWAPES (GW4 AMR Plasmid Epidemiology and Surveillance) |
Organisation | University of Exeter |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | A network funded under the third round of the GW4 generator fund. The project focuses on managing the spread of antimicrobial resistance (AMR) by exploring how the genes spread on plasmids between different bacterial strains, different ecological settings, and different geographical regions. Members of the network represent the four GW4 Universities ; Bath, Bristol, Cardiff and Exeter Also partners Cefas (Weymouth), MicrobesNg and the centre for genomic pathogen surveillance (university of Oxford). |
Collaborator Contribution | Hybrid meetings, sharing of data and research resources. |
Impact | Further network funding (JPIAMR network TEAPOTS), and further collaboration (eg with Khalifa University in UAE). Multidiscplinary 'One-Health' (agricultural + clinical) plus modelling and experimental aspects. |
Start Year | 2022 |
Description | JPIAMR 7th Joint Programme Initiative on AMR - SOLIDNESS |
Organisation | University of Groningen |
Country | Netherlands |
Sector | Academic/University |
PI Contribution | This network has just started (kick off meeting in March) |
Collaborator Contribution | This network has just started (kick off meeting in March) |
Impact | This network has just started. Kick off meeting in March. |
Start Year | 2019 |
Description | KlebNet: a One Health network bridging science and surveillance on antimicrobial resistant Klebsiella |
Organisation | Pasteur Institute, Paris |
Country | France |
Sector | Charity/Non Profit |
PI Contribution | Attended kick-off meeting in April 2019. I have been invited to present at the next meeting in April 2020 in Paris |
Collaborator Contribution | 31 leading experts in Kp in distinct sectors located in 12 different countries (Europe, Africa, North America, South America, Asia). Consortium headed by Slyvain Brisse who is a SpARK partner |
Impact | Kick off meeting last year resulting in new collaborations. I have been invited to present outputs from the the SpARK project at this years meeting. |
Start Year | 2019 |
Description | Landscape ecology of antimicrobial resistance |
Organisation | University of Glasgow |
Department | School of Mathematics and Statistics |
Country | United Kingdom |
Sector | Academic/University |
PI Contribution | We have established a new collaboration with the statistics department to develop novel statistical tools to analyse emerging regional and national scale antimicrobial resistance datasets. We bring expertise in the analysis of diversity and epidemiology of antimicrobial resistance spread. |
Collaborator Contribution | Advanced statistical tools |
Impact | Fully funded studentship to commence October 2016 plus a Pump-priming NERC application |
Start Year | 2015 |
Description | Nor-Kleb-Net and Kleb-Gap |
Organisation | University of Tromso |
Country | Norway |
Sector | Academic/University |
PI Contribution | I am on the advisory board of Nor-Kleb-Gap. I have provided advise and data for the Nor-Kleb and Kel-Gap networks and will be attending a workshop in June. |
Collaborator Contribution | NA |
Impact | This is a multidisciplinary partnership covering all aspects of Klebsiella population biology, with a focus on Norway. |
Start Year | 2019 |
Description | STARCS consortium |
Organisation | Utrecht University |
Country | Netherlands |
Sector | Academic/University |
PI Contribution | I am attending and presenting at the final meeting of the STARCS consortium on the outputs of the SpARK project |
Collaborator Contribution | NA |
Impact | I will present at the final meeting in June 2020 |
Start Year | 2019 |
Description | Sharing/collaboration on Klebsiella sequences |
Organisation | Washington State University |
Country | United States |
Sector | Academic/University |
PI Contribution | A BBSRC funded project in Tanzania has provided Klebsiella isolates for sequencing which will provide input into SPARK plus and a currently funded MRC funded project in Tanzania looking at the drivers of antibtioic resistance. |
Collaborator Contribution | A BBSRC funded project in Tanzania has provided Klebsiella isolates for sequencing which will provide input into SPARK plus and a currently funded MRC funded project in Tanzania looking at the drivers of antibtioic resistance. |
Impact | Analysis of sequence data in progress. |
Start Year | 2019 |
Description | Special Training Network on bacterial evolution (funded by ESEB) https://eseb.org/prizes-funding/special-topic-networks/stn-current-networks/synthesizing-micro-and-macro-evolutionary-processes-shaping-prokaryotic-genomes/ |
Organisation | Bangalore University |
Country | India |
Sector | Academic/University |
PI Contribution | STN on prokaryotic evolution, funded by the ESEB (40K Euros). I am a co-PI with Deepa Agashe (Bangalore). Co-write the proposal and organising meetings. This was due to start in 2019 but has been delayed 2 years because of the pandemic. |
Collaborator Contribution | Deepa Agashe co-wrote the proposal and helping to organise meetings (with other co-organisers). |
Impact | Funding secured - 1 st meeting organised for May 2022 (in Bath, UK) |
Start Year | 2019 |
Description | UofG-USYD |
Organisation | University of Sydney |
Department | Faculty of Veterinary Science |
Country | Australia |
Sector | Academic/University |
PI Contribution | Prof Zadoks was lead applicant (HAZEL; SNAP-AMR) or co-applicant on the proposals listed in ResearchFish and continues to contribute to ongoing activities despite having moved to the University in Sydney. The University of Sydney covers her salary as in-kind contribution to enable her to continue to contribute to meetings, publications, ResearchFish reporting, etc. |
Collaborator Contribution | All listed projects were initiated by the partners, including by Prof. Zadoks when she was still employed by the University of Glasgow. |
Impact | Prof. Zadoks continues to engage with several projects, including through meetings, preparation of manuscripts, and reporting in ResearchFish. Prof. Zadoks' time investment in various projects is still significant and is contributed in-kind by her current employer, the University of Sydney. Multiple disciplines are involved in each project, as reported under various projects where appropriate. |
Start Year | 2019 |
Description | WSU |
Organisation | Washington State University |
Country | United States |
Sector | Academic/University |
PI Contribution | I led the write up of the grant proposal HAZEL, submitted under the ZELS call, with contributions from my research team incl. Dr Margaret Davis at WSU. Prof Douglas Call, also at WSU, led a NSF-BBSRC project on AMR in Northern Tanzania and Klebsiella isolates or sequences from that project will be included in data analysis under SpARK. |
Collaborator Contribution | Dr. Margaret Davis contributed to the writing of the grant proposal HAZEL; that was submitted under the ZELS call. Dr Davis contributes intellectual input into project activities and attends annual in-person meetings and monthly skype calls. Conference Presentations: G. Prinsen, J. Benschop, N. French, E. Swai, R. Zadoks, J. Sharp, L. Waldman. Food Safety Awareness and Practices in Urban and Rural Butcheries and Eateries in Northern Tanzania. 34th Tanzania Veterinary Association Conference, 6-8 December 2016, Arusha, Tanzania. Audience: veterinarians, policy makers, PhD students, researchers. G. Prinsen, J. Benschop, N. French, E. Swai, R. Zadoks, J. Sharp, L. Waldman. Food Safety Awareness and Practices in Urban and Rural Butcheries and Eateries in Northern Tanzania. 9th Biennial Conference New Zealand International Development Studies Network, 5-7 December 2016, Wellington, New Zealand. Audience: researchers, development experts. R. Zadoks, K. Thomas, G. Barker, J. Benschop, J. Buza, S. Cleaveland, M. Davis, N. French, E. Karimuribo, R. Kazwala, B. Mmbaga, N. Mtui, G. Prinsen, J. Sharp, E. Swai, L. Waldman, J. Crump. Of Meat and Men, Models and Microbes - Understanding Salmonella risks in Tanzania's Meat Supply Chain. . 34th Tanzania Veterinary Association Conference, 6-8 December 2016, Arusha, Tanzania. Audience: veterinarians, policy makers, PhD students, researchers. Since then, the collaboration has been extended to include Professor Douglas Call, who has shared a collection of ~600 AMR resistant E. coli isolates with us to inform writing of a follow-on grant proposal. He is also contributing material to the Klebsiella-focussed SpARK project, funded by MRC through a JPI-AMR grant. |
Impact | (1) Successful application for funding of the HAZEL project. This is a multi-disciplinary collaboration involving medics, veterinarians, quantitative scientists, social scientists, and molecular epidemiologists. (2) Submission of a grant application to MRC. This is a multi-disciplinary collaboration involving representatives of the following disciplines: anthropology, bioinformatics, health economics, epidemiology, human geography, mathematics, medicine, microbiology, pharmacology, sociology, veterinary medicine |
Start Year | 2012 |
Description | Departmental Seminar University of Edinburgh (online) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Departmental seminar at the University of Edinburgh - dissemination of the results form the SpARK project. Made new collaborative links. |
Year(s) Of Engagement Activity | 2021 |
Description | Invited Seminar as part of ESGEM seminar series |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | Online seminar as part of the EsGEM (an ESCMID working group) Webinar series titled "The transmission of resistant, virulent strains and plasmids within complex ecological landscapes: does Klebsiella challenge the focus on One-Health?" |
Year(s) Of Engagement Activity | 2022 |
Description | Invited presentation National Consortium for Microbial Genomics Meeting Olso |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Study participants or study members |
Results and Impact | Research seminar Oslo National Consortium for Microbial Genomics Meeting titled "Host adaptation and 'spillover' in Staphylococcus aureus and Klebsiella pnuemoniae." |
Year(s) Of Engagement Activity | 2022 |
URL | https://www.fhi.no/en/about/conferences/national-consortium-for-microbial-genomics-meeting/ |
Description | Invited presentation at BIRS-CMO workshop |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | 30 minute presentation of work from the SpARK project, with 30 minute discussion with other workshop attendees. |
Year(s) Of Engagement Activity | 2020 |
URL | http://www.birs.ca/events/2020/5-day-workshops/20w5222 |
Description | Lay article for 'The Conversation' 'Superbugs in the environment rarely transfer to humans - new study' |
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 | Published a lay-article in the conversation summarising the results of the Spark study (after these results were published in Nature Microbiology). 3,812 Reads, 10 publishers |
Year(s) Of Engagement Activity | 2022 |
URL | https://theconversation.com/superbugs-in-the-environment-rarely-transfer-to-humans-new-study-195075 |
Description | Outreach event for local schools |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | In my capacity as Head of Outreach for the Milner Centre for Evolution, I organised a major outreach activity in September 2018. 150 local school children (year 4-6) were invited from local schools to take part in a range of activities, including the use of a lego DNA "sequencer", and understanding AMR and bacteria. |
Year(s) Of Engagement Activity | 2018 |
URL | https://www.youtube.com/watch?v=TkwIiB72itY&feature=youtu.be |
Description | Podcasts on AMR/MLST |
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 | Professional Practitioners |
Results and Impact | These podcast have had around 300 listens (a short time after being released) and have several 'likes' and shares on twitter. Micro Binfie podcast on MLST https://soundcloud.com/microbinfie/early-days-of-mlst Micro Binfie podcast on 'One Health': https://soundcloud.com/microbinfie/one-health |
Year(s) Of Engagement Activity | 2023 |
URL | https://soundcloud.com/microbinfie/one-health |
Description | Public Lecture (Norwich) |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Undergraduate students |
Results and Impact | I gave an invited lecture at the Quadram Institute in Norwich on 12 Feb 2020 as part of the "Darwin Day" symposium. The lecture was on bacterial adaptation and included some discussion of the research output form SpARK and other ongoing projects. |
Year(s) Of Engagement Activity | 2020 |
Description | Research seminar |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Study participants or study members |
Results and Impact | Research seminar given to the Kleb-Gap consortium (Norway) titled 'The SpARK study: Klebsiella spp. transmission modelling across niches' |
Year(s) Of Engagement Activity | 2021 |
Description | Research seminar |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Study participants or study members |
Results and Impact | Research seminar titled 'Gauging the risk from environmental reservoirs of AMR' for inaugural meeting of the GW4 Alliance on AMR |
Year(s) Of Engagement Activity | 2022 |
URL | https://gw4amr.com/events/ |
Description | Workshop |
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 | Attendance at UK - Canada One Health Workshop on Antimicrobial Resistance in Agriculture and the Environment (UKRI, UCalgary) |
Year(s) Of Engagement Activity | 2021 |
Description | open symposium |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Professional Practitioners |
Results and Impact | Open symposium on project progress at the University of Pavia |
Year(s) Of Engagement Activity | 2017 |