Using genome sequence data to combat antimicrobial resistance
Lead Research Organisation:
University of Edinburgh
Department Name: Sch of Molecular. Genetics & Pop Health
Abstract
Antibiotic resistance is a truly global health challenge of our time, with the rates of infection by resistant bacteria consistently increasing year-on-year; particularly alarming is the relative growth in the number of infections by multi-drug resistant strains. In September 2016 world leaders at the UN pledged an unprecedented level of commitment to tackling antibiotic resistance - only the fourth time such action has been taken with respect to infectious disease.
In line with this aim, action needs to be taken to curtail the indiscriminate use of antibiotics in the clinical setting - to address this my current project focuses upon using whole sequence data to speed up the process of bacterial infection diagnostics by taking advantage of Oxford Nanopore's mobile sequencer (MinION). By determining the antibacterial resistance genes present in clinical samples, appropriate antibiotics can be administered more rapidly so decreasing the selective pressures for incidental antibiotic resistance to arise within populations, improving treatment outcome, and providing a substantial base for antibiotic resistance surveillance.
In line with this aim, action needs to be taken to curtail the indiscriminate use of antibiotics in the clinical setting - to address this my current project focuses upon using whole sequence data to speed up the process of bacterial infection diagnostics by taking advantage of Oxford Nanopore's mobile sequencer (MinION). By determining the antibacterial resistance genes present in clinical samples, appropriate antibiotics can be administered more rapidly so decreasing the selective pressures for incidental antibiotic resistance to arise within populations, improving treatment outcome, and providing a substantial base for antibiotic resistance surveillance.
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| MR/N013166/1 | 01/10/2016 | 30/09/2025 | |||
| 1805073 | Studentship | MR/N013166/1 | 01/09/2016 | 29/02/2020 | Stefan Rooke |
| Title | ZooLinK dataset |
| Description | Bacterial genomic data from sequencing |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Sequence data from underrepresented region (Kenya), with genomes of antibiotic resistant bacteria. Will be uploaded to public databases on publication |
| Description | ZooLinK (Zoonoses in Livestock in Kenya) project partnership |
| Organisation | International Livestock Research Institute (ILRI) |
| Country | Kenya |
| Sector | Charity/Non Profit |
| PI Contribution | As part of this project we implemented in-country sequencing using novel sequencing technologies. Allowing us to add significant value to the bacterial surveillance data which was being collected as a major part of the fieldwork that was conducted. We were able to conduct high quality sequencing at the field-lab from which the project was based a significant distance outside of the Kenyan capital; demonstrating the ability to somewhat decentralised sequence based surveillance, even in countries with less well developed infrastructure. We also implemented novel bioinformatics strategies to determine the presence and relationship between mobile vehicles of antibiotic resistance. |
| Collaborator Contribution | Our partners conducted the entirety of fieldwork for this project, where an enormous effort was placed on generating samples from very intensive field-work sampling over the course of 3 years. Our partners set up our field-lab from which we based our own sequencing efforts, also providing the bacterial samples with which we worked. |
| Impact | My PhD thesis is based on the work conducted as part of this project - with a view to publish a number of chapters as papers after submission. As yet, current outcomes are limited to those listed elsewhere in this portfolio. |
| Start Year | 2016 |
| Description | Sequencing workshop/demonstration held in Kenyan lab |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Held workshop for fellow researchers and colleagues from a project I was involved with in Kenya. I demonstrating Nanopore sequencing to them, as a full demonstration from DNA to sequencing. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Uk Parliament POST - Superbugs event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | We attended to highlight our work on the problem of antibiotic resistance. Specifically how we use sequencing to provide surveillance capacity for antibiotic resistance. This involved a interaction and discussion with members of the public. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.eventbrite.co.uk/e/superbugs-registration-92717521603# |