The Vivli AMR Surveillance Open Data Re-Use Data Challenge, funded by Wellcome, was launched in April 2023, as a catalyst for innovation and support for the inventive reutilization of the wealth of surveillance data available within the AMR Register.
Vivli is pleased to announce the awardees. Please see official press release for further information.
The WHO has declared that antimicrobial resistance (AMR) is one of the top 10 global public health threats facing humanity, and antimicrobial resistant infections may become the leading cause of death globally by 2050.
The Vivli AMR Register was successfully launched in June 2022 and is sharing surveillance data from GSK, Johnson & Johnson, Merck, Pfizer, Shionogi, Paratek and Venatorx, and welcomes data from other potential data contributors in pharmaceutical, diagnostic, biotech and generics companies who generate surveillance data.
The open sharing of these industry data through a single platform enables researchers to:
Note: all the datasets on the AMR Register are available as part of the challenge, with the exception of the Merck datasets. These datasets from Merck can still be requested via the AMR Register, but not as part of the data challenge.
Vivli AMR Surveillance Open Data Re-use Challenge, funded by Wellcome
Our hope is that the research projects enabled by this platform will further advance understanding, inform decision-making and drive policy and behavioral changes in the medical community, by global organizations and wider society.
The key goal of this Vivli AMR Surveillance Open Data Re-use Data Challenge, funded by Wellcome, is to promote utilization of the Vivli AMR Register to more researchers and drive advances in the AMR field. We believe that important questions in surveillance would be answered, or tools developed through this Data Challenge.
This Challenge is in direct alignment with Wellcome and Vivli’s open science goals in that through this project it will:
Here are some potential examples of how the data sets can be utilised:
Entries were scored from 1 lowest-5 highest on
A short list of finalists were chosen for the “pitch” phase involving a live Zoom presentation. This pitch phase enabled the judges to have an interactive Q&A session and allowed finalists to bring a demonstration dimension and more depth to their solutions.
Awardees were decided by the highest scores – if the case of a tie, the judges’ decision was final.
Judges
The judging panel included:
Final Awards
A total of 5 awards were made associated with monetary awards/travel:
The 5 winning teams are invited to submit an abstract of their project to ECCMID 2024. If the abstract is accepted, the successful teams will be provided with $5,000 (or equivalent in GBP) funding to be used towards travel, registration, and other related expenses for ECCMID 2024 to present their abstract.
One Runner-Up Innovation award team was also invited to submit an abstract of their project to ECCMID 2024. If the abstract is accepted, the successful teams will be provided with $2,000 (or equivalent in GBP) funding to be used towards travel, registration, and other related expenses for ECCMID 2024 to present their abstract.
All final solutions will be published in an open access journal, platform or repository, such as OSF or GitHub. Outputs will be accompanied by documentation or metadata to allow the solutions to be interpreted and used by others.
Links to the solutions are posted on the AMR Register website.
AMR surveillance is the monitoring of changes in populations of microbes to help understand evolving patterns of resistance to anti-infectives.
Antimicrobial resistance surveillance entails the collection of clinical samples from patients with infections in hospital or in the community. These samples are then tested to determine what microbes or isolates they contain. The isolates are then exposed to a bank of different antibiotics to determine whether the microbe is susceptible to the antibiotic, i.e., the infection would be cured by the antibiotic, or whether they are resistant to the antibiotic, i.e., another antibiotic would have to be identified to treat the infection.
The pharmaceutical industry routinely collects surveillance data that could be highly valuable to support the collective global efforts to curb AMR. These industry programmes monitor the susceptibility of clinical isolates to marketed antibiotics and record pre-launch resistance levels of new products compared to antibiotic generic drugs to resistance trends. While there is no requirement for industry to run surveillance on marketed antibiotics, regulatory bodies need surveillance data before launching a new antibiotic as part of approval requirements. Research using this data, shared through the AMR Register, could guide appropriate antibiotic prescription, set up breakpoints for antibiotics, define strategies for new drug discovery and development, reveal unmet needs and allow the modelling of future trends in resistance.
This Data Challenge invites researchers from all fields, including those working in AMR, data scientists, AI/ML researchers etc., to put forward their ideas initially as an Expression of Interest (EOI).
The Data Challenge is in the form of an open question. Participants are challenged to come up with innovative insights or uses for the AMR surveillance data. Participants might combine the data available on the AMR Register with their own open datasets to address questions related to AMR. Success will be determined by innovative and original ideas backed up with robust methods.
The data are available in the form of Excel spreadsheets and contain information on minimal inhibitory concentrations (MICs), plus country of collection, infection & specimen type, year, microorganisms and antimicrobial used, plus most datasets include basic demographics such as patient’s age range and gender. The available data was collected in 85 countries over 17 years and contains nearly one million isolates.