Data Challenge Overview

Please note that the submission deadline has expired and the data challenge is now closed for new entries.

The aim of the 2024 Vivli AMR Surveillance Data Challenge, funded by GARDP, Paratek, Pfizer and Vivli, 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 could be answered, or tools developed through this Data Challenge.

HOW TO PARTICIPATE

1. Sign up to the AMR Register
2. Form a team
3. Learn about the datasets on the Register
4. Submit a 300-word expression of interest (complete a team form)
5. Access the data for 30 days
6. Create and upload your final submission
7. Finalists notified

Data Challenge Goals

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:

Detect trends in multi-drug resistance over time
Inform national and international policy, and antibiotic stewardship
Allow modelling of future resistance trends

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.

2024 Vivli AMR Surveillance Challenge, funded by GARDP, Paratek, Pfizer and Vivli

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 the 2024 Vivli AMR Surveillance Data Challenge 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:

Maximize the reach and discoverability of research
Maximize the potential for research to be used and have real world impact
Facilitate collaboration, engagement and dialogue around research
Expand the user-base of the AMR surveillance data available on the AMR Register

To see the potential of the data, see the 2023 Data Challenge winners’ solutions here.

*Wellcome funded the 2023 Vivli AMR Surveillance Data Challenge

Data Challenge Entries

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.

Details of the data available can be reviewed at https://amr.vivli.org/members/research-programs/

Note – all the datasets on the Register are available for the Data Challenge, with the exception of the Merck datasets. The Merck data can still be requested, but outside of the Data Challenge.

Expressions of Interest for the Data Challenge should be submitted on the AMR Register at https://amr.vivli.org. For details of how to take part, see How to Participate.

For any questions, please read the FAQs, or ask them via the Slack channel.

Expressions of Interest must be submitted by midnight Eastern Time on July 28, 2024
Teams must comprise of at least 2 and a maximum of 5 team members
Teams entering for the AMR Student Innovation Prize must comprise of a majority of students, with a maximum of one named non-student mentor. Teams entering for this prize should indicate this by checking the box on the Research Team Form.
Expressions of Interest will be reviewed by Vivli to ensure they meet basic high-level criteria
- Uses some data that is available in the AMR register
- Have a minimum of 2 and maximum of 5 team members
- Pose a scientific question related to AMR
Individuals or teams who lack teammates or particular skillsets should sign up for the dedicated 2024 Vivli AMR Surveillance Data Challenge Slack channel and post a message in the #i-want-to-join-a-team channel to advise other researchers they are interested in a collaboration.
Datasets will be downloadable, and teams will have 30 days to download and work with the data, and submit their written submission document.
Researchers may bring their own data to the challenge to supplement the data available.
Teams will present their concept as a written submission document. Guidelines for the submission document may be found here. These guidelines must be followed and final results submitted within the 30-day period to be considered a valid submission.
Each submission document will be scored by an independent judging panel.
Finalists will be chosen for the “pitch” phase involving a live Zoom presentation. This pitch phase will enable the judges to have an interactive Q&A session and allow finalists to bring a demonstration dimension and more depth to their solutions.
Awardees will be decided by the highest scores – if there is a tie, the judges’ decision will be final.
This is an open competition, and we aim to receive entries from all interested teams. Applications are invited from researchers based in both high and low resource settings.

About the Datasets on the AMR Register

The pharmaceutical industry routinely collects surveillance data that is 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.

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 89 countries over 20 years and contains over one million isolates.

Browse the datasets available on the AMR Register.

Note – all the datasets on the Register are available for the Data Challenge, with the exception of the Merck datasets. The Merck data can still be requested, but outside of the Data Challenge.

Data Challenge Judging and Awards

How will the final submission be judged?

Each submission document will be scored by an independent judging panel. Submissions will be judged on the following criteria. Entries for the AMR Student Innovation Prize will be judged separately.

Each solution will be judged on methodology and design as well as:

Innovation – how creative is this idea, technique or solution?
Impact – how would you rate the impact of this solution or tool on the field if successfully implemented?

A short list of finalists will be chosen for the “pitch” phase involving a live Zoom presentation. This pitch phase will enable the judges to have an interactive Q&A session and allow finalists to bring a demonstration dimension and more depth to their solutions.
Awardees will be decided by the highest scores – if there is a tie, the judges’ decision will be final.

Judges

The independent judging panel includes:

Diane Anastasiou, Director of Microbiology, Paratek Pharmaceuticals
Patricia Bradford, PhD, Consultant and Owner of Antimicrobial Development Specialists LLC
Ana Gales, MD, PhD, Professor of Infectious Diseases, Universidade Federal de São Paulo
Direk Limmathurotsakul, MD, PhD, Associate Professor and Head of Microbiology, Mahidol-Oxford Tropical Medicine Research Unit
Anand Manoharan, PhD, Scientific and Antibiotic Susceptibility Program Lead, GSK
Marc Mendelson, MBBS, PhD, Professor of Infectious Diseases, University of Cape Town
Seamus O’Brien, PhD, R&D Director, Global Antibiotic Research and Development Partnership (GARDP)
Katherine Perez, PharmD, BCIDP, RWE – Anti-infective & ID Surveillance, Pfizer

Final Awards

A total of 6 awards will be provided that are associated with monetary awards/travel grants

Grand Prize Award – $10,000 (or equivalent in GBP) and a travel grant of $5,000 to travel to ESCMID Global or ASM Microbe in 2025, if their abstract is accepted
4 awards – Each receiving $5,000 and a travel grant of $2,500 to travel to ESCMID Global or ASM Microbe in 2025, if their abstract is accepted – 2 in Innovation and 2 in Impact
1 AMR Student Innovation Award – a travel grant of $5,000 to travel to ESCMID Global or ASM Microbe in 2025, if their abstract is accepted. Teams must indicate that they are entering for this award up front, as the entries will be judged separately.
All finalist teams will be invited to submit a publication to the peer reviewed Wellcome Open Research Journal. The Vivli AMR Open Data Reuse Data Challenge is a “Collection” or compilation of articles from data challenges related to the AMR Register, funded by Wellcome. https://wellcomeopenresearch.org/collections/vivli/about

The significant outputs of this data challenge may be tools, applications, reports, publications or software. As strong proponents of Open Science, to ensure that the outcomes of the Data Challenge can be used for the greatest impact, participating teams are expected to make their outputs openly and publicly accessible.

All final solutions would be published in an open access journal, platform or repository, such as OSF or GitHub. Teams would be best placed to identify the most appropriate repository for their outputs and would be expected to share them in line with the timeline outlined in the FAQs on the data challenge webpage. Outputs would be accompanied by documentation or metadata to allow the solutions to be interpreted and used by others.

Finalist teams will be invited to submit a manuscript to be included in the Wellcome Open Research collection, Vivli AMR Open Data Reuse Data Challenge.

Links would be posted on the AMR website at https://amr.vivli.org/, and shared by Vivli on LinkedIn and X. Any researcher solutions that are created remain the intellectual property of the research team(s). Delays or restrictions on data or software sharing may be appropriate in limited cases to protect intellectual property.

About AMR Surveillance

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.