Combining datasets to address AMR surveillance gaps

Expression of Interest Title: Data Challenge – Combining datasets to address AMR surveillance gaps
Team 9057, led by Quentin Leclerc of Institut Pasteur, France with Aleksandra Kovacevic (Institut Pasteur), Eve Rahbe (Institut Pasteur) and Lulla Opatowski (Institut Pasteur)

Summary of Research:

Recent efforts to estimate the global burden of antimicrobial resistance (AMR) have highlighted multiple gaps in existing surveillance systems. Surveillance datasets from the pharmaceutical industry currently represent an under-utilised resource to monitor trends in AMR. Firstly, these datasets can focus on different bacterial species, countries, and years, hence combining them instead of analysing them separately could substantially increase our AMR surveillance coverage. Secondly, even in cases where these datasets describe isolates belonging to the same bacterial species and country, these are obtained from different institutions, therefore combining them could increase the robustness of national AMR estimates. However, the feasibility and value of these combinations is currently unclear. In this project, we aim to discuss the value of comparing and combining these datasets to fill current surveillance gaps. First, we plan to review the methods used to generate these datasets, to highlight potential common ground but also important differences which may limit a global analysis, and identify overlapping key pathogens, years, and countries we can compare across datasets. We will then compare resistance estimates across these datasets, and determine the “agreement” of these different systems with the latest available GLASS data, the global surveillance system led by WHO. We will further test how grouping several of these datasets might drive resistance estimates closer to or away from the WHO GLASS estimates. Finally, we will visualise the global coverage of these datasets with maps, to facilitate discussion of surveillance gaps. Overall, our project aims to strengthen health systems by clarifying the validity and role of industry surveillance systems as part of global efforts to fill the gaps in AMR surveillance.

Requested Datasets:

Data Contributor: Pfizer Inc.

Bedaquiline Drug Resistance Assessment in MDR-TB (DREAM)
Data Contributor: Johnson & Johnson

GEARS (Global Evaluation of Antimicrobial Resistance via Surveillance)
Data Contributor: Venatorx Pharmaceuticals

Data Contributor: Paratek Pharmaceuticals, Inc.

Data Contributor: Shionogi

SOAR 201818
Data Contributor: GSK