H2020 COMPARE Project: Collaborative management platform for the detection and analysis of (re)emerging and foodborne outbreaks in Europe

Just over five years ago, a consortium of 29 partners, coming from very different scientific fields, came together to collect samples, sequence samples, share the data and sequence metadata, and analyze/visualize the data, all within a secure "playground." Each area came with its own perspective, vocabulary, ways of working, and biases. At the end of this grand experiment called 'COMPARE,' we have demonstrated, not only within the Consortium but also beyond its boundaries, that, at least to some extent, a common sample and laboratory preparation system can be defined, a secure data hub with multiple ways to upload sequences and metadata can be created and used by various types of users, and that the combined data can be visualized into actionable information and used for the detection, surveillance, and monitoring of clinical infections, foodborne outbreaks, and emerging infectious diseases.

During the initial phases of COMPARE, significant efforts were devoted to preparing, evaluating, and comparing protocols for sampling and sequencing data generation, as well as to creating informatics infrastructures and bioinformatics workflows that would enable the secure storage and analysis of sequencing data. These infrastructures were tested using various real-life studies focusing on clinical microbiology, foodborne infections, and emerging infectious diseases. Most pilot studies involved a single organism, but some met the ultimate goal of combining all domains of life.

Furthermore, we have explored the economic potential of including next-generation sequencing in diagnostics, surveillance, and outbreak detection, as well as the political, legal, ethical, and other barriers to the rapid sharing of sequencing data, and we have also been a global voice and advocate for data sharing for the benefit of public health. In addition to a large number of scientific achievements, documented by numerous scientific publications, COMPARE has established standard workflows, protocols, ring-testing, data-sharing centers, and bioinformatics pipelines that, both during the project and in the years to come, have been and will be used by other scientists involved in next-generation sequencing. A key component of the project has been the in-depth exploration of the barriers to data sharing, as viewed by scientists and data end-users, leading to an agreed-upon code of conduct and governance models that have been presented well beyond COMPARE.

Therefore, the COMPARE project and the established solutions have changed the landscape, and we see a huge demand for tools, infrastructure, and data centers beyond.