Periodic Reporting for period 4 - COMPARE (COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe) Reporting period: 2019-06-01 to 2019-11-30 Summary of the context and overall objectives of the project COMPARE is a multidisciplinary research network that envisions a globally linked data and information sharing platform system for the rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks.The main objectives of COMPARE were:• to improve rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks,• by developing a cross-sector and cross-pathogen analytic framework and globally linked data and information sharing platform,• that integrates state-of-the-art strategies, tools, technologies and methods for collecting, processing and analysing sequence-based pathogen data in combination with associated (clinical, epidemiological, and other) data,• for the generation of actionable information to relevant authorities and other users in the human health, animal health and food safety domains.COMPARE has successfully delivered on all objectives and has here at the end of the project, general SOPs for sampling, data generation and analyses, as well as data hubs for sharing data. The workflows have already been used for surveillance, clinical investigations and outbreak detection and will also in the future be embedded in the clinical and public health response improving local and global human and animal health. The tools and infrastructure developed have been taken forward through new EU projects (ECRAID, RECODID, VEO) where new advances will be added, building from the same basic concepts. Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far Just over five years ago, a Consortium of 29 partners, from widely different scientific fields, was brought together to simply gather samples, sequence samples, share the sequence data and metadata, and analyze/visualize the data, all within a secure ‘playground’. Each area came with their own perspective, vocabulary, ways of working and prejudices. At the end of this grand experiment called ‘COMPARE’, we have now demonstrated, not only within the Consortium, but beyond its confines as well, that, at least to some degree, a common sample and laboratory prep can be determined, a secure data hub with multiple ways of uploading sequences as well as metadata can be created and used by several types of users, and that the mix of data can be visualized into information of action and used for detection, surveillance and tracking of clinical infections, foodborne outbreaks and emerging infectious diseases.During the initial phases of COMPARE, major efforts were put into preparing, evaluating and comparing protocols for sampling and generating sequencing data, as well as creating IT-infrastructures and bioinformatics workflows allowing for secure storage and analyses of sequencing data. These infrastructures were piloted using different real-life studies focusing on clinical microbiology, foodborne infections and emerging infectious diseases. Most pilot studies involved only a single organism, but some fulfilled the end goal of combining all domains of life. In addition, we have explored the economical potentials of including next-generation sequencing in diagnostic, surveillance and outbreak detection, as well as the political, legal, ethical and other barriers for rapid sharing of sequencing data, and we have also been a global voice and advocate for sharing data for the benefit of public health. Besides a huge number of scientific conquests, documented by many scientific publications, COMPARE has established standard workflows, protocols, ring-tests, data-sharing hubs and bioinformatics pipelines that both during the project, but also 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 deep exploration of barriers to data sharing, as seen by scientists and end-users of data, and has led to an agreed code of conduct and governance models that have been brought forward far beyond COMPARE. The COMPARE project, and the solutions established, have thus, made a change in the landscape, and we see great demand for taking tools, infrastructure and data hubs further. Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far) COMPARE has set standards that will find their way well beyond this project. COMPARE-branded SOPs are being taken up by many laboratories in the field, the cross-consortium ring trials are in popular demand and these trials have been opened up to outside users and advocated through the Global Microbial Identifier alliance (www.globalmicrobialidentifier.org) and will to a large extent continue by support from other funds and have also been taken up by WHO/FAO. Requests to help shape future challenges in data generation and analysis have been received from other EU-funded consortia (RECODID), and the data hub concept has been presented as a model for potential support of the mission of the GLOPID-R coalition. Several COMPARE bioinformatics tools and pipelines are not only publicly available for the global scientific community, but continue to be running as web-services heavily accessed by people all over the world. Further development of new data integration platforms is foreseen in the VEO project that will build from the foundation laid through the COMPARE project. The potential utility of the data hub concept and governance are also explored in the ECRAID project, which aims to build a sustainable model for clinical trial infrastructure in Europe.The direct implications for society are difficult to quantify, but there is in our mind no doubt that the scientific progress made by COMPARE has and will continue to improve the use of next-generation sequencing for rapid diagnostic, identification of pathogens, surveillance and outbreak detection for the benefit of patients and society as a whole. Genomic information as the pathogen-independent language
