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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 3 - COMPARE (COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe)

Teaser

Summary

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 system will collect, process and analyse 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 aims to make as much data as possible publicly available and will thus, contribute significantly to global Open Science.

The Specific Objectives of COMPARE include the following:
A. Risk-assessment models and risk-based sampling and data collection strategies that enhance our capacity to detect potential disease outbreaks;
B. From samples and associated metadata to comparable data: harmonised standards for sample processing and sequencing to obtain high quality and comparable sequence data from and metadata associated with a specimen;
C. From comparable data to actionable information: designing analytical workflows for turning comparable data into actionable information for addressing questions in frontline diagnostics, foodborne infections and (re-) emerging infections.
o Frontline diagnostics
o Public health
o (Re)-emerging infections research
D. Designing and building a common data and information platform supporting rapid sharing, integration and analysis of sequence-based pathogen data in combination with other contextual metadata; The system will be linked to existing and future complementary systems, networks and databases such as those used by ECDC, NCBI and EFSA.
E. Risk communication tools will be developed enabling authorities in the human and animal health and food safety sectors to effectively communicate the results obtained.
F. Studies on the barriers (ethical, regulatory, administrative, logistical, political) to the implementation and widespread use of open-data sharing platforms
G. Development of a framework for estimating the cost-effectiveness of the COMPARE system, including the value of safety.

Work performed

As the structure of the COMPARE project is different from typical research projects, and requires a shared commitment to goals that help develop the COMPARE infrastructure in addition to the individual scientific ambitions, coordination of the WPs has been crucially important. All WPs initially spent time and organized teleconferences and meetings to better understand the needs and capacities of each participant, and the potential synergies, overlaps and knowledge / expertise gaps as a start to the organisation of the WP activities. These initial investments have especially paid off during this reporting period, as there was extensive collaboration between institutes, across work packages, and with partners outside the COMPARE consortium. The project results are also increasingly becoming visible for outside users, as envisioned from the onset.

The outputs are beyond (a high number of) scientific publications, and includes development of searchable repositories providing guidance on sampling, investigation of disease outbreaks or unusual events in humans and animals, and general guidelines (SOPs) for future sample and data collection. During this 3rd reporting period, several of the initial products were evaluated by other partners inside and outside of the consortium as part of the translational activities.

A key development has been the use of quality assurance standards that are a starting point for routine implementation of NGS-based analytics particularly for public health, clinical environments.

After the initial exploratory data sharing in the first period, several data hubs followed and the user feedback was extremely helpful to guide improvements towards user-friendly infrastructure.

The COMPARE project, and the solution established, has made a change in the landscape, and we see great demand for taking tools, infrastructure and data hubs further. We therefore are keen on further developing this integrated concept. It is clear that we are still at version 1.0, and work is needed to further develop the data hubs regarding user-friendliness and flexibility. We currently aim to do that through the COMPARE foundation, supported by new funding initiatives, as well as more targeted funding.

Final results

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). Requests to help shape future challenges in data generation and analysis have been received from two other EU-funded consortia (ZIKALLIANCE and RECODID), and the data hub concept has been presented as a model for potential support of the mission of the GLOPID-R coalition.

Based on the feedback from these interactions, as well as from our extensive panel of stakeholders, we are strengthened in our belief that the data hub concept and initial version of a â€˜safe spaceâ€™ for collaborative analysis of next generation sequencing data should be sustained and developed further. As was expected, the development of the COMPARE solution was never going to be a simple website as a finished product. Like many research-based solutions, the technology behind it, the science supporting it and the maintenance demanded by it continues after version 1.0 is released. We have therefore started to consider new funding applications as well as the establishment of a foundation, while developing a longer-term sustainability plan. In all, as coordinators, COMPARE has performed beyond what we ever imagined. At the General Meeting 2019, the 125 participants continued to avidly discuss future work, exchange ideas, and promote the COMPARE solution; in short â€œa buzzâ€ about COMPARE still exists. We hope to be able to continue this through future projects.