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Imprint
Collaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe
Project
Project code: FLI-IVD-08-Ri-0368
Contract period: 01.12.2014
- 30.11.2019
Budget: 1,000,000 Euro
Purpose of research: Basic research
COMPARE is a multidisciplinary research network that is set up with the common vision to become the enabling analytical framework and globally linked data and information sharing platform system for the rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks. The system sets out to integrate state-of-the-art strategies, tools, technologies and methods for collecting, processing and analyzing 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 will establish a 'one serves all' analytical framework and data exchange platform that will allow real-time analysis and interpretation of sequence-based pathogen data in combination with associated data (e.g., clinical, epidemiological data) in an integrated international intersectorial ‘One Health' approach. The framework will link research, clinical and public health organisations active in human health, animal health, and food safety in Europe and beyond, to develop integrated risk assessment and risk-based collection of samples and data, harmonised workflows for generating comparable sequence and associated data, state-of-the-art analytical workflows and tools for generating actionable information for support of patient diagnosis, treatment, outbreak detection and investigation, and risk communication tools. COMPARE has the following objectives: To improve rapid identification, containment and mitigation of emerging infectious diseases and foodborne outbreaks, To develop a cross-sector and cross-pathogen analytical framework and globally linked data- and information-sharing platform, To integrate state-of-the-art strategies, tools, technologies and methods for collecting, processing and analysing sequence-based pathogen data in combination with associated data (clinical, epidemiological, and other), and To generate actionable information for relevant authorities and other users in human health, animal health and food safety domains.
FLI contributed to several work packages (WP) but was mainly involved in WP2. The basic challenge of WP2 was to adapt and improve protocols to develop a „one-serves-all“ sample processing workflow for metagenomics sequencing using NGS, which is applicable for samples of different matrices to detect various pathogens with samples related to different sectors (human health, animal health, and food safety). The work with COMPARE-WP2 resulted in a much-improved rapid identification workflow of emerging infectious diseases and foodborne outbreaks. A sophisticated analytical framework was provided describing a universal sample analysis pipeline and providing a whole set of Standard Operating Procedures (SOPs and laboratory LOPs, https://www.compare-europe.eu/library/protocols-and-sops) for the consortium and also to the public. One generic workflow consisting of harmonized modules is presented as pathogen- and matrix-independent approach and was released as a key article of COMPARE (Wylezich et al. 2018, see also Wylezich et al. 2019). The established and strengthened collaboration among European institutions working on infectious diseases will persist beyond COMPARE and will further enhance detection and characterization of re-emerging pathogens to speed up medical responses. Ring trials / proficiency tests were conducted within the COMPARE network to validate the established LOPs and SOPs for the first time for high-throughput sequencing (HTS). Their outcome will shape the development of standards and the implementation of HTS in laboratory diagnostics in the near future. In terms of publications, COMPARE was a very successful project with 168 publications that can be found via Web of Science that mentioned COMPARE as/in the “funding agency” (77 publications are related to WP2, FLI scientists contributed to 33 publications, see below). Selected publications: Höper D, Mettenleiter TC, Beer M (2016) Metagenomic approaches to identifying infectious agents. Rev Sci Tech. 35(1):83-93. doi: 10.20506/rst.35.1.2419 Lycett et al. 2016. Role for migratory wild birds in the global spread of avian influenza H5N8. Science 354:213-217, 10.1126/science.aaf8852 Wylezich et al. 2018. A versatile sample processing workflow for metagenomic pathogen detection. Scientific Reports Aug 30, 8:13108, DOI: 10.1038/s41598-018-31496-1 Brinkmann et al. 2019. Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets. Journal of Clinical Microbiology 57(8):e00466-19 doi: 10.1128/JCM.00466-19 Wylezich et al. 2019. Metagenomics for broad and improved parasite detection: A proof-of-concept study using swine faeces samples. Int J Parasitol 49(10):769-777 https://doi.org/10.1016/j.ijpara.2019.04.007
Section overview
Subjects
- Food microbiology
