Initiative & background

COMPARE is a collaboration of founding members of the Global Microbial Identifier (GMI) initiative ( and institutions with hands-on experience in outbreak detection and response. 

COMPARE aims to harness the rapid advances in Whole Genome Sequencing (WGS)/Whole Community Sequencing (WCS) technologies to improve identification and mitigation of emerging infectious diseases and foodborne outbreaks. 

International research activities linked to COMPARE include a number of EU funded research networks in the area of emerging epidemics research in the human, animal and food sectors. Partners in COMPARE have coordinating or leading roles in these networks that can either serve as a basis for COMPARE, building on results and data from these networks, and/or as an outlet of COMPARE activities/ results. A selection of these EU-funded projects is presented here.

EMPERIE (223498)

EMPERIE is a large-scale integrated project funded in FP7 Health, coordinated by EMC and involving the COMPARE partners FLI, AMC, UK-Bonn, CAM and WTSI. EMPERIE has built Europe’s leading pathogen identification and characterization platform using state of the art sequencing technologies. COMPARE will build from this expertise and the available biobanks, as well as access the wider network for stakeholder consultations.  
ANTIGONE (278976)
ANTIGONE is a large-scale integrated project funded in FP7 Health, coordinated by EMC and involving COMPARE partners AMC, AHVLA, UCLM, UK-Bonn, AUTH and UCAM. Its main purpose is to identify the factors (at the molecular, host or  population level) that promote the pandemic potential of zoonotic bacteria and viruses. The pathogen identification efforts in COMPARE can feed into ANTIGONE for subsequent research and the promoting factors identified in ANTIGONE can inform the sampling strategies in COMPARE.
PREPARE (602525):
PREPARE is a large-scale integrated project, coordinated by COMPARE partners UA and AMC (deputy), and with EMC and UK-Bonn as partners. The purpose of PREPARE is to transform Europe’s response to severe epidemics or pandemics by providing infrastructure, co-ordination and integration of existing clinical research networks, both in community and hospital settings. The clinical research networks in PREPARE can make use of COMPARE (e.g. the communication toolbox, linked to the dissemination of clinical guidelines developed in PREPARE). Vice versa, the findings in PREPARE can inform the sampling strategies in COMPARE and can be used as the platform for further testing COMPARE’s results.
EVA: European Virus Archive 
EVA is an EU funded infrastructures project, that mobilises a European network of scientific centres with expertise in virology to collect, characterize, standardize and distribute viruses and derived products. UK-Bonn, EMC, FLI, and AHVLA are partners in EVA. This will provide COMPARE direct access to a European repository of reference strains and sequences, and the COMPARE system will be a potential hub for storage of the data generated by EVA.
The Med-Vet-Net association plays a central role in one-health by increasing and disseminating scientific knowledge on zoonoses through collaboration between Public Health and Animal Health organisations across Europe. The Association’s key goal is the provision and dissemination of knowledge and expertise in order to support the scientific community in combating zoonoses. Six COMPARE partners are Med-Vet-Net members.
Microbial Research Resource Infrastructure (MIRRI) The mirror image of EVA for non-viral pathogens is MIRRI, an EU funded infrastructures project with the goal to improve access to the microbial resources and services that are needed to accelerate research and discovery processes. MIRRI is building a Pan-European distributed research infrastructure that gives access to reference strains, their derivatives and associated data for research, development and application. COMPARE partner DSMZ is a central partner in MIRRI.
 RAPIDIA-FIELD (Rapid Field Diagnostics and Screening in Veterinary Medicine) is an EU FP7 funded project aimed to develop rapid diagnostics systems for livestock, companion animal and wildlife diseases. For molecular test systems NGS data are generated and used as a basis of assay design and results confirmation. COMPARE partners FLI and ANSES are central partners and will ensure close links with RAPIDIA.
RiskSUR (Risk Based Animal Health Surveillance) is an EU FP7 funded project with AHVLA as partner aimed to develop and validate conceptual and decision support frameworks and associated tools for designing efficient risk-based animal health surveillance systems. It will support the Community Animal Health Policy and EFSA activities relating to cost-effective animal disease surveillance programmes. It will inform COMPARE on the current and future animal disease surveillance strategies and structures including economic aspects.
EPI-SEQ (219235)
EPI-SEQ is an EMIDA ERA net funded network that aims to exploit NGS technologies to generate improved tools that can be used during epidemics of viral diseases threatening livestock industries in Europe. FLI is partner of Epi-Seq. Experiences of and data generated within Epi-Seq will help COMPARE to optimize NGS data management, providing a perfect starting point allowing the immediate optimization within COMPARE without any delay.
APHAEA (“harmonised Approaches in monitoring wildlife Population Health, And Ecology and Abundance” is an EMIDA ERA-NET (s) project, coordinated by COMPARE partner IREC and including investigators from DTU, FLI, ISVZ and Artemis. APHAEA a.o. aims at establishing harmonized procedures for wildlife population abundance estimation, sampling and diagnosis and provide data on key host abundance and key pathogens in their wild hosts. As such its results will feed primarily in to WPs 1 and 2.
TELL-ME (278723)
The EU FP7 funded TELL ME project is an integrated research project involving experts in social and behavioral sciences, communication and media, health professionals at various levels and specialties and representatives of civil society organizations to develop an evidence-based behavioral and communication package to respond to major epidemic outbreaks, notably flu pandemics. The TELL ME Integrated Communication Kit for Outbreak Communication and simulation software will be at the basis of the Communication Toolkit of COMPARE, brought by partner 26 RT.
GESTURE GESTURE was an EU funded project led by COMPARE partners EMC and RIVM exploring barriers to sharing of sequence data in emerging disease outbreaks under the framework of the International Health Regulations. The detailed background investigation of the current legal and ethical framework, law and regulations, as well as experiences of a broad range of stakeholders, will be used as input for the COMPARE legal and ethical barriers and solutions.
Ecology from Farm to Fork Of microbial drug Resistance and Transmission (EFFORT) is a newly started (2014) EU-project that will study the complex epidemiology and ecology of antimicrobial resistance between bacterial communities, commensals and pathogens in animals, the food chain and the environment. The measurement of antimicrobial resistance will mainly be though meta-genomic analysis coordinated by COMPARE partner DTU.
FLURISK This recently completed EFSA project developed and validated an influenza risk assessment framework (IRAF) for the ranking of animal influenza A strains in their potential to cross the species barrier and cause human infection. AHVLA and EMC were partners in FLURISK.
 BASELINE is an EU FP7 large integrated project coordinated by COMPARE partner UNIBO that aims to improve sampling plans for microbial risk analysis by 1) definition of fit-for purpose sampling plans; 2) proposal of Food Safety Criteria in different animal food chains (egg, meat and milk); 3) harmonization and validation of new, fast and sensitive molecular methods for detection and quantification of foodborne pathogens (bacteria and viruses).
24 FEBRUARY 2017