Workpackage 1
Risk assessment and risk-based strategies for sample and data collection
WP leader: Emma Snary, DEFRA/APHA (10) emma.snary@apha.gsi.gov.uk
co-leader: Christian Gortazar, UCLM (18) Christian.Gortazar@uclm.es
Overall task: To develop risk assessment models and risk-based sampling and data collection strategies for NGS-based analyses of foodborne and (re-) emerging infections.
Workpackage 2
Harmonised standards for sample processing and sequencing
WP leader: Martin Beer, FLI (4) martin.beer@fli.bund.de
co-leaders: Simone Caccio, ISS (8) simone.caccio@iss.it
Overall task: To develop harmonized analytical workflows for generation of high-quality NGS data in combination with relevant metadata for pathogen detection and typing across sample types, pathogens and domains.
Workpackage 3
From comparable data to actionable information: Analytical workflows for frontline diagnostics
WP leader: Surbhi Malhotra, UA (14) surbhi.malhotra@uantwerpen.be
co-leaders: Constance Schultsz, AMC (13) schultsz@gmail.com, & Anne Pohlmann, FLI (4) anne.pohlmann@fli.bund.de
Overall task: To develop an analytical workflow for the use of single isolate and metagenomic NGS in human and veterinary clinical microbiology.
Workpackage 4
From comparable data to actionable information: Analytical workflows for foodborne pathogen surveillance, outbreak detection and epidemiological analysis
WP leader: Eva Møller Nielsen, SSI (3) emn@ssi.dk
co-leaders: Tine Hald, DTU (1) tiha@food.dtu.dk, & Michel-Yves Mistou, ANSES (5) michel-yves.mistou@anses.fr
Overall task: To develop a general analytical workflow for population-based disease surveillance, outbreak detection and epidemiological modeling of foodborne infections.
Workpackage 5
From comparable data to actionable information: Additional tools for detection of and response to (re-) emerging infections
WP leader: Ron Fouchier, EMC (2) r.fouchier@erasmusmc.nl
co-leader: Mark Woolhouse, UEDIN (11) mark.woolhouse@ed.ac.uk
Overall task: To develop cross-sector and cross-pathogen methods for support of emerging pathogen identification and characterization in support of outbreak investigations and epidemiological analysis.
Workpackage 6
Underpinning research: Frontline diagnostics using the COMPARE analytical framework
WP leader: Surbhi Malhotra, UA (14) surbhi.malhotra@uantwerpen.be
co-leaders: Constance Schultsz, AMC (13) schultsz@gmail.com, & Anne Pohlmann, FLI (4) anne.pohlmann@fli.bund.de
Overall task: To assess feasibility of NGS/WGS/WCS for clinical diagnostic use and hospital epidemiology.
Workpackage 7
Underpinning research on food outbreaks using the COMPARE analytical framework
WP leader: Eva Møller Nielsen, SSI (3) emn@ssi.dk
co-leaders: Tine Hald, DTU (1) tiha@food.dtu.dk, & Michel-Yves Mistou, ANSES (5) michel-yves.mistou@anses.fr
Objectives:
- To establish robust analytic procedures of NGS/WGS data for Salmonella, STEC/EHEC, Listeria, norovirus, hepatitis A, and Cryptosporidium to be able to identify epidemiologically linked isolates and differentiate these from similar unrelated isolates.
- To develop guidelines for interpretation criteria for defining clusters of disease and linking of isolates from various sources and reservoirs.
- To enable backward compatibility to important previous nomenclature (e.g. serotypes, species, MLST).
- To perform pilot studies in collaboration with global partners and networks including ECDC and EFSA.
Workpackage 8
Underpinning research: Novel approaches to (re-) emerging disease detection and outbreak response using the COMPARE analytical framework
WP leader: Ron Fouchier, EMC (2) r.fouchier@erasmusmc.nl
co-leader: Mark Woolhouse, UEDIN (11) mark.woolhouse@ed.ac.uk
Objectives:
1. To develop and pilot early detection and surveillance of enteric pathogens and genes through strategic sampling and metagenomic analysis.
2. To develop and pilot ”hot-spot” based syndromic surveillance in animals and humans.
3. To develop and pilot early detection of surveillance of emerging zoonoses from the wildlife reservoir through strategic sampling and metagenomic analysis.
4. To develop and pilot early detection of changes in pathogen traits enhancing the risk for outbreaks and pandemic.
Workpackage 9
COMPARE data and information platform
WP leader: Guy Cochrane, EMBL (7) cocharne@ebi.ac.uk
co-leaders: Ole Lund, DTU (1) lund@cbs.dtu.dk, & Istvan Csabai, WIGNER (24) csabai.istvan@wigner.mta.hu
Objectives:
- To create and operate the COMPARE Data Resource, workflow engine and portal.
- To create user spaces for COMPARE workflow development and pilot projects.
- To ensure the long-term sustainability of the tools developed and data generated.
Workpackage 10
COMPARE risk communication tools
WP leader: Emilio Mordini, RT (26) emilio.mordini@responsibletechnology.eu
Overall task: To design and develop appropriate risk communication tools and strategies for stakeholders involved in the process, as well as a set of management tools for authorities to handle uncertainties and available options according to the input received through the COMPARE system.
Workpackage 11
User consultations
WP leader: Marion Koopmans, EMC (2) m.koopmans@erasmusmc.nl
co-leader: Frank Aarestrup, DTU (1) fmaa@food.dtu.dk
Overall task: To design the COMPARE systems’ analytical workflow and its main components based on the expert inputs and associated information needs of its intended future users and other stakeholders working in human, animal and wildlife health and food safety.
Workpackage 12
Barriers to open data sharing
WP leader: George Haringhuizen, RIVM (9) george.haringhuizen@rivm.nl
co-leader: Jørgen Schlundt, DTU (1) jschlundt@ntu.edu.sg
Overall task: To identify, clarify and, as far as feasible, develop practical solutions for Political, Ethical, Administrative, Regulatory and Legal (PEARL) barriers that hamper the timely and openly sharing of data through COMPARE.
Workpackage 13
Dissemination and training
WP leader: Frank Aarestrup, DTU (1) fmaa@food.dtu.dk
co-leader: Marion Koopmans, EMC (2) m.koopmans@erasmusmc.nl
Overall task: To ensure that relevant stakeholders of COMPARE are adequately informed about COMPARE’s progress and results and have access to the training they need in order to apply the harmonized workflows, analytical tools and data resources developed and implemented by COMPARE in their pathogen detection and outbreak response activities.
Workpackage 14
Cost-effectiveness framework
WP leader: Pieter van Baal, EUR (22) vanbaal@bmg.eur.nl
co-leader:
Overall task: To develop a standardised framework for estimating the cost-effectiveness of the COMPARE system and related methods and tools, including the value of safety.
Workpackage 15
Management
WP leader: Frank Aarestrup, DTU (1) fmaa@food.dtu.dk
co-leader: Marion Koopmans, EMC (2) m.koopmans@erasmusmc.nl
Overall task: To implement the appropriate organizational structures and processes to ensure COMPARE’s compliance to the EC Grant Agreement and the COMPARE Consortium Agreement (CA).