The objective of ENGAGE is to establish collaboration between the public health, food and veterinary sectors across the European Union (EU) for building and enhancing the use of real-time whole genome sequencing (WGS) and analysis in food safety and public health protection.

ENGAGE will pursue the following specific objectives I – V to be realized within the format of a two-year program. Together these five specific project objectives will shape the overall framework of ENGAGE.


I. At least two joint “proof of concept” WGS projects targeting emerging E. coli and Salmonella lineages will be established among the consortium partners within the first quarter of the project period.


Comparable datasets suitable for joint analyses will be obtained by the consortium partners. Data will be generated and collected by the consortium and affiliated partners starting from the first quarter of the project period until the end ensuring data collection based on a robust, statistically-based sampling design and data analysis in real time. A minimum of 3,000 strains / genomes continually collected through the daily routine and the national / EU monitoring programs will be sequenced. To provide a broader European representation of the circulation strains, the consortium will reach out to other European laboratories inviting them to submit genomes or strains of the target organisms. Data from the United States of America (US) Genome Trakr Network, Global Microbial Identifier (GMI) and the H2020 COMPARE project will also be available to ENGAGE. The two joint “proof of concept” WGS projects will focus on outbreak investigations, transmission routes, epidemiological markers for virulence and, AMR.


II. Creation of a temporary database for hosting genome data.


The genome data of emerging E. coli and Salmonella lineages will be hosted in mirrored genome databases developed in the first quarter of the project period and subsequently released to the European Nucleotide Archive (ENA) and the European Food Safety Authority (EFSA) database by the end of the project period. Consortium partner will have full access to the database including raw reads and a minimum set of metadata, but not compromising legal, individual or national needs for anonymity.


III. Benchmarking of bioinformatic analytic tools to investigate the following issues: 1) genetic exchange, selection, and clonal expansion; 2) epidemiological relationships between the target microorganisms; 3) identification of biologically successful microbial clones; and 4) microbial determination of virulence, AMR, and other putative markers. In addition, the benchmarking will also assess the applicability and integration of WGS into public health.


Currently, there is no international standard on how to analyze WGS data. Thus, it is important to validate the bioinformatic methods being used to ensure that no matter what tool is being applied, the scientist would be able to detect the same epidemiological links, success-clones, virulence factors and AMR. To circumvent this problem, various commercial and online open access bioinformatic analytic tools will be used in a comparative benchmarking analysis to ensure comparable results despite the differences of the tools being utilized. The comparative benchmarking analysis will be launched as a pilot project in the 1st quarter of the project period and subsequently rolled out in the 2nd quarter.


IV. To establish and conduct WGS proficiency tests.


To ensure reliable genome data from research organizations, it is of paramount importance to establish and conduct WGS proficiency tests (PTs) regularly (e.g. at least once a year). In addition to the PTs, best practices guidelines, protocols and standard operating procedures (SOPs) for quality assurance (QA) will be developed as well as reference materials. In the framework of GMI, the Technical University of Denmark, National Food Institute (DTU Food) and Public Health England (PHE) are already involved setting up a PT scheme. Overall, the PTs assess the quality of the obtained genome sequences and suitability of the bioinformatic tools applied by the participants to the detection of outbreak strains and the characterization of emerging successful clones. The results of the PT trials will be disseminated annually through a report.


V. To boost scientific collaboration between scientists, clinicians, and risk assessors to exchange expertise and knowledge as well as to build capacity.


In contrast to most other ongoing WGS projects, ENGAGE focuses on using the joint “proof of concept” WGS projects for in real-time surveillance and identifying potential problems through learning-by-doing. In the first year of the project, the consortium will develop and execute training courses and twinning projects for consortium/affiliated partners and the target group in order to transfer knowledge and exchange expertise as well as to build WGS capacity. In addition, to boost scientific collaboration e-learning modules will be developed to build WGS capacity. The consortium will host workshops for the consortium/affiliated partners and the target group to boost scientific collaboration. The consortium partners will monthly, with participation of EFSA and European Centre for Disease Prevention and Control (ECDC), discuss the latest results through conference calls. In cases of emergency, alert calls will autonomously be arranged to disseminate urgent information.

16 AUGUST 2022