Multinational outbreaks of food-borne pathogens cause considerable threats to European public health. Implementing a whole genome sequencing (WGS) in routine surveillance and outbreak investigations is becoming a strategic goal for many public health authorities all over the world. With this in mind a group of researchers have developed an initiative called INNUENDO, which aims to deliver a cross-sectorial framework of bacterial WGS integration in routine surveillance and epidemiological investigations. The potential of widespread, routine use of WGS analysis for public health protection is essentially restricted by the absence of accessible IT framework, and the limited skills of public health microbiologists in handling these novel methodologies. The aim of the INNUENDO project is aligned with the European Food Safety Authority (EFSA) mission to promote the development and validation of new approaches in microbial characterization throughout coordinate efforts between all public health and food safety stakeholders. The project will start on 15 January and the agreed duration is 30 months. EFSA is funding the project. Who is involved? To design an affordable and sustainable diagnostic infrastructure, the INNUENDO consortium includes governmental organizations, authorities and research institutes from the food, veterinary and human sectors, from small countries. The project is coordinated by Ass. Prof. Mirko Rossi (University of Helsinki) and includes organizations from Finland, Estonia, Latvia, Portugal, Basque Autonomous Community in Spain and Austria. Allowing project stakeholders to assess design choices early on in the development cycle, this multinational collaboration in the ‘One-health’ context will ensure that the planned infrastructure will address the requirement for the integration of WGS in routine analysis in the food chain. How to maximize the food safety? Standardization and calibration of process and simplification of data analysis and interpretation are the two basic conditions allowing the transition from the current diagnostic paradigm to a full WGS consolidation. Moreover, the lack of accessible informatics infrastructure for data processing and integration is still the major obstacle to implementation of WGS. Thus, it is now essential that advances in bioinformatics and bacterial genomics encounter the needs of the public health microbiology. This goal is reachable only throughout an integration of competencies across different disciplines and professions. Therefore, throughout active cooperation between experts in bacterial genomics, evolution, bioinformatics, epidemiology and specialists in validation, food control and public health, the INNUENDO consortium will use a cross-sectorial approach in developing a common framework for maximizing the benefit to use WGS in food safety. Small countries with limited resources might not be able to succeed in reaching this goal in the near future, putting several EU member states in a condition of inferior capabilities for outbreak detection and investigation. To guarantee the reinforcement of European capacities to ensure protection of citizens against cross border health threats, EU must enable wider access to the new methodologies. An increased level of cooperation between the local, national and European competent authorities by dedicated training, development of a common pathogen database and validation of new approaches in microbial characterization is warranted.