Saara Salmenlinna, Janne Lundén, Marjaana Hakkinen, Crista Hämäläinen, Diogo N. Silva, Friederike Hilbert, Jani Halkilahti, João Paulo Gomes, João A. Carriço, Ilargi Martinez-Ballesteros, Bruno Ribeiro-Gonçalves, Rosario San Millán, Javier Garaizar, Vítor Borges, Miguel P. Machado, Lorena Laorden, Joana Isidro, Mickael Silva, Riikka Laukkanen-Ninios, Anniina Jaakkonen, Mihael Mäesaar, Mari Nevas, Cristina Correia, Jasmin Joenperä, Lelde Grantina-Ievina, Joseba Bikandi, Mónica Oleastro, Luis Viera, Mirko Rossi, Maria Fredriksson-Ahomaa, Ann-Katrin Llarena, Mirko Rossi Research Group, Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, Janne Lundén / Principal Investigator, Maria Fredriksson-Ahomaa / Principal Investigator, Hannu Korkeala / Principal Investigator, Mari Nevas / Principal Investigator, and Food Control research group
In response to the EFSA call New approaches in identifying and characterizing microbial and chemical hazards, the project INNUENDO (https://sites.google.com/site/theinnuendoproject/) aimed to design an analytical platform and standard procedures for the use of whole-genome sequencing in surveillance and outbreak investigation of food-borne pathogens. The project firstly attempted to identify existing flaws and needs, and then to provide applicable cross-sectorial solutions. The project focused in developing a platform for small countries with limited economical and personnel resources. To achieve these goals, we applied a user-centered design strategy involving the end-users, such as microbiologists in public health and veterinary authorities, in every step of the design, development and implementation phases. As a result, we delivered the INNUENDO Platform V1.0 (https://innuendo.readthedocs.io/en/latest/), a stand-alone, portable, open-source, end-to-end system for the management, analysis, and sharing of bacterial genomic data. The platform uses Nextflow workflow manager to assemble analytical software modules in species-specific protocols that can be run using a user-friendly interface. The reproducibility of the process is ensured by using Docker containers and throught the annotation of the whole process using an ontology. Several modules, available at https://github.com/TheInnuendoProject, have been developed including: genome assembly and species confirmation; fast genome clustering; in silico typing; standardized species-specific phylogenetic frameworks for Campylobacter jejuni, Yersinia enterocolitica, Salmonella enterica and Escherichia coli based on an innovative gene-by-gene methodology; quality control measures from raw reads to allele calling; reporting system; a built-in communication protocols and a strain classification system enabling smooth communication during outbreak investigation. As proof-of-concepts, the proposed solutions have been thoroughly tested in simulated outbreak conditions by several public health and veterinary agencies across Europe. The results have been widely disseminated through several channels (web-sites, scientific publications, organization of workshops). The INNUENDO Platform V1.0 is effectively one of the models for the usage of open-source software in genomic epidemiology.