INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens

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Llarena , A-K , Ribeiro-Gonçalves , B F , Nuno Silva , D , Halkilahti , J , Machado , M P , Da Silva , M S , Jaakkonen , A , Isidro , J , Hämäläinen , C , Joenperä , J , Borges , V , Viera , L , Gomes , J P , Correia , C , Lunden , J , Laukkanen-Ninios , R , Fredriksson-Ahomaa , M , Bikandi , J , Millan , R S , Martinez-Ballesteros , I , Laorden , L , Mäesaar , M , Grantina-Ievina , L , Hilbert , F , Garaizar , J , Oleastro , M , Nevas , M , Salmenlinna , S , Hakkinen , M , Carriço , J A & Rossi , M 2018 , ' INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens ' , EFSA Supporting Publications , vol. 15 , no. 11 , pp. 1498E . https://doi.org/10.2903/sp.efsa.2018.EN-1498

Title: INNUENDO: A cross-sectoral platform for the integration of genomics in the surveillance of food-borne pathogens
Author: Llarena, Ann-Katrin; Ribeiro-Gonçalves, Bruno Filipe; Nuno Silva, Diogo; Halkilahti, Jani; Machado, Miguel Paulo; Da Silva, Mickael Santos; Jaakkonen, Anniina; Isidro, Joana; Hämäläinen, Crista; Joenperä, Jasmin; Borges, Vítor; Viera, Luìs; Gomes, João Paulo; Correia, Cristina; Lunden, Janne; Laukkanen-Ninios, Riikka; Fredriksson-Ahomaa, Maria; Bikandi, Joseba; Millan, Rosario San; Martinez-Ballesteros, Ilargi; Laorden, Lorena; Mäesaar, Mihael; Grantina-Ievina, Lelde; Hilbert, Friederike; Garaizar, Javier; Oleastro, Mónica; Nevas, Mari; Salmenlinna, Saara; Hakkinen, Marjaana; Carriço, João André; Rossi, Mirko
Contributor organization: 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
Food Control research group
Date: 2018-11-26
Language: eng
Number of pages: 142
Belongs to series: EFSA Supporting Publications
ISSN: 2397-8325
DOI: https://doi.org/10.2903/sp.efsa.2018.EN-1498
URI: http://hdl.handle.net/10138/298892
Abstract: Abstract 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.
Subject: 416 Food Science
1183 Plant biology, microbiology, virology
Peer reviewed: Yes
Usage restriction: openAccess
Self-archived version: publishedVersion


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