The Italian information system for the collection and analysis of complete genome sequence of pathogens isolated from animal, food and environment

Abstract

Background: The development of integrated information systems is a guarantee for farmers and consumers, because these systems allow to turn data into actions. For this reason the IZSAM has realized the VETINFO portal, a platform where several national information systems in the veterinary field are available. What is missing is a link to be promptly used to connect results of molecular typing, in particular of WGS (Whole Genome Sequencing) that is progressively replacing older techniques, with the VETINFO systems. The Italian Ministry of Health appointed the IZSAM as National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatics analysis. The first activity of the Centre was the design of a national platform for the collection and analysis of complete genome sequence isolated from animal, food and environment (BioinfoDB). Methods & Materials: IZSAM provides the technical infrastructure, the developers team, the service desk needed for the management of BioinfoDB, ensuring the interoperability with other national information systems through the VETINFO platform and provides the database with information coming from other veterinary laboratories. A working group made up of pathogens, genomics and bioinformatics experts ensures standardized, harmonized and improved bioinformatics analyses among the different local organizations. Results: BioinfoDB provides IT tools and data that are quickly available, usable and helpful in outbreak situations allowing to link molecular typing and bioinformatics analyses results with time and position of sampling as well as the others epidemiological information available. In this way it is possible to compare the classification results obtained by WGS for two or more distinct isolates and to measure their relatedness to support an epidemiological investigation as experienced in 2015 during a severe listeriosis outbreak in the Marche region. Conclusion: Access to information allow to know the health risk to which the livestock and food processing chain is exposed and how the risks can affect the public health, perform real-time assessments to adjust technical and organizational responses, plan actions and check their effectiveness afterwards. The national platform for the collection and analysis of complete genome sequence together with the veterinary information systems adopted in Italy during the years fully meet these needs.