ReporTree and SPREAD: INNOVATIVE TOOLS FOR GENOMIC SURVEILLANCE OF PATHOGENIC MICROORGANISMS

International collaboration and open source philosophy to enhance the fight against infectious diseases

ReporTree is an advanced bioinformatics resource designed to enhance the genomic surveillance of pathogens, developed through a collaboration between the Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA) in Portugal and the Bioinformatics Unit of the Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise (IZS-TE).

Described in a paper in Genome Medicine, ReporTree uses advanced algorithms capable of processing and interpreting complex and heterogeneous genomic data, quickly identifying the emergence and evolution of bacterial and viral outbreaks. This tool, applied in international investigations, has already demonstrated its effectiveness in linking epidemiological and genetic data, showing great versatility and ease of use. "The fact that it can be applied to a wide range of pathogens, both bacteria and viruses - explains Vítor Borges, coordinator of the Bioinformatics Platform at the Instituto de Saúde Pública Doutor Ricardo Jorge in Lisbon - makes ReporTree an extremely flexible resource that can be easily integrated into disease monitoring processes and can become an essential tool in modern health surveillance strategies. It is currently used in Portugal and Italy, at the GENPAT Reference Center platform, and is generating increasing interest internationally."

To exploit the full potential of ReporTree, the Bioinformatics Department of IZS-TE has also developed and integrated the SPREAD software into the GENPAT platform: an open source dashboard that graphically combines genomic and epidemiological data. This result was presented at the international GEOVET-2023 conference and published in the journal Veterinaria Italiana.

"The collaboration between public institutes and the sharing of open source tools like ReporTree and SPREAD - comments Adriano Di Pasquale, from the National Reference Center for Genomic Sequences of Pathogenic Microorganisms at IZS-TE - demonstrate an advanced vision in the field of health surveillance. These tools not only improve the efficiency of genomic analyses but also promote interoperability and scientific transparency."

In this regard, the announcement by the ARIES Genomics team (Istituto Superiore di Sanità) about the integration of ReporTree and SPREAD into their IRIDA-ARIES genomic platform [https://irida.iss.it] is significant.

The ability to integrate genetic and epidemiological data in a flexible and automated way is now indispensable for public health agencies worldwide. The collaborative approach, and the open source philosophy, are therefore crucial tools for advancements in the global fight against infectious diseases.