A novel cross-sectorial platform for the integration of genomics in surveillance of foodborne pathogens

Multinational outbreaks of foodborne pathogens cause considerable threats to European public health. Implementing 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 we developed the initiative INNUENDO, which aims to deliver a cross-sectorial framework for the integration of bacterial WGS in routine surveillance and epidemiologic investigations.

INNUENDO platform is divided into two distinct applications that communicate between each other. The first one, the INNUENDO frontend server, comprises the user web interface and mechanisms to allow secure user authentication with LDAP and data storage into a dedicated database. It also communicates with the INNUENDO process controller, which was developed with the aim of working as a bridge to allow running analytical procedures on a laptop or in a High Performance Computer (HPC), with the help of SLURM process manager and Nextflow.

There is also a docker-compose version of the platform that can be easily installed with a few commands.