IRIDA-ARIES Genomics, a key player in the One Health surveillance of diseases caused by infectious agents in Italy

Abstract

Pathogen genomics is transforming surveillance of infectious diseases, deepening our understanding of evolution and diffusion of etiological agents, host-pathogen interactions and antimicrobial resistance. This discipline is playing an important role in the development of One Health Surveillance with public health experts of various disciplines integrating methods applied to pathogen research, monitoring, management and prevention of outbreaks. Especially with the notion that foodborne diseases may not be transmitted by food only, the ARIES Genomics project aimed to deliver an Information System for the collection of genomic and epidemiological data to enable genomics-based surveillance of infectious epidemics, foodborne outbreaks and diseases at the animal-human interface. Keeping in mind that the users of the system comprised persons with expertise in a wide variety of domains, the system was expected to be used with a low learning curve directly by the persons target of the analyses' results, keeping the information exchange chains as short as possible. As a result, the IRIDA-ARIES platform (https://irida.iss.it/) provides an intuitive web-based interface for multisectoral data collection and bioinformatic analyses. In practice, the user creates a sample and uploads the Next-generation sequencing reads, then an analysis pipeline is launched automatically performing a series of typing and clustering operations fueling the information flow. Instances of IRIDA-ARIES host the Italian national surveillance system for infections by Listeria monocytogenes (Lm) and the surveillance system for infections by Shigatoxin-producing Escherichia coli (STEC). As of today, the platform does not provide tools to manage epidemiological investigations but serves as an instrument of aggregation for risk monitoring, capable of triggering alarms on possible critical situations that might go unnoticed otherwise.

Keywords: One Health surveillance; data integration; foodborne pathogens; genomic; molecular typing workflows; multisectorial.

Figure 1

The IRIDA-ARIES platform: when a sample is created, metadata is recovered from both the local molecular and epidemiological information systems. Then, when genomic sequences are uploaded, quality control is performed and consequently the sequences are analyzed by ARIES using the pathogen-specific pipeline PHANtAsTiC. Results are returned to IRIDA and displayed in a specific analysis web page. Schematic design of the IRIDA-ARIES information flow. The flow is triggered at the local level by a clinical center which sends a sample of a case to a diagnostic laboratory (could be in-house) performing the whole genome sequencing. The sequences are uploaded to IRIDA-ARIES and the results are returned to the local level as well as forwarded to the regional and national level. If necessary, the data can be advanced to the European level.