Multi-layered networks of SalmoNet2 enable strain comparisons of the Salmonella genus on a molecular level

Abstract

Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens has the potential to identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here we present SalmoNet2, a major update to SalmoNet, the first multi-layered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory and enzyme-enzyme interactions. The new version extends the number of Salmonella genomes from 11 to 20, including strains such as Salmonella Typhimurium D23580, an epidemic multidrug-resistant strain leading to invasive non-typhoidal Salmonella Disease (iNTS), and a strain from Salmonella bongori, another species in the Salmonella genus. The database now uses strain specific metabolic models instead of a generalised model to highlight differences between strains. This has increased the coverage of high-quality protein-protein interactions, and enhances interoperability with other computational resources by adopting standardised formats. The resource website has been updated with tutorials to help researchers analyse their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/.</SPAN>