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TyphiNET is a web application for viewing genome-derived data on antimicrobial resistance (AMR) and lineage variants (genotypes), for the typhoid fever pathogen Salmonella Typhi.
This wiki explains how to use the TyphiNET dashboard (hosted at https://www.typhi.net/) via a web browser. The dashboard is regularly updated with Typhi genome data drawn from non-targeted sampling frames, curated by contributors to the Global Typhoid Genomics Consortium (GTGC) as described in this paper, and uploaded to the Typhi Pathogenwatch platform for consistent analysis of genotypes and antimicrobial resistance (AMR) determinants (see Data sources and definitions for more info).
The TyphiNET dashboard can be viewed at https://www.typhi.net/. The numbers at the top of the dashboard indicate the total number of genomes and genotypes currently available in the dashboard, which are used for prevalence estimates and visualisations in TyphiNET. You can further filter by time period or data source (local or travel-associated) (see here for more info). The map view shows the global distribution of AMR, genotypes, and sample sizes by country. Click a country to view details of national annual AMR and genotype prevalence, and the distribution of resistances and underlying determinants within genotypes. See Plots for more details.
The full TyphiNET database (CSV format) is available for download at the bottom of the dashboard. Note this includes the full set of GTGC curated Typhi genomes, including those from targeted sampling frames; however only data from non-targeted sampling frames, suitable for estimation of national annual genotype and AMR prevalences, are included in TyphiNET dashboard visualisations. The date of last database update is shown at the bottom of the dashboard. You can also download individual plots, or reports of current views; see Downloads for more info.
The code to run your own version of the dashboard is also available in this repository, see the README for install info.