AMRnet: a data visualization platform to interactively explore pathogen variants and antimicrobial resistance

Antimicrobial resistance (AMR) poses a substantial threat to global public health. Whole genome sequencing is increasingly used as a core method for pathogen characterization to support AMR surveillance. As a result, a vast amount of bacterial sequence data are available in public archives, yet the AMR-related information they encode is not readily accessible to those without bioinformatics expertise and is essentially invisible to policy makers. The AMRnet platform aims to make publicly available genome-derived AMR data accessible to a diverse user base. The underlying data are drawn from public genomic databases and used to calculate pooled estimates of national annual prevalence that can be visualized interactively, and broken down and explored in terms of underlying pathogen variants, resistance mechanisms, and geographic and temporal distributions. Users can download dynamically generated reports, summary and line-list data from the web-based dashboard (https://www.amrnet.org), and query the database via application programming interface. For selected organisms, data are curated for purpose of sampling, to reduce the public data bias towards sequencing of resistant or severe infections. By improving the accessibility and utility of publicly archived data, AMRnet aims to encourage wider sequencing initiatives and collaborative data-sharing efforts while providing crucial data insights for researchers and policy makers.