Pathogenwatch: A public health platform for rapid interpretation of pathogen genomics

Abstract Pathogen genomic data provide important insights for public health microbiology, yet genome analysis options often remain highly technical and beyond the reach of many microbiologists and public health practitioners. Pathogenwatch ( https://pathogen.watch ) is a platform that translates pathogen genome data into outputs directly usable for surveillance and public health action. The platform contextualises bacterial, viral, and fungal genomes within a unified framework integrating organism identity, variant or lineage assignment, antimicrobial resistance and virulence gene detection, and geographic and temporal context. Pathogenwatch provides multilocus sequence typing (MLST) for more than 37 bacterial species and core genome MLST (cgMLST) schemes for over 20 priority organisms, with user-uploaded genomes automatically compared against over 875,000 curated public bacterial genomes. The platform has been adopted by 14,389 registered users across 165 countries. In 2025, users uploaded 328,676 genome assemblies and 20,830 read datasets. Pathogenwatch replicates analysis results of complex bioinformatics pipelines. Benchmarking of SARS-CoV-2 lineage assignment against an established reference dataset demonstrated complete concordance for all Variants of Concern and Interest, and full concordance with contemporary Pangolin calls across non-VOC/VOI lineages. Pathogenwatch operates as a continuously deployed, containerised system designed for scalability, reproducibility, and rapid incorporation of new pathogens, positioning it as durable infrastructure for both endemic surveillance and genomic response to emerging threats.