Always-on web tools for genomic epidemiology: from Pathogenwatch to amr.watch
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| Verfasser: | |
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| Format: | artículo original |
| Status: | Versión publicada |
| Publikationsdatum: | 2026 |
| Beschreibung: | Whole-genome sequencing (WGS) is transforming infectious-disease surveillance, yet many settings still lack accessible, scalable analysis environments that turn raw genomes into epidemiologically actionable insights. Pathogenwatch was designed to close this gap: a web platform that lets users upload or stream public asssemblies, performs species assignment and typing (MLST/cgMLST and species-specific genotyping), predicts antimicrobial resistance (AMR) determinants, and instantaneously contextualizes genomes against large, curated public references—delivering trees, maps, timelines, and shareable collections in the browser. Building on this foundation, amr. watch will be introduced, as an interactive dashboard that continuously synthesizes genomes for WHO-priority bacterial pathogens via an “always-on” Pathogenwatch pipeline (automated retrieval/QC/assembly, variant typing, and AMR calling) and exposes geotemporal trends in lineages and mechanisms for exploration and policy planning. We will show how integrating WGS with sampling metadata delivers situational awareness of AMR dynamics and supports decisions spanning empiric therapy, infection control, and vaccine/diagnostic targeting. Together, Pathogen- watch and amr.watch demonstrate how web-first, analysis-as-a-service can democratize genomic surveillance—turning shared WGS data into timely, interpretable evidence for public-health action. |
| Land: | Portal de Revistas UNA |
| Institution: | Universidad Nacional de Costa Rica |
| Repositorio: | Portal de Revistas UNA |
| Sprache: | Inglés |
| OAI Identifier: | oai:www.revistas.una.ac.cr:article/22337 |
| Online Zugang: | https://www.revistas.una.ac.cr/index.php/veterinaria/article/view/22337 |
| Stichwort: | Whole-genome sequencing antimicrobial resistance |