PDN’s central node, the Pathogens Portal, has launched a new wastewater data page to improve visibility and access to sequencing data from wastewater metagenomic samples. This new feature supports public health agencies, researchers, and environmental monitoring teams by bringing together relevant datasets in one place – helping them track pathogens and antimicrobial resistance (AMR) more effectively.
Supporting faster public health response
Wastewater surveillance is increasingly used to detect emerging health threats—including novel pathogens and AMR—before clinical cases rise. However, these datasets have often been difficult to locate. By automatically surfacing relevant nucleotide sequence data (assemblies and raw reads), this new page of the Pathogen Portal, hosted at EMBL-EBI, helps users act more quickly and confidently.
Users can explore datasets by country or project, with direct access to raw data and metadata that can feed into surveillance systems or genomic analysis pipelines.
“By making these datasets more visible and accessible, we help public health agencies and researchers identify early signals of public health concern—whether that’s the spread of new variants or resistance genes emerging in the environment.”
Zahra Waheed
Senior Bioinformatician
EMBL-EBI (UK)
This resource contributes directly to PDN’s objectives by:
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- Fostering global data discovery in an emerging, high-priority surveillance area
- Enabling timely, evidence-based public health response
- Creating trust and alignment through shared, open data infrastructure
It also demonstrates the practical application of FAIR principles (Findable, Accessible, Interoperable, Reusable) in supporting real-time decision-making.
This achievement was made possible thanks to an existing and well-structured taxonomy tree/ontology in NCBI Taxonomy, enabling the team to pull appropriate wastewater datasets through the wastewater metagenome taxonomy.
What’s next?
In upcoming updates, the page aims to include:
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- Improved metadata linking and visualisation to enhance interpretation
- Antimicrobial resistance (AMR) gene profiles extracted from metagenomic data
- Summarised organism-level findings, providing quicker biological insights
Together, these additions will further strengthen the portal’s role in enabling environmental genomic surveillance as part of the broader global public health response toolkit.
For questions, feedback or collaboration: ena-path-collabs@ebi.ac.uk
Workstreams involved: WS1 Pathogens Portals