New coastal pathogen database maps microbial risks across global waters

Coastal environments connect terrestrial and marine systems and are increasingly affected by wastewater discharge, aquaculture, urbanization and climate-driven changes in temperature and rainfall.

Existing databases have improved access to information on waterborne bacteria or aquaculture pathogens, but many lack geographic and temporal abundance data, broad coverage of viruses and fungi, or integrated records of antibiotic resistance and virulence.

These gaps limit pollution tracing, cross-region comparisons and assessments of how environmental change may alter pathogen transmission, creating a need for a more comprehensive and spatially resolved resource.

New pathogen database

A study published in Biocontaminant  by Lu Fan’s team, Southern University of Science and Technology, reports that CWPD integrates global coastal metagenomic datasets to map pathogens and associated risk factors while providing interactive searches, visualization and online analysis of user-submitted samples.

To build the platform, the researchers first created a biological risk-factor dictionary using authoritative resources, including the National Center for Biotechnology Information, public-health agencies, the International Committee on Taxonomy of Viruses, the Comprehensive Antibiotic Resistance Database and the Virulence Factor Database.

Pathogen names and synonyms were standardized through taxonomy identifiers, while antibiotic resistance genes and virulence factors were organized into searchable categories.

Users can search by pathogen or location, explore regional abundance patterns and upload metagenomic reads to receive profiles of microbial communities, pathogens, resistance genes and virulence factors.

Multistep pipeline

The team then screened publicly available shotgun metagenomic datasets from coastal, estuarine and inland-sea environments, retaining high-depth Illumina sequencing data and excluding 16S ribosomal RNA surveys. Raw reads were quality-filtered, classified and assembled through a multistep pipeline.

MetaPhlAn profiled microbial communities, MegaPath identified pathogens, DeepARG annotated resistance genes, and searches against the Virulence Factor Database detected virulence factors. Processed information was stored in a PostgreSQL and PostGIS framework and displayed through maps, heatmaps, word clouds, search tools and sample-level reports.

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The current version contains 158 samples from six coastal regions on three continents. Its knowledge dictionary includes 1,904 pathogenic microorganisms, 2,373 antibiotic resistance genes across 47 categories and 541 virulence factors. In the analyzed samples, the researchers detected 361 pathogenic bacterial taxa, 42 pathogenic viral taxa, 287 resistance-gene subtypes from 30 classes and 10 virulence factors.

Supported by more than 700 central processing units, the system can process a typical 10-gigabyte dataset in approximately 12 hours. Its modular architecture and application programming interfaces are designed for future connections with ecological, clinical and public-health databases. The authors nevertheless caution that current geographic coverage remains limited and that the dataset is not yet suitable for robust temporal comparisons.

Accessible framework

CWPD brings environmental sequencing, spatial mapping and biological risk information into one accessible framework. With planned semiannual updates and expansion into densely populated and underrepresented coastlines, it could improve surveillance of pathogen movement, antibiotic resistance and emerging environmental threats.

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The platform may also help researchers and policymakers connect microbial hazards with wastewater discharge, aquaculture, climate variability and other drivers of coastal change, supporting evidence-based disease prevention, environmental policy development and sustainable water-resource management.