New coastal pathogen database maps microbial risks across global waters
image: When the user hovers the mouse over the bar representing a specific pathogen, the annual average abundance of top pathogens is shown as the size of dots with their geographic distribution on the map of a specific coastal region.
Credit: Biocontaminant
A research team has developed the Coastal Water Pathogen Database (CWPD), an open-access platform that integrates metagenomic evidence on pathogenic bacteria, viruses and fungi in coastal waters with information on antibiotic resistance genes and virulence factors. Through geographic visualization, searchable records and an online annotation service, the platform allows users to examine where biological hazards occur and analyze their own sequencing data without constructing a complex bioinformatics workflow. The resource could strengthen One Health research, public-health surveillance, pandemic preparedness and the management of estuaries, aquaculture zones and other vulnerable coastal ecosystems.
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.
A study (DOI: 10.48130/biocontam-0026-0006) published in Biocontaminant on 01 May 2026 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. 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. 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. 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. 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.
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. 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.
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References
DOI
Original Source URL
https://doi.org/10.48130/biocontam-0026-0006
Funding information
This work was supported by the National Natural Science Foundation of China (Grant Nos 42376113 LF, 52321005 AJW, 42206122 MS, and 52293441 SHG), the Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology (Grant No. SYSPG20241211173725010 LF), the Basic and Applied Basic Research Foundation of Guangdong Province (Grant Nos 2021B1515120080 LF and 2024A1515010085 SHG), Shenzhen Science and Technology Program (Grant Nos GXWD20231127195344001 AJW and JCYJ20241202123735045 SHG), and the Open Project of Key Laboratory of Environmental Biotechnology, CAS (Grant No. KF2021006 AJW and LF).
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Biocontaminant (e-ISSN 3070-359X) is a multidisciplinary platform dedicated to advancing fundamental and applied research on biological contaminants across diverse environments and systems. The journal serves as an innovative, efficient, and professional forum for global researchers to disseminate findings in this rapidly evolving field.