A new global database brings together information on disease-causing microorganisms, antibiotic resistance genes, and virulence factors in coastal waters, giving researchers and public health professionals a practical tool for assessing biological risks in estuaries and other nearshore environments.
"Coastal waters connect human communities, wildlife, wastewater systems, and marine ecosystems, but information about their microbial hazards has often been scattered across separate studies," said corresponding author Lu Fan of the Southern University of Science and Technology. "The Coastal Water Pathogen Database was developed to make these complex data easier to explore, compare, and use for environmental and public health decision-making."
Coastal regions are home to a large proportion of the global population and support fisheries, aquaculture, recreation, transportation, and tourism. However, these waters can also receive pathogens from domestic sewage, livestock wastewater, aquaculture operations, and other human activities. Rising water temperatures and changing rainfall patterns may further increase the movement and growth of some microorganisms, making effective surveillance increasingly important.
To address this challenge, the research team developed the Coastal Water Pathogen Database, or CWPD, an open-access platform that integrates shotgun metagenomic sequencing data from coastal environments. Unlike databases that focus mainly on individual bacterial species or aquaculture pathogens, CWPD covers pathogenic bacteria, viruses, and fungi, together with antibiotic resistance genes and virulence factors.
The current version includes data from 158 samples collected across six coastal regions on three continents, including the Pearl River Estuary, Cochin Estuary, Columbia River Estuary, Chesapeake Bay, Delaware Bay, and Baltic Sea. The samples span coastal conditions ranging from low-salinity estuarine waters to seawater and cover collection periods between 2010 and 2019.
Across these samples, the researchers detected 361 pathogenic bacterial species, 42 pathogenic viral species, 287 antibiotic resistance gene subtypes from 30 classes, and 10 virulence factors. The platform's underlying knowledge dictionary is even broader, containing 1,904 pathogen entries, 2,373 antibiotic resistance genes, and 541 virulence factors.
CWPD presents the information through interactive maps, word clouds, heat maps, and bar charts. Users can explore the geographic distribution and abundance of specific pathogens or search by location, year, and biological risk category. This visual approach allows complex metagenomic information to be interpreted without requiring users to work directly with large raw sequencing datasets.
The platform also provides an online analysis service for newly generated metagenomic data. Registered users can upload raw Illumina paired-end sequencing files, after which the system performs quality control, sequence assembly, and annotation of microbial communities, pathogens, antibiotic resistance genes, and virulence factors. For a typical 10-gigabyte environmental metagenomic sample, the full analysis takes approximately 12 hours, and users receive an email when the results are ready.
The researchers designed CWPD with a modular architecture and standardized application programming interfaces, allowing it to be connected with ecological, clinical, and public health databases in the future. The platform is also intended to support the One Health approach, which recognizes that human health, animal health, and environmental conditions are closely linked.
The authors caution that the current database represents an initial version and does not yet provide complete global coverage. The available samples are concentrated in several well-studied coastal systems, so comparisons between regions or time periods should be interpreted carefully. The team plans to update the database every six months and expand coverage to densely populated deltas, industrialized coastlines, and underrepresented regions in Africa and South America.
By combining pathogen detection, antibiotic resistance information, geographic visualization, and online data analysis, CWPD provides a foundation for coastal ecosystem management, biological risk assessment, and future pandemic preparedness.
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Journal reference: Song S, Lei Z, Feng Y, Wang W, Huang F, et al. 2026. Coastal Water Pathogen Database profiles pathogenic microorganisms in coastal environments. Biocontaminant 2: e009 doi: 10.48130/biocontam-0026-0006
https://www.maxapress.com/article/doi/10.48130/biocontam-0026-0006
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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.
