A new open-access Coastal Water Pathogen Database (CWPD) is designed to bring together scattered evidence on microbial hazards in nearshore environments. By linking disease-causing organisms with antibiotic resistance genes and virulence factors, the platform aims to help researchers and public health professionals evaluate biological risk in estuaries and coastal waters.
Coastal systems connect wastewater inputs, wildlife, fisheries, and human recreation, yet microbial hazard data often live in separate studies. “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,” said corresponding author Lu Fan of the Southern University of Science and Technology.
CWPD is built on shotgun metagenomic sequencing, capturing DNA from entire microbial communities rather than focusing only on single cultivated species. Unlike pathogen resources limited to bacteria or aquaculture-related threats, CWPD integrates pathogenic bacteria, viruses, and fungi alongside resistance and virulence determinants.
The current CWPD release includes 158 samples collected from six coastal regions spanning three continents: the Pearl River Estuary, Cochin Estuary, Columbia River Estuary, Chesapeake Bay, Delaware Bay, and the Baltic Sea. Sample collection periods range from 2010 to 2019 and cover conditions from low-salinity waters to marine environments.
Across these datasets, researchers report 361 pathogenic bacterial species and 42 pathogenic viral species, plus 287 antibiotic resistance gene subtypes across 30 classes and 10 virulence factors. The CWPD knowledge dictionary is broader, containing 1,904 pathogen entries, 2,373 antibiotic resistance genes, and 541 virulence factors.
To make metagenomic outputs usable without requiring users to run heavy bioinformatics pipelines, CWPD presents findings through interactive maps, word clouds, heat maps, and bar charts. Users can search by location, year, and biological risk category, supporting rapid cross-site comparisons of relative abundance.
A key feature is an online analysis service for newly generated metagenomic data. Registered users can upload Illumina paired-end reads; the system performs quality control, assembly, and annotation for microbial communities, pathogens, antibiotic resistance genes, and virulence factors, with turnaround reported at about 12 hours for a typical 10 GB sample.
CWPD is also designed with modular architecture and standardized interfaces, enabling future integration with ecological, clinical, and public health resources. The team positions the platform to support One Health workflows that connect environmental exposure to human and animal health outcomes.
The authors emphasize that this is an initial version with incomplete global coverage, as sampling is concentrated in well-studied coastal systems. They plan semiannual updates and expansion toward densely populated deltas, industrial coastlines, and underrepresented regions in Africa and South America.
Subject of Research: Coastal Water Pathogen Database (CWPD) using shotgun metagenomics
Article Title: Coastal Water Pathogen Database profiles pathogenic microorganisms in coastal environments
News Publication Date: 1-May-2026
Web References: https://doi.org/10.48130/biocontam-0026-0006
References: 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
Image Credits: Shangheng Song, Zelin Lei, Yuan Feng, Wenxiu Wang, Fang Huang, Yanmei Zhao, Jiping Jiang, Mengqi Sun, Ai-Jie Wang, Shu-Hong Gao, Marwan Majzoub & Lu Fan
Keywords
Coastal pathogens; shotgun metagenomics; antibiotic resistance genes; virulence factors; One Health; environmental risk assessment; interactive bioinformatics; microbial surveillance
