Hybridization capture sequencing for Vibrio spp. and associated virulence factors

• Published in: mBio Vol. 16; no. 8; p. e0051625
• Main Authors: Brumfield, Kyle D., Enke, Sana, Swan, Brandon K., Carrasquilla, Lakeshia, Lee, Michael D., Stern, David B., Gieser, Linn, Hasan, Nur A., Usmani, Moiz, Jutla, Antarpreet S., Huq, Anwar, Caviness, Katie, Goodrich, Jennifer S., Bull, Robert, Colwell, Rita R.
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 25.06.2025
• Subjects: Animals; Environmental Microbiology; hybridization capture; metagenomics; Metagenomics - methods; microbiome; next generation sequencing; Ostreidae - microbiology; Research Article; targeted enrichment; Vibrio - classification; Vibrio - genetics; Vibrio - isolation & purification; Vibrio - pathogenicity; Virulence Factors - genetics; Water Microbiology; Whole Genome Sequencing; virulence; metagenomics; next generation sequencing; whole-genome sequencing; microbiome; targeted enrichment; hybridization capture; Vibrio
• ISSN: 2150-7511; 2150-7511
• DOI: 10.1128/mbio.00516-25

The increasing prevalence of pathogenic Vibrio spp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundance Vibrio spp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing of Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples. Results suggest pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.