Hybridization capture sequencing for spp. and associated virulence factors.

Proliferation of spp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic 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 (HCS) was employed to profile low-abundance spp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69 spp. and 162 -specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition, and strains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenic spp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specific spp., yielded significantly greater metagenomic insight, notably a variety of other spp., including detection of , , and , in addition to and , and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenic spp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios.IMPORTANCEThe increasing prevalence of pathogenic 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 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 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 and strains isolated from the samples. Results suggest pathogenic spp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.