Hybridization capture sequencing for <i>Vibrio</i> spp. and associated virulence factors

Proliferation of <i>Vibrio</i> 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 <i>Vibrio</i> 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 <i>Vibrio</i> spp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69 <i>Vibrio</i> spp. and 162 <i>Vibrio</i>-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, <i>Vibrio parahaemolyticus</i> and <i>Vibrio vulnificus</i> strains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenic <i>Vibrio</i> spp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specific <i>Vibrio</i> spp., yielded significantly greater metagenomic insight, notably a variety of other <i>Vibrio</i> spp., including detection of <i>Vibrio cholerae</i>, <i>Vibrio fluvialis</i>, and <i>Vibrio aestuarianus</i>, in addition to <i>Vibrio parahaemolyticus</i> and <i>Vibrio vulnificus</i>, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenic <i>Vibrio</i> 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 <i>Vibrio</i> 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 <i>Vibrio</i> 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 <i>Vibrio</i> 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 <i>Vibrio parahaemolyticus</i> and <i>Vibrio vulnificus</i> strains isolated from the samples. Results suggest pathogenic <i>Vibrio</i> spp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.