Phylogenetic and Biogeographic Patterns of Vibrio parahaemolyticus from North America Inferred from Whole Genome Sequence Data.

Vibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States. Draft genomes of 132 North American clinical and oyster V. parahaemolyticus isolates were sequenced to investigate their phylogenetic and biogeographic relationships. The majority of oyster isolate sequence types (STs) were from a single harvest location; however, four were identified from multiple locations. There was population structure along the Gulf and Atlantic Coasts of North America, with what seemed to be a hub of genetic variability along the Gulf Coast with some of the same STs occurring along the Atlantic Coast and one shared between the coastal waters of the Gulf and those of Washington state. Phylogenetic analyses found nine well-supported clades. Two clades were composed of isolates from both clinical and oyster sources. Four were composed entirely from clinical sources and three entirely from oyster sources. Each single source clade consisted of one ST. Some human isolates lack tdh and trh and some T3SS genes, which are established virulence genes of V. parahaemolyticus Thus, these genes are not essential for pathogenicity. However, isolates in the monophyletic groups from clinical sources were enriched in several categories of genes when compared to those from monophyletic groups of oyster isolates. These functional categories include: cell signaling, transport, and metabolism. Identification of genes in these functional categories provides a basis for future in-depth pathogenicity investigations of V. parahaemolyticus IMPORTANCE Vibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States and is frequently associated with shellfish consumption. This study contributes to our knowledge of the biogeography and functional genomics of this species around North America. STs shared between the Gulf Coast and the Atlantic seaboard as well as Pacific waters suggests possible transport via oceanic currents or large shipping vessels. STs frequently isolated from humans, but rarely if ever from the environment, are likely more competitive in the human gut compared to other STs. This could be due to additional functional capabilities in areas like cell signaling, transport, and metabolism which may give these isolates an advantage in novel nutrient replete environments like the human gut.