Gastric infections caused by the environmentally transmitted pathogen, Vibrio parahaemolyticus, have increased over the last two decades, including in many parts of the United States (US). However, until recently, infections linked to shellfish from the cool northeastern US waters were rare. Cases have risen in the Northeast, consistent with changes in local V. parahaemolyticus populations toward greater abundance or a shift in constituent pathogens. We examined 94 clinical isolates from a period of increasing disease in the region and compared them to 200 environmental counterparts to identify resident and non-indigenous lineages and to gain insight into the emergence of pathogenic types. Genotyping and multi-locus sequence analysis (MLSA) of clinical isolates collected from 2010 to 2013 in Massachusetts, New Hampshire, and Maine revealed their polyphyletic nature. Although 80% of the clinical isolates harbored the trh hemolysin either alone or with tdh, and were urease positive, 14% harbored neither hemolysin exposing a limitation for these traits in pathogen detection. Resident sequence type (ST) 631 strains caused seven infections, and show a relatively recent history of recombination with other clinical and environmental lineages present in the region. ST34 and ST674 strains were each linked to a single infection and these strain types were also identified from the environment as isolates harboring hemolysin genes. Forty-two ST36 isolates were identified from the clinical collection, consistent with reports that this strain type caused a rise in regional infections starting in 2012. Whole-genome phylogenies that included three ST36 outbreak isolates traced to at least two local sources demonstrated that the US Atlantic coastal population of this strain type was indeed derived from the Pacific population. This study lays the foundation for understanding dynamics within natural populations associated with emergence and invasion of pathogenic strain types in the region.

dVibrio parahaemolyticus sequence type 36 (ST36) strains that are native to the Pacific Ocean have recently caused multistate outbreaks of gastroenteritis linked to shellfish harvested from the Atlantic Ocean. Whole-genome comparisons of 295 genomes of V. parahaemolyticus, including several traced to northeastern U.S. sources, were used to identify diagnostic loci, one putatively encoding an endonuclease (prp), and two others potentially conferring O-antigenic properties (cps and flp). The combination of all three loci was present in only one clade of closely related strains of ST36, ST59, and one additional unknown sequence type. However, each locus was also identified outside this clade, with prp and flp occurring in only two nonclade isolates and cps in four. Based on the distribution of these loci in sequenced genomes, prp identified clade strains with >99% accuracy, but the addition of one more locus increased accuracy to 100%. Oligonucleotide primers targeting prp and cps were combined in a multiplex PCR method that defines species using the tlh locus and determines the presence of both the tdh and trh hemolysin-encoding genes, which are also present in ST36. Application of the method in vitro to a collection of 94 clinical isolates collected over a 4-year period in three northeastern U.S. states and 87 environmental isolates revealed that the prp and cps amplicons were detected only in clinical isolates identified as belonging to the ST36 clade and in no environmental isolates from the region. The assay should improve detection and surveillance, thereby reducing infections. Vibrio parahaemolyticus is typically harmless, but pathogenic strains can cause severe inflammatory gastroenteritis infections that rarely progress to lethal sepsis (1). It is the leading cause of bacterial seafood-borne illness worldwide, with raw or improperly handled seafood as a major vector. In the United States, it has been of greatest concern for shellfish harvested in the Gulf of Mexico and the Pacific Northwest (2-5). Infections linked to shellfish from the northeastern United States have been rare, but a steep rise in infections occurred in 2012 to 2013 that was concurrent with the probable ecological invasion of a serotype O4:K12 sequence type 36 (ST36) strain. This strain type has been linked to recurrent infections in the Pacific Northwest for more than a decade, suggesting that it may have expanded its geographic range (6, 7). Furthermore, unlike native strains present in the northern Atlantic that cause infrequent infections, the ST36 strain is responsible for an ongoing multistate outbreak (7) (Fig. 1). Rapid identification of this strain complex in clinical samples might aid in the prevention of more widespread infections. Additionally, accurate quantification of this strain in shellfish growing areas could inform harvest strategies that maintain a safe product.Identifying rare pathogenic strains among mostly nonpathogenic populations of V. parahaemolyticus has been a long-standing challenge. A few strains, such as tho...

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