Genetic characterization of clinical and environmental Vibrio parahaemolyticus from the Northeast USA reveals emerging resident and non-indigenous pathogen lineages

Abstract

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.

Parallel Evolution of Two Clades of an Atlantic-Endemic Pathogenic Lineage of Vibrio parahaemolyticus by Independent Acquisition of Related Pathogenicity Islands

“…The two distinct ST631 clades shared 85% of their DNA in common and displayed polymorphisms in Յ12% of the shared DNA content. The most closely related sister lineage to ST631 was formed by trh-harboring ST1127 isolates that have been exclusively reported from clinical sources in the Northeast United States (21).…”

“…Prior to 2012, resident lineages contributed to low but increasing sporadic infection rates on the Northeast U.S. coast (https://www.cdc.gov/vibrio/surveillance.html, 2017; see also reference 21), with ST631 emerging as the major lineage that is endemic to nearshore areas of the Atlantic Ocean bordering North America (the northwest Atlantic Ocean) (31). However, we previously identified a single ST631 isolate lacking hemolysins (21,27), suggesting this pathogen lineage may have recently evolved through VPaI acquisition.…”

“…In contrast, islands containing T3SS2␤ linked to trh and a urease (ure) cluster, which confers a useful diagnostic phenotype, (where similar islands are described by others as Vp-PAI TH3966 [16] or trhVPA [17,20]) have received only modest attention. Pathogenic variants harboring both tdh and trh are increasingly associated with disease in North America (21)(22)(23)(24)(25)(26), and yet, to our knowledge, the exact configuration of hemolysin-associated VPaI in isolates that contain both tdh and trh has not yet been described (see also reference 20). Thus, it is unclear how virulence loci and islands in these emergent pathogen lineages carrying both hemolysins evolved and spread.…”

“…S2 in the supplemental material; also, data not shown). Because clade I isolate G149 lacked these islands, this could be the ancestral state of the ST631 lineage (21).…”

“…A related complex of Asia-derived pandemic strains, most often identified as serotype O3:K6 and also known as sequence type 3 (ST3; based on allele combinations of seven housekeeping genes) causes the most disease globally (28). An unrelated Pacific native lineage called ST36 (also described as serotype O4:K12) currently dominates infections in North America, including from the Northeast United States (21,26,29). The introduction of ST36 into the Atlantic Ocean by an unknown route precipitated a series of outbreaks from Atlantic shellfish starting in 2012 (29,30).…”