Vibrio parahaemolyticus is the most common cause of seafood-borne gastroenteritis worldwide and a blight on global aquaculture. This organism requires a horizontally acquired type III secretion system (T3SS2) to infect the small intestine, but knowledge of additional factors that underlie V. parahaemolyticus pathogenicity is limited. We used transposon-insertion sequencing to screen for genes that contribute to viability of V. parahaemolyticus in vitro and in the mammalian intestine. Our analysis enumerated and controlled for the host infection bottleneck, enabling robust assessment of genetic contributions to in vivo fitness. We identified genes that contribute to V. parahaemolyticus colonization of the intestine independent of known virulence mechanisms in addition to uncharacterized components of T3SS2. Our study revealed that toxR, an ancestral locus in Vibrio species, is required for V. parahaemolyticus fitness in vivo and for induction of T3SS2 gene expression. The regulatory mechanism by which V. parahaemolyticus ToxR activates expression of T3SS2 resembles Vibrio cholerae ToxR regulation of distinct virulence elements acquired via lateral gene transfer. Thus, disparate horizontally acquired virulence systems have been placed under the control of this ancestral transcription factor across independently evolved human pathogens.Vibrio parahaemolyticus | transposon-insertion sequencing | type III secretion | bacterial pathogenesis | pathogen evolution T he gram-negative γ-proteobacterium Vibrio parahaemolyticus thrives in either pathogenic or symbiotic association with marine organisms and as a planktonic bacterium (1). This facultative human pathogen, abundant in aquatic environments, was first isolated following a food poisoning outbreak in 1952 and has emerged as the leading cause of seafood-associated gastroenteritis worldwide and a blight on global aquaculture (2, 3). Sequencing of the V. parahaemolyticus genome and the development of animal models of infection have demonstrated a critical role for type III secretion in V. parahaemolyticus virulence (4, 5).Pathogenic isolates of V. parahaemolyticus encode two type III secretion systems (T3SSs), which are multiprotein structures that mediate the translocation of bacterial effector proteins directly into eukaryotic cells (4, 6). All V. parahaemolyticus strains encode a T3SS on the large chromosome (T3SS1), and the vast majority of clinical isolates, but few environmental isolates possess a horizontally acquired pathogenicity island (VPaI-7) encoding a second T3SS (T3SS2) and one or more pore-forming toxins (TDH) (7). Studies using the infant rabbit model of V. parahaemolyticus infection, which recapitulates manifestations of human gastrointestinal disease (e.g., profuse diarrhea, enteritis, epithelial disruption), revealed that although T3SS1 and TDH are dispensable for intestinal colonization and pathogenesis, colonization and pathology are dependent on T3SS2, consistent with the epidemiological association between T3SS2 and pathogenicity (5). Furthermor...