T he genus Bordetella contains nine species, three of which have been studied in detail: B. pertussis, B. parapertussis, and B. bronchiseptica. B. pertussis and B. parapertussis are the causative agents of whooping cough. While long considered a disease of infants and children, it is now recognized that infections occur in adults, although they are milder than the classic whooping cough described in children (1-5). B. pertussis is considered the major pathogen of whooping cough; however, the prevalence of B. parapertussis in disease is not well understood but may be a significant contributor to the overall burden (6). Symptoms of B. parapertussis and B. pertussis disease are clinically indistinguishable and include a prolonged cough, whooping, paroxysms, vomiting, and cyanosis (7), leading to increased mortality in infected children; however, B. parapertussis is often considered to cause milder disease than B. pertussis (7). In many countries, whooping cough is controlled by vaccination against B. pertussis. However, many countries have recently suffered major outbreaks despite continuous high levels of vaccine coverage, initiating renewed interest in whooping cough vaccinology. The acellular pertussis vaccines (DTaP and Tdap) used in most developed countries do not result in protection against B. parapertussis, likely due to the B. parapertussis lipopolysaccharide (LPS) O antigen inhibiting the binding of antibodies to the bacterium (8).LPS is the major component of the outer leaflet of the outer membrane of Gram-negative bacteria. The lipid A region imparts the endotoxin activity of LPS (9) that arises when lipid A binds to a host membrane complex that includes and activates signaling by Toll-like receptor 4 (TLR4) (10), resulting in the expression of many proinflammatory cytokines and chemokines in cells of the innate immune system. TLR4 signaling is also important for the activation of adaptive immunity, particularly through the activation of dendritic cells (DCs), which act as antigen-presenting cells (APCs) for T cells. Thus, lipid A-TLR4 interactions are central to the host immune response to Gram-negative bacteria, including Bordetella species.Bordetella subspecies exhibit extensive heterogeneity in their lipid A structure, arising from both species-specific differences in and species-variable expression of specific lipid A-modifying enzymes (11,12). Previously, we demonstrated that B. bronchiseptica pagP (pagP BB ) encodes a lipid A palmitoyl transferase that is responsible for the presence of palmitate in lipid A. The expression of pagP BB is regulated by the Bvg two-component system (13) that regulates the expression of many Bordetella genes that are involved in pathogenesis (14). pagP BB is maximally expressed in the Bvgplus (Bvg ϩ ) phase that is adopted when the system is active and includes the expression of many of the toxins and adhesins considered important for infection. When the Bvg system is inactive, the bacteria adopt the Bvg-minus (Bvg Ϫ ) phase, and the expression of these virulence gene...