Bordetella pertussis, the Causative Agent of Whooping Cough, Evolved from a Distinct, Human-Associated Lineage of B. bronchiseptica

Abstract

Bordetella pertussis, B. bronchiseptica, B. parapertussis_hu, and B. parapertussis_ov are closely related respiratory pathogens that infect mammalian species. B. pertussis and B. parapertussis_hu are exclusively human pathogens and cause whooping cough, or pertussis, a disease that has resurged despite vaccination. Although it most often infects animals, infrequently B. bronchiseptica is isolated from humans, and these infections are thought to be zoonotic. B. pertussis and B. parapertussis_hu are assumed to have evolved from a B. bronchiseptica–like ancestor independently. To determine the phylogenetic relationships among these species, housekeeping and virulence genes were sequenced, comparative genomic hybridizations were performed using DNA microarrays, and the distribution of insertion sequence elements was determined, using a collection of 132 strains. This multifaceted approach distinguished four complexes, representing B. pertussis, B. parapertussis_hu, and two distinct B. bronchiseptica subpopulations, designated complexes I and IV. Of the two B. bronchiseptica complexes, complex IV was more closely related to B. pertussis. Of interest, while only 32% of the complex I strains were isolated from humans, 80% of the complex IV strains were human isolates. Comparative genomic hybridization analysis identified the absence of the pertussis toxin locus and dermonecrotic toxin gene, as well as a polymorphic lipopolysaccharide biosynthesis locus, as associated with adaptation of complex IV strains to the human host. Lipopolysaccharide structural diversity among these strains was confirmed by gel electrophoresis. Thus, complex IV strains may comprise a human-associated lineage of B. bronchiseptica from which B. pertussis evolved. These findings will facilitate the study of pathogen host-adaptation. Our results shed light on the origins of the disease pertussis and suggest that the association of B. pertussis with humans may be more ancient than previously assumed. Bordetella pertussis causes whooping cough, which kills 300,000 persons annually, and is reemerging despite vaccination. This human-restricted species is closely related to the respiratory pathogens B. parapertussis_hu, which is also human restricted, and B. bronchiseptica, which infects a broad range of mammals. Based on its limited genetic diversity and lack of historical descriptions, it has been suggested that the association between B. pertussis and humans is recent. In this study, the authors examined the genetic diversity and evolutionary relationships of these three Bordetella species. Their results suggest that B. parapertussis evolved from an animal-associated lineage of B. bronchiseptica, while B. pertussis evolved from a distinct B. bronchiseptica lineage that may already have had a preference for hominids up to 2.5 million years ago. Extant members of this newly identified B. bronchiseptica lineage were found to circulate in human populations. Comparisons of gene content revealed genomic features that are shared by and specific to B. pertussis and the B. bronchiseptica human-associated lineage and that may be important for association with the human host. These two lineages also have differences in key virulence genes that may reflect immune competition in the human host. By elucidating the evolutionary origins of human-adapted Bordetella, this study sets the stage for identification of key molecular events in host adaptation.