Pathogens of the bacterial genus Bordetella cause respiratory disease in humans and animals. Although virulence and host specificity vary across the genus, the genetic determinants of this diversity remain unidentified. To identify genes that may underlie key phenotypic differences between these species and clarify their evolutionary relationships, we performed a comparative analysis of genome content in 42 Bordetella strains by hybridization of genomic DNA to a microarray representing the genomes of three Bordetella species and by subtractive hybridization. Here we show that B. pertussis and B. parapertussis are predominantly differentiated from B. bronchiseptica by large, species-specific regions of difference, many of which encode or direct synthesis of surface structures, including lipopolysaccharide O antigen, which may be important determinants of host specificity. The species also exhibit sequence diversity at a number of surface protein-encoding loci, including the fimbrial major subunit gene, fim2. Gene loss, rather than gene acquisition, accompanied by the proliferation of transposons, has played a fundamental role in the evolution of the pathogenic bordetellae and may represent a conserved evolutionary mechanism among other groups of microbial pathogens.Bacteria of the genus Bordetella are important pathogens that cause respiratory disease in humans and animals. B. pertussis is the causative agent of whooping cough (8), which is responsible for up to 500,000 annual deaths worldwide in unvaccinated populations (52) and is increasing in incidence in some countries with established vaccination programs, including the United States (e.g., see references 15, 30, and 38). Although most Bordetella species can cause similar disease in the upper respiratory tract, their host specificities vary dramatically. B. pertussis infects only humans; B. parapertussis strains can be classified in two groups, one of which infects only humans and one of which infects only sheep (16,17,25); B. bronchiseptica causes respiratory infections in a wide variety of mammals and birds but only rarely in humans (22,41,51).These three Bordetella species are closely related at the nucleotide sequence level (4, 24), and their relatedness has been further established using a variety of common molecular strain typing techniques (reviewed in reference 29). Phylogenetic analyses of the genus Bordetella, using pulsed-field gel electrophoresis, multilocus enzyme electrophoresis (MLEE), and IS typing data, suggested that B. pertussis, human-derived B. parapertussis, and sheep-derived B. parapertussis arose independently from B. bronchiseptica-like ancestors (46, 47). Comparative genome sequencing of a representative strain of each species (33) confirmed that nucleotide sequence similarity is very high in conserved regions of the genome but demonstrated that B. pertussis and B. parapertussis evolved by genome decay from a B. bronchiseptica-like ancestor.Although a number of critical conserved virulence mechanisms have been identified in the bor...