Comparative genomics of the toxin.

is a zoonotic pathogen whose genetic heterogeneity is well known. Five serogroups (A, B, D, E, and F) and 16 serotypes of have been recognized thus far based on capsular polysaccharide typing and lipopolysaccharide typing, respectively. Progressive atrophic rhinitis in domestic pigs is caused by strains containing , which encodes a 146 kDa heat-labile toxin. Among the five serogroups, only some strains of serogroups A and D are toxigenic. In this study, by comparative analyses of the genomes of many strains, it has been shown that is sparsely distributed in . Furthermore, full-length homologs of were found only in two other bacterial species. It has also been shown that is usually associated with a prophage, and that some strains contain an orthologous prophage but not . Among the -containing prophages that were compared, an operon putatively encoding a type II restriction-modification system was present only in strains LFB3, HN01, and HN06. These results indicate that the selection and maintenance of the heat-labile toxin and the type II restriction-modification system are evolutionarily less favorable among strains. Phylogenetic analysis using the alignment- and parameter-free method CVTree3 showed that deduced proteome sequences can be used as effectively as whole/core genome single nucleotide polymorphisms to group strains in relation to their serotypes and (or) genotypes. It remains to be determined if the -containing prophages in strains HN01 and HN06 are inducible, and if they can be used for lysogenic transfer of to other bacteria.