Numerical analyses of the sequence data.

The sequences of bvgA and bvgS originate from this study, while those of the 7 housekeeping gene fragments (HKG) were obtained from a previous study [28] and concatenated for the analyses. All three sets of sequences were obtained from similar sets of isolates. The Shannon-Wiener index represents the genetic diversity. Complex I includes B. bronchiseptica isolates mainly of animal origin and the B. parapertussis ovine isolates (Bppov), complex II all B. pertussis isolates, complex III all B. parapertussis human isolates (Bpphu) and complex IV B. bronchiseptica isolates mainly of human origin.