The aim of this project is to analyze the genomic diversity of Bordetella pertussis isolates collected in France since the 1990s in the frame of the French programme for the surveillance of whooping cough These genome sequence datasets are scrutinized for defining, over several decades of continuous surveillance, the genomic determinants of the lack of production of vaccine antigens, switches in fimbrial serotypes, sublineage changes and variants emergence, and phylogeography.