Differences in the genomic content of Bordetella pertussis isolates before and after introduction of pertussis vaccines in four European countries

► At least three clusters of Bordetella pertussis circulated in Europe in pre-vaccine era. ► The genomes of European B. pertussis isolates were distinct from that of the international reference strain Tohama I. ► Progressive gene loss occurs in European B. pertussis population with time. ► Difference in frequency of the lost genes was observed among the countries. ► In contrast to many European countries, the novel pertussis toxin promoter allele ptxP3 was not found in Poland.