No innocent bystanders: pertussis vaccination epitomizes evolutionary parallelisms between Bordetella parapertussis and B. pertussis

Pathogens adapting to the human host and to vaccination-induced immunity may follow parallel evolutionary paths. Bordetella parapertussis (Bpp) contributes significantly to the burden of whooping cough (pertussis), shares vaccine antigens with Bordetella pertussis (Bp), and both pathogens are phylogenetically related and ecological competitors. Bp vaccine antigen-coding genes have accumulated variation, including pertactin disruptions, after introduction of acellular vaccines in the 1990s. We aimed to evaluate evolutionary parallelisms in Bpp, even though pertussis vaccines were designed against Bp. We investigated the temporal evolution of Bpp sublineages, by sequencing 242 Bpp isolates collected in France, the USA and Spain between 1937 and 2019, spanning pre-vaccine and two vaccines eras. We estimated the evolutionary rate of Bpp at 2.12x10-7 substitutions per site{middle dot}year-1, with a most recent common ancestor of all sequenced isolates around year 1877, and found that pertactin deficiency in Bpp was driven by 18 disruptive mutations, including deletion prn:{Delta}G-1895 estimated to have occurred around 1998 and observed in 73.8% (149/202) of post-2007 isolates. In addition, we detected two mutations in the bvgA-fhaB intergenic region (controlling expression of the master transcriptional regulator BvgA and the filamentous hemagglutinin), that became fixed in the early 1900s. Our findings suggest early adaptation of Bpp to humans through modulation of the bvgAS regulon, and a rapid adaptation through the loss of pertactin expression, representing a late evolutionary parallelism concomitant with acellular vaccination against whooping cough. IMPORTANCEVaccination against Bordetella pertussis (Bp) has strongly affected the recent evolution of this main agent of whooping cough. Whether it may have done so co-incidentally on Bordetella parapertussis (Bpp), which is genetically and ecologically very similar to Bp, has not been described in detail. Our findings show striking evolutionary parallelisms of Bpp with Bp, including early changes in a critical regulatory region, and strong evidence of adaptation to vaccine-driven population immunity, even though whooping cough vaccines were not designed explicitly against Bpp. The rapid populational loss of pertactin in countries where acellular pertussis vaccines are used may also reduce protection by vaccination against Bpp, the second agent of whooping cough.