Global population structure and evolution of Bordetella pertussis and their relationship with vaccination

Abstract

Bordetella pertussis causes pertussis, a respiratory disease that is most severe for infants. Vaccination was introduced in the 1950s, and in recent years, a resurgence of disease was observed worldwide, with significant mortality in infants. Possible causes for this include the switch from whole-cell vaccines (WCVs) to less effective acellular vaccines (ACVs), waning immunity, and pathogen adaptation. Pathogen adaptation is suggested by antigenic divergence between vaccine strains and circulating strains and by the emergence of strains with increased pertussis toxin production. We applied comparative genomics to a worldwide collection of 343 B. pertussis strains isolated between 1920 and 2010. The global phylogeny showed two deep branches; the largest of these contained 98% of all strains, and its expansion correlated temporally with the first descriptions of pertussis outbreaks in Europe in the 16th century. We found little evidence of recent geographical clustering of the strains within this lineage, suggesting rapid strain flow between countries. We observed that changes in genes encoding proteins implicated in protective immunity that are included in ACVs occurred after the introduction of WCVs but before the switch to ACVs. Furthermore, our analyses consistently suggested that virulence-associated genes and genes coding for surface-exposed proteins were involved in adaptation. However, many of the putative adaptive loci identified have a physiological role, and further studies of these loci may reveal less obvious ways in which B. pertussis and the host interact. This work provides insight into ways in which pathogens may adapt to vaccination and suggests ways to improve pertussis vaccines. IMPORTANCE Whooping cough is mainly caused by Bordetella pertussis, and current vaccines are targeted against this organism. Recently, there have been increasing outbreaks of whooping cough, even where vaccine coverage is high. Analysis of the genomes of 343 B. pertussis isolates from around the world over the last 100 years suggests that the organism has emerged within the last 500 years, consistent with historical records. We show that global transmission of new strains is very rapid and that the worldwide population of B. pertussis is evolving in response to vaccine introduction, potentially enabling vaccine escape.

FIG 1

Global phylogeny of B. pertussis. (A) Outline of the maximum likelihood phylogeny of all B. pertussis samples sequenced, showing the deep divergence between lineages I and II. The complete tree is shown in Fig. S1 in the supplemental material. (B) Bayesian phylogeny of samples for which date information was available within the most common clade of B. pertussis. The position of a node along the x axis of the tree represents the median date reconstructed for that node across all sampled trees. Dates of whole-cell vaccine (WCV) and acellular vaccine (ACV) periods are shown as background colors behind the tree. To the right of the tree, the continent of origin of isolates is indicated by the first column of horizontal bars, colored according to the inset key. The remaining nine columns represent loci within the ptx operon, the fim2 and fim3 loci, and the prn locus, with assigned numerical alleles colored according to the key. The positions of reference strains 18323 and Tohama I (T) are indicated in panels A and B with green filled circles. Black filled circles represent the American vaccine strains B308 (A) and B310 (B) (Table S1). Red circles indicate the major changes in antigen gene alleles in proteins used in current ACVs (from ptxA2 to ptxA1, fim2-1 to fim2-2, ptxP1 to ptxP3, and fim3-1 to fim3-2).

FIG 2

Temporal trends in strain frequencies for the fim2 (A), fim3 (B), ptxA (C), ptxP (D), and prn (E) alleles. Four periods were defined to reflect the worldwide changes in pertussis vaccination, the early WCV period (earlier than 1960), the period in which mainly WCVs were used (WCV period, 1960 to 1995), the period in which both WCVs and ACVs were used (WCV/ACV period, 1996 to 2000), and a period in which mainly ACVs were used (ACV period, later than 2000).

FIG 3

SNP densities per functional category (A), subcellular localization (B), and Bvg regulation (C). Red bars indicate the chromosomal average. Green bars refer to categories with an SNP density significantly higher than the chromosomal average (P < 0.05).