Changes in the genomic content of circulating Bordetella pertussis strains isolated from the Netherlands, Sweden, Japan and Australia: adaptive evolution or drift?

Abstract

BackgroundBordetella pertussis is the causative agent of human whooping cough (pertussis) and is particularly severe in infants. Despite worldwide vaccinations, whooping cough remains a public health problem. A significant increase in the incidence of whooping cough has been observed in many countries since the 1990s. Several reasons for the re-emergence of this highly contagious disease have been suggested. A particularly intriguing possibility is based on evidence indicating that pathogen adaptation may play a role in this process. In an attempt to gain insight into the genomic make-up of B. pertussis over the last 60 years, we used an oligonucleotide DNA microarray to compare the genomic contents of a collection of 171 strains of B. pertussis isolates from different countries.ResultsThe CGH microarray analysis estimated the core genome of B. pertussis, to consist of 3,281 CDSs that are conserved among all B. pertussis strains, and represent 84.8% of all CDSs found in the 171 B. pertussis strains. A total of 64 regions of difference consisting of one or more contiguous CDSs were identified among the variable genes. CGH data also revealed that the genome size of B. pertussis strains is decreasing progressively over the past 60 years. Phylogenetic analysis of microarray data generated a minimum spanning tree that depicted the phylogenetic structure of the strains. B. pertussis strains with the same gene content were found in several different countries. However, geographic specificity of the B. pertussis strains was not observed. The gene content was determined to highly correlate with the ptxP-type of the strains.ConclusionsAn overview of genomic contents of a large collection of isolates from different countries allowed us to derive a core genome and a phylogenetic structure of B. pertussis. Our results show that B. pertussis is a dynamic organism that continues to evolve.

The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement

“…Although no evidence of gene gain has been reported, many previous studies have identified regions of difference resulting from apparent deletions conserved among circulating isolates in comparison with older references (12, 14, 50, 51). The conserved structural features identified here, specifically those which differentiated isolates with the ptxP3 allele and vaccine reference strains, included deletions flanked by IS481 insertions, each of which corresponds to regions of difference identified previously (12,14,25,(50)(51)(52)(53). However, conserved rearrangements and inversions were also identified, illustrating that structural genome evolution in B. pertussis is not limited to reduction.…”

Better colonisation of newly emerged Bordetella pertussis in the co-infection mouse model study

“…The SNP in sphB1 was a common SNP found in all Australian B. pertussis SNP profile 13 (cluster I) isolates from the 2008-2012 epidemic that were sequenced previously while the SNP in fliM was only found in a subset of the isolates [15]. Genomic content of currently circulating B. pertussis strains has been reduced compared to other SNP clusters [38][39][40]. One or more of these changes may provide a selective advantage to the SNP cluster I strains for increased colonisation of the host.…”

BpsR Modulates Bordetella Biofilm Formation by Negatively Regulating the Expression of the Bps Polysaccharide

“…This, combined with very high levels of nucleotide sequence identity in the bpsA-D promoter regions, the similar arrangement of the bpsR ORF with respect to the bpsA-D locus, and the highly homologous amino acid sequences of the BpsR proteins among these three species, suggests the preservation of a common bacterial strategy to regulate virulence and biofilm development. By analyzing the genomic content of a large collection of B. pertussis strains isolated over the last 60 years from six different countries, a core genome for B. pertussis has been derived (4,33). In addition, a group of 589 variable genes that were either absent or divergent in one or more of these strains were also iden-tified (33).…”

“…By analyzing the genomic content of a large collection of B. pertussis strains isolated over the last 60 years from six different countries, a core genome for B. pertussis has been derived (4,33). In addition, a group of 589 variable genes that were either absent or divergent in one or more of these strains were also iden-tified (33). None of the genes of the bpsA-D locus, the intervening gene, BP1945, or the bpsR gene was found to be missing or divergent in these strains, strongly suggesting that these genes are part of the B. pertussis pan-genome.…”