| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Bordetella pertussis </it>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 <it>B. pertussis </it>over the last 60 years, we used an oligonucleotide DNA microarray to compare the genomic contents of a collection of 171 strains of <it>B. pertussis </it>isolates from different countries.</p> <p>Results</p> <p>The CGH microarray analysis estimated the core genome of <it>B. pertussis</it>, to consist of 3,281 CDSs that are conserved among all <it>B. pertussis </it>strains, and represent 84.8% of all CDSs found in the 171 <it>B. pertussis </it>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 <it>B. pertussis </it>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. <it>B. pertussis </it>strains with the same gene content were found in several different countries. However, geographic specificity of the <it>B. pertussis </it>strains was not observed. The gene content was determined to highly correlate with the <it>ptxP</it>-type of the strains.</p> <p>Conclusions</p> <p>An 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 <it>B. pertussis</it>. Our results show that <it>B. pertussis </it>is a dynamic organism that continues to evolve.</p>
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