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Background  Whooping cough caused by  Bordetella pertussis  in humans, is re-emerging in many countries despite vaccination. Several studies have shown that significant shifts have occurred in the  B. pertussis  population resulting in antigenic divergence between vaccine strains and circulating strains and suggesting pathogen adaptation. In the Netherlands, the resurgence of pertussis is associated with the rise of  B. pertussis  strains with an altered promoter region for pertussis toxin ( ptxP3 ).    Results  We used Multi-Locus Sequence Typing (MLST), Multiple-Locus Variable Number of Tandem Repeat Analysis (MLVA) and microarray-based comparative genomic hybridization (CGH) to characterize the  ptxP3  strains associated with the Dutch epidemic. For CGH analysis, we developed an oligonucleotide (70-mers) microarray consisting of 3,581 oligonucleotides representing 94% of the gene repertoire of the  B. pertussis  strain Tohama I. Nine different MLST profiles and 38 different MLVA types were found in the period 1993 to 2004. Forty-three Dutch clinical isolates were analyzed with CGH, 98 genes were found to be absent in at least one of the  B. pertussis  strains tested, these genes were clustered in 8 distinct regions of difference.    Conclusion  The presented MLST, MLVA and CGH-analysis identified distinctive characteristics of  ptxP3 B. pertussis  strains -the most prominent of which was a genomic deletion removing about 23,000 bp. We propose a model for the emergence of  ptxP3  strains.

bmc genomics

Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: Identification of genes absent from epidemic strains