Abstract
BackgroundBordetella pertussis, the causative agent of whooping cough, is a highly clonal pathogen of the respiratory tract. Its lack of genetic diversity, relative to many bacterial pathogens, could limit its ability to adapt to a hostile and changing host environment. This limitation might be overcome by phase variation, as observed for other mucosal pathogens. One of the most common mechanisms of phase variation is reversible expansion or contraction of homopolymeric tracts (HPTs).ResultsThe genomes of B. pertussis and the two closely related species, B. bronchiseptica and B. parapertussis, were screened for homopolymeric tracts longer than expected on the basis of chance, given their nucleotide compositions. Sixty-nine such HPTs were found in total among the three genomes, 74% of which were polymorphic among the three species. Nine HPTs were genotyped in a collection of 90 geographically and temporally diverse B. pertussis strains using the polymerase chain reaction/ligase detection reaction (PCR/LDR) assay. Six HPTs were polymorphic in this collection of B. pertussis strains. Of note, one of these polymorphic HPTs was found in the fimX promoter, where a single base insertion variant was present in seven strains, all of which were isolated prior to introduction of the pertussis vaccine. Transcript abundance of fimX was found to be 3.8-fold lower in strains carrying the longer allele. HPTs in three other genes, tcfA, bapC, and BP3651, varied widely in composition across the strain collection and displayed allelic polymorphism within single cultures.ConclusionAllelic polymorphism at homopolymeric tracts is common within the B. pertussis genome. Phase variability may be an important mechanism in B. pertussis for evasion of the immune system and adaptation to different niches in the human host. High sensitivity and specificity make the PCR/LDR assay a powerful tool for investigating allelic variation at HPTs. Using this method, allelic diversity and phase variation were demonstrated at several B. pertussis loci.
Highlights
Bordetella pertussis, the causative agent of whooping cough, is a highly clonal pathogen of the respiratory tract
Multilocus enzyme electrophoresis (MLEE) [10], comparative genome hybridization (CGH) [11] and multilocus sequence typing (MLST) of seven housekeeping genes [4] have established that B. pertussis is highly clonal with nearly invariant genome content
The apparent scarcity of variation in the B. pertussis genome is unusual among bacterial pathogens, in which extensive genomic plasticity is thought to contribute to host immune evasion [12]
Summary
Bordetella pertussis, the causative agent of whooping cough, is a highly clonal pathogen of the respiratory tract. Its lack of genetic diversity, relative to many bacterial pathogens, could limit its ability to adapt to a hostile and changing host environment. This limitation might be overcome by phase variation, as observed for other mucosal pathogens. Re-emergence of pertussis in certain vaccinated populations [5,6] suggests that B. pertussis may be adapting to vaccine-induced host immunity [5] In support of this hypothesis, shifts in the allelic frequencies of genes encoding at least three vaccine components (pertussis toxin, pertactin, and fimbriae) have been documented in B. pertussis from Finland, Sweden, France and the Netherlands [5,7,8,9]. The apparent scarcity of variation in the B. pertussis genome is unusual among bacterial pathogens, in which extensive genomic plasticity is thought to contribute to host immune evasion [12]
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