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Open Access Highly Accessed Research article

Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis

Emily B Gogol135, Craig A Cummings13*, Ryan C Burns4 and David A Relman123

Author Affiliations

1 Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA

2 Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA

3 VA Palo Alto Health Care System, Palo Alto, California 94304, USA

4 2030 3rd. St., Unit #2, San Francisco, CA 94107, USA

5 Present address : University of California San Francisco, Biomedical Sciences Graduate Program, 513 Parnassus Ave., Room HSE-1285, San Francisco, CA, 94143, USA

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BMC Genomics 2007, 8:122  doi:10.1186/1471-2164-8-122

Published: 17 May 2007

Abstract

Background

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. One of the most common mechanisms of phase variation is reversible expansion or contraction of homopolymeric tracts (HPTs).

Results

The 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.

Conclusion

Allelic 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.