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One of the most common mechanisms of phase variation is reversible expansion or contraction of homopolymeric tracts (HPTs).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The genomes of <jats:italic>B. pertussis<\/jats:italic> and the two closely related species, <jats:italic>B. bronchiseptica<\/jats:italic> and <jats:italic>B. parapertussis<\/jats:italic>, 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 <jats:italic>B. pertussis<\/jats:italic> strains using the polymerase chain reaction\/ligase detection reaction (PCR\/LDR) assay. Six HPTs were polymorphic in this collection of <jats:italic>B. pertussis<\/jats:italic> strains. Of note, one of these polymorphic HPTs was found in the <jats:italic>fimX<\/jats:italic> 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 <jats:italic>fimX<\/jats:italic> was found to be 3.8-fold lower in strains carrying the longer allele. HPTs in three other genes, <jats:italic>tcfA<\/jats:italic>, <jats:italic>bapC<\/jats:italic>, and BP3651, varied widely in composition across the strain collection and displayed allelic polymorphism within single cultures.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>Allelic polymorphism at homopolymeric tracts is common within the <jats:italic>B. pertussis<\/jats:italic> genome. Phase variability may be an important mechanism in <jats:italic>B. pertussis<\/jats:italic> 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 <jats:italic>B. pertussis<\/jats:italic> loci.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2164-8-122","type":"journal-article","created":{"date-parts":[[2007,5,18]],"date-time":"2007-05-18T00:40:56Z","timestamp":1179448856000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Phase variation and microevolution at homopolymeric tracts in Bordetella pertussis"],"prefix":"10.1186","volume":"8","author":[{"given":"Emily B","family":"Gogol","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Craig A","family":"Cummings","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ryan C","family":"Burns","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David A","family":"Relman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,5,17]]},"reference":[{"issue":"4","key":"835_CR1","first-page":"31","volume":"80","author":"World Health Organization","year":"2005","unstructured":"World Health Organization: Pertussis vaccines--WHO position paper. 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