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The strains investigated comprised a well defined collection of 58 invasive and carriage isolates that were sequenced typed and included eight different <jats:italic>S. pneumoniae<\/jats:italic> serotypes (1, 3, 5, 6A, 11, 14, 19\u2009F and 23\u2009F) of varying invasive disease potential.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>The core genome of the isolates was estimated to be 38% and was mainly represented by gene functional categories associated with housekeeping functions. Comparison of the gene content of invasive and carriage isolates identified at least eleven potential genes that may be important in virulence including surface proteins, transport proteins, transcription factors and hypothetical proteins. Thirteen accessory regions (ARs) were also identified and did not show any loci association with the eleven virulence genes. Intraclonal diversity (isolates of the same serotype and MLST but expressing different patterns of ARs) was observed among some clones including ST 1233 (serotype 5), ST 3404 (serotype 5) and ST 3321 (serotype 14). A constructed phylogenetic tree of the isolates showed a high level of heterogeneity consistent with the frequent <jats:italic>S. pneumoniae<\/jats:italic> recombination. Despite this, a homogeneous clustering of all the serotype 1 strains was observed.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Comparative phylogenomics of invasive and carriage <jats:italic>S. pneumoniae<\/jats:italic> isolates identified a number of putative virulence determinants that may be important in the progression of <jats:italic>S. pneumoniae<\/jats:italic> from the carriage phase to invasive disease. Virulence determinants that contribute to <jats:italic>S. pneumoniae<\/jats:italic> pathogenicity are likely to be distributed randomly throughout its genome rather than being clustered in dedicated loci or islands. Compared to other <jats:italic>S. pneumoniae<\/jats:italic> serotypes, serotype 1 appears most genetically uniform.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2164-13-569","type":"journal-article","created":{"date-parts":[[2012,10,29]],"date-time":"2012-10-29T21:54:20Z","timestamp":1351547660000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Comparative phylogenomics of Streptococcus pneumoniae isolated from invasive disease and nasopharyngeal carriage from West Africans"],"prefix":"10.1186","volume":"13","author":[{"given":"Eric S","family":"Donkor","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard A","family":"Stabler","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jason","family":"Hinds","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard A","family":"Adegbola","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Antonio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brendan W","family":"Wren","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,10,29]]},"reference":[{"key":"4513_CR1","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/0-387-33026-7_10","volume":"582","author":"TJ Mitchell","year":"2006","unstructured":"Mitchell TJ: Streptococcus pneumoniae: infection, inflammation and disease. 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