Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae.

Jennifer E Cornick; Chrispin Chaguza; Simon R Harris; Feyruz Yalcin; Madikay Senghore; Anmol M Kiran; Shanil Govindpershad; Sani Ousmane; Mignon Du Plessis; Gerd Pluschke; +12 more... Chinelo Ebruke; Lesley McGee; Beutel Sigaùque; Jean-Marc Collard; Martin Antonio; Anne von Gottberg; Neil French; Keith P Klugman; Robert S Heyderman; Stephen D Bentley; Dean B Everett; For The PAGe Consortium; (2015) Region-specific diversification of the highly virulent serotype 1 Streptococcus pneumoniae. Microbial genomics, 1 (2). e000027-. ISSN 2057-5858 DOI: 10.1099/mgen.0.000027
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Serotype 1 Streptococcus pneumoniae is a leading cause of invasive pneumococcal disease (IPD) worldwide, with the highest burden in developing countries. We report the whole-genome sequencing analysis of 448 serotype 1 isolates from 27 countries worldwide (including 11 in Africa). The global serotype 1 population shows a strong phylogeographic structure at the continental level, and within Africa there is further region-specific structure. Our results demonstrate that region-specific diversification within Africa has been driven by limited cross-region transfer events, genetic recombination and antimicrobial selective pressure. Clonal replacement of the dominant serotype 1 clones circulating within regions is uncommon; however, here we report on the accessory gene content that has contributed to a rare clonal replacement event of ST3081 with ST618 as the dominant cause of IPD in the Gambia.


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