D, Oxford PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28878015 OX3 7FZ, UK. 17Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland. 18School of Pathology, University of the Witwatersrand, Johannesburg, South Africa. 19Division of Infection and Immunity, University College London, London WC1E 6BT, UK.Abbreviations CI: Confidence interval; HPD: Highest posterior density; ICE: Integrative conjugative element; IPD: Invasive pneumococcal disease; PCR: Polymerase chain reaction; PCV: Pneumococcal conjugate vaccine; SC: Sequence cluster; SNP: Single nucleotide polymorphism Acknowledgements We would like to thank all the clinical and laboratory staff at all the collaborating institutions, the sequencing teams at the Wellcome Trust Sanger Institute for their expertise. We are also grateful to the Global Pneumococcal Strain Bank (a PATH-funded collaboration between the US Centre for Disease Control and Prevention (CDC), Emory University, and others) for providing additional isolates for the study. Funding This work was supported by funds from the Bill and Melinda Gates Foundation (BMGF) (grant number: OPP1023440 awarded to DBE [http:// www.pagegenomes.org/page/consortium]) and The Wellcome Trust Major Overseas programme core award (Award number: 084679/Z/08/Z). CC acknowledges support in form of a PhD scholarship from the Commonwealth Scholarship Commission, UK.Chaguza et al. BMC Infectious Diseases (2016) 16:Page 13 ofPneumococcal African Genomics (PAGe) Consortiumhttp:// www.pagegenomes.org/. Received: 25 May 2016 Accepted: 30 OctoberReferences 1. O’Brien KL, Wolfson LJ, Watt JP, Henkle E, Deloria-Knoll M, McCall N, Lee E, Mulholland K, Levine OS, MLN9708 price Cherian T. Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. Lancet. 2009;374(9693):893?02. 2. Johnson HL, Deloria-Knoll M, Levine OS, Stoszek SK, Freimanis Hance L, Reithinger R, Muenz LR, O’Brien KL. Systematic Evaluation of Serotypes Causing Invasive Pneumococcal Disease among Children Under Five: The Pneumococcal Global Serotype Project. PLoS Med. 2010;7(10):e1000348. 3. Bentley SD, Aanensen DM, Mavroidi A, Saunders D, Rabbinowitsch E, Collins M, Donohoe K, Harris D, Murphy L, Quail MA, et al. Genetic Analysis of the Capsular Biosynthetic Locus from All 90 Pneumococcal Serotypes. PLoS Genet. 2006;2(3):e31. 4. Calix JJ, Nahm MH. A new pneumococcal serotype, 11E, has a variably inactivated wcjE gene. J Infect Dis. 2010;202(1):29?8. 5. Jin P, Kong F, Xiao M, Oftadeh S, Zhou F, Liu C, Russell F, Gilbert GL. First report of putative Streptococcus pneumoniae serotype 6D among nasopharyngeal isolates from Fijian children. J Infect Dis. 2009;200(9):1375?0. 6. Park IH, Pritchard DG, Cartee R, Brandao A, Brandileone MC, Nahm MH. Discovery of a new capsular serotype (6C) within serogroup 6 of Streptococcus pneumoniae. J Clin Microbiol. 2007;45(4):1225?3. 7. Oliver MB, van der Linden MP, Kuntzel SA, Saad JS, Nahm MH. Discovery of Streptococcus pneumoniae serotype 6 variants with glycosyltransferases synthesizing two differing repeating units. J Biol Chem. 2013;288(36):25976?5. 8. Calix JJ, Porambo RJ, Brady PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28192408 AM, Larson TR, Yother J, Abeygunwardana C, Nahm MH. Biochemical, genetic, and serological characterization of two capsule subtypes among Streptococcus pneumoniae Serotype 20 strains: discovery of a new pneumococcal serotype. J Biol Chem. 2012;287(33):27885?4. 9. Park IH, Geno KA, Yu J, Oliver MB, Kim KH, Nahm MH. Genetic, biochemical, and serological characterization of a n.