title: Region-specific diversification of the highly virulent serotype 1Streptococcus pneumoniae.
abstract: Serotype 1Streptococcus pneumoniaeis 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.
authors.affiliation: The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.|University of Liverpool, Institute of Infection and Global Health, Liverpool, UK.
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Cornick
authors.affiliation: The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.|University of Liverpool, Institute of Infection and Global Health, Liverpool, UK.
authors.forename: Chrispin
authors.initials: C
authors.lastname: Chaguza
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Harris
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Feyruz
authors.initials: F
authors.lastname: Yalcin
authors.affiliation: Medical Research Council, Banjul, The Gambia.|Division of Translational and Systems Medicine, Microbiology and Infection Unit, The University of Warwick, Coventry, UK.
authors.forename: Madikay
authors.initials: M
authors.lastname: Senghore
authors.affiliation: The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.|University of Liverpool, Institute of Infection and Global Health, Liverpool, UK.
authors.forename: Anmol M
authors.initials: AM
authors.lastname: Kiran
authors.affiliation: National Institute for Communicable Diseases, Division of the National Health Laboratory Service; and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Shanil
authors.initials: S
authors.lastname: Govindpershad
authors.affiliation: Centre de Recherche Médicale et Sanitaire, Niamey, Niger.
authors.forename: Sani
authors.initials: S
authors.lastname: Ousmane
authors.affiliation: National Institute for Communicable Diseases, Division of the National Health Laboratory Service; and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Mignon Du
authors.initials: MD
authors.lastname: Plessis
authors.affiliation: Swiss Tropical and Public Health Institute, Basel, Switzerland.
authors.forename: Gerd
authors.initials: G
authors.lastname: Pluschke
authors.affiliation: Medical Research Council, Banjul, The Gambia.|Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
authors.forename: Chinelo
authors.initials: C
authors.lastname: Ebruke
authors.affiliation: Centers for Disease Control and Prevention, Atlanta, GA, USA.
authors.forename: Lesley
authors.initials: L
authors.lastname: McGee
authors.affiliation: Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique.
authors.forename: Beutel
authors.initials: B
authors.lastname: Sigaùque
authors.affiliation: Centre de Recherche Médicale et Sanitaire, Niamey, Niger.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Collard
authors.affiliation: Medical Research Council, Banjul, The Gambia.|Division of Translational and Systems Medicine, Microbiology and Infection Unit, The University of Warwick, Coventry, UK.|Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Antonio
authors.affiliation: National Institute for Communicable Diseases, Division of the National Health Laboratory Service; and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
authors.forename: Anne
authors.initials: A
authors.lastname: von Gottberg
authors.affiliation: University of Liverpool, Institute of Infection and Global Health, Liverpool, UK.
authors.forename: Neil
authors.initials: N
authors.lastname: French
authors.affiliation: Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
authors.forename: Keith P
authors.initials: KP
authors.lastname: Klugman
authors.affiliation: The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.
authors.forename: Robert S
authors.initials: RS
authors.lastname: Heyderman
authors.affiliation: The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
authors.affiliation: The Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.|University of Liverpool, Institute of Infection and Global Health, Liverpool, UK.
authors.forename: Dean B
authors.initials: DB
authors.lastname: Everett
authors.lastname: For The PAGe Consortium
keywords: Africa; Antibiotic Resistance; Genomics; PAGe; Phylogeny; Pneumococcal Disease; Recombination