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Title: Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages
Authors: Markus Hilty
Daniel Wüthrich
Susannah J. Salter
Hansjürg Engel
Samuel Campbell
Raquel Sá-Leão
Hermínia De Lencastre
Peter Hermans
Ewa Sadowy
Paul Turner
Claire Chewapreecha
Mathew Diggle
Gerd Pluschke
Lesley McGee
Özgen Köseoʇlu Eser
Donald E. Low
Heidi Smith-Vaughan
Andrea Endimiani
Marianne Kü Ffer
Mélanie Dupasquier
Emmanuel Beaudoing
Johann Weber
Rémy Bruggmann
William P. Hanage
Julian Parkhill
Lucy J. Hathaway
Kathrin Mü Hlemann
Stephen D. Bentley
University of Bern
UniversitatsSpital Bern
Swiss Institute of Bioinformatics
Wellcome Trust Sanger Institute
Instituto de Tecnologia Quimica e Biologica - Univesidade Nova de Lisboa
Rockefeller University
Radboud University Nijmegen
National Medicines Institute, Warsaw
Mahidol University
Nuffield Department of Clinical Medicine
Queen's Medical Centre
Universitat Basel
National Center for Immunization and Respiratory Diseases
Hacettepe Universitesi
Mount Sinai Hospital of University of Toronto
Menzies School of Health Research
Universitat Lausanne Schweiz
Harvard School of Public Health
University of Cambridge
Keywords: Agricultural and Biological Sciences;Biochemistry, Genetics and Molecular Biology
Issue Date: 1-Jan-2014
Citation: Genome Biology and Evolution. Vol.6, No.12 (2014), 3281-3294
Abstract: © The Author(s) 2014. The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence factor and is targeted by pneumococcal conjugate vaccines (PCV). However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also been isolated globally, mainly in carriage studies. It is unknown if non-Ec-Sp evolve sporadically, if they have high antibiotic nonsusceptiblity rates and a unique, specific gene content. Here, whole-genome sequencing of 131 non-Ec-Sp isolates sourced from 17 different locations around the world was performed. Results revealed a deep-branching classic lineage that is distinct from multiple sporadic lineages. The sporadic lineages clustered with a previously sequenced, global collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic lineage is comprised mainly of the frequently identified multilocus sequences types (STs) ST344 (n = 39) and ST448 (n = 40). All ST344 and nine ST448 isolates had high nonsusceptiblity rates to β-lactams and other antimicrobials. Analysis of the accessory genome reveals that the classic non-Ec-Sp contained an increased number of mobile elements, than Ec-Sp and sporadic non-Ec-Sp. Performing adherence assays to human epithelial cells for selected classic and sporadic non-Ec-Sp revealed that the presence of a integrative conjugative element (ICE) results in increased adherence to human epithelial cells (P = 0.005). In contrast, sporadic non-Ec-Sp lacking the ICE had greater growth in vitro possibly resulting in improved fitness. In conclusion, non-Ec-Sp isolates from the classic lineage have evolved separately. They have spread globally, are well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due to continued use of PCV, non-Ec-Sp may become more prevalent.
ISSN: 17596653
Appears in Collections:Scopus 2011-2015

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