Global Phylogenomic Analysis of NonencapsulatedStreptococcus pneumoniaeReveals a Deep-Branching Classic Lineage That Is Distinct from Multiple Sporadic Lineages
Year: 2014
Type: article
Abstract: 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.
Source: Genome Biology and Evolution
DOI: 10.1093/gbe/evu263
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 Köseoğlu Eser, Donald E Low, Heidi Smith-Vaughan, Andrea Endimiani, Marianne Küffer, Mélanie Dupasquier, Emmanuel Beaudoing, Johann Weber, Rémy Bruggmann, William P Hanage, Julian Parkhill, Lucy J Hathaway, Kathrin Mühlemann, Stephen D Bentley
Institutions: University of Bern, University Hospital of Bern, SIB Swiss Institute of Bioinformatics, Wellcome Sanger Institute, University of Lisbon, Rockefeller University, Radboud University Nijmegen, Radboud University Medical Center, Narodowy Instytut Leków, Mahidol University, University of Oxford, Shoklo Malaria Research Unit, Mahidol Oxford Tropical Medicine Research Unit, Queen's Medical Centre, Swiss Tropical and Public Health Institute, University of Basel, Centers for Disease Control and Prevention, Hacettepe University, Mount Sinai Hospital, Charles Darwin University, Menzies School of Health Research, University of Lausanne, Harvard University, University of Cambridge, Addenbrooke's Hospital
Language: English
Subfield: Epidemiology
Field: Medicine
Domain: Health Sciences
Open Access status: gold
Estimated APC paid: $2,850
Awards: G1119336897, G1683598284, Nutrition, capsule and virulence in Streptococcus pneumoniae, A study of the epidemiology of lower respiratory tract infection and pneumococcal carriage in refugee infants living on the Thai-Burmese border., Wellcome Trust Sanger Institute - generic account for deposition of all core- funded research papers, G9000087992, G9000292789
OpenAlex ID: W2134752242