Global Phylogenomic Analysis of Nonencapsulated Streptococcus pneumoniae Reveals a Deep-Branching Classic Lineage That Is Distinct from Multiple Sporadic Lineages. (24th December 2014)

• Record Type: Journal Article
• Authors: Hilty, Markus; Wüthrich, Daniel; Salter, Susannah J; Engel, Hansjürg; Campbell, Samuel; Sá-Leão, Raquel; de Lencastre, Hermínia; Hermans, Peter; Sadowy, Ewa; Turner, Paul; Chewapreecha, Claire; Diggle, Mathew; Pluschke, Gerd; McGee, Lesley; Eser, Özgen Köseoğlu; Low, Donald E; Smith-Vaughan, Heidi; Endimiani, Andrea; Küffer, Marianne; Dupasquier, Mélanie; Beaudoing, Emmanuel; Weber, Johann; Bruggmann, Rémy; Hanage, William P; Parkhill, Julian; Hathaway, Lucy J; Mühlemann, Kathrin; Bentley, Stephen D
• Editors: Gojobori, Takashi
• Is Part Of: Genome biology and evolution. Volume 6:Number 12(2014:Dec.)
• Page Start: 3281
• Page End: 3294
• Publication Date: 2014-12-24
• Subjects: pneumococcal isolates -- whole-genome sequencing -- comparative genomics -- integrative conjugative elements -- antibiotic nonsusceptibility; Genomics -- Periodicals; Genes -- Periodicals; 572.8605
• DOI: 10.1093/gbe/evu263
• Languages: English
• ISSNs: 1759-6653

Abstract

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.