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ERX075299: Whole Genome Sequencing of Streptococcus pneumoniae
1 ILLUMINA (Illumina Genome Analyzer II) run: 2.4M spots, 371.7M bases, 179.9Mb downloads

Design: Illumina sequencing of library 1713627, constructed from sample accession ERS096009 for study accession ERP000413. This is part of an Illumina multiplexed sequencing run (5737_6). This submission includes reads tagged with the sequence CTTGTACT.
Submitted by: The Wellcome Trust Sanger Institute (SC)
Study: Population structure and diversity in non-encapsulated Streptococcus pneumoniae
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“Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.” Pubmed ID: 25480686. 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 ?-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.
Sample: 0155-sc-2012-02-20T16:31:05Z-1010995
SAMEA1022928 • ERS096009 • All experiments • All runs
Name: 1713627
Instrument: Illumina Genome Analyzer II
Strategy: WGS
Selection: RANDOM
Layout: PAIRED
Construction protocol: Standard
Spot descriptor:
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Runs: 1 run, 2.4M spots, 371.7M bases, 179.9Mb
Run# of Spots# of BasesSizePublished


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