SRA STUDY
SRA Study Id ERP000152  (Link to NCBI )
Study Title Genetic diversity on Streptococcus pneumoniae in Malawi 2
SRA Experiments
SRA Experiment Id ERX2007491  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201493P
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007481  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201483N
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007021  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT206813I
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007483  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201485P
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2004260  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201501V
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007490  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201492O
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2005207  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201472K
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2005205  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201470I
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2005204  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201469P
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2004258  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201499V
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007489  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201491N
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007016  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT206808L
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007005  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT206762O
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007006  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT206763P
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007007  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT206764Q
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007022  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT206814J
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007023  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT206815K
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007486  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201488S
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2005212  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201477P
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
   
SRA Experiment Id ERX2007487  (Link to NCBI )
Experiment Title Illumina Genome Analyzer II paired end sequencing
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name NT201489T
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
Study Abstract BACKGROUND: Carriage of either single or multiple pneumococcal serotypes (multiple carriage) is a prerequisite for developing invasive pneumococcal disease. However, despite the reported high rates of pneumococcal carriage in Malawi, no data on carriage of multiple serotypes has been reported previously. Our study provides the first description of the prevalence of multiple pneumococcal carriage in Malawi. METHODS: The study was conducted in Blantyre and Karonga districts in Malawi, from 2008 to 2012. We recruited 116 children aged 0-13 years. These children were either HIV-infected (N = 44) or uninfected (N = 72). Nasopharyngeal samples were collected using sterile swabs. Pneumococcal serotypes in the samples were identified by microarray. Strains that could not be typed by microarray were sequenced to characterise possible genetic alterations within the capsular polysaccharide (CPS) locus. RESULTS: The microarray identified 179 pneumococcal strains (from 116 subjects), encompassing 43 distinct serotypes and non-typeable (NT) strains. Forty per cent (46/116) of children carried multiple serotypes. Carriage of vaccine type (VT) strains was higher (p = 0.028) in younger (0-2 years) children (71 %, 40/56) compared to older (3-13 years) children (50 %, 30/60). Genetic variations within the CPS locus of known serotypes were observed in 19 % (34/179) of the strains identified. The variants included 13-valent pneumococcal conjugate vaccine (PCV13) serotypes 6B and 19A, and the polysaccharide vaccine serotype 20. Serotype 6B variants were the most frequently isolated (47 %, 16/34). Unlike the wild type, the CPS locus of the 6B variants contained an insertion of the licD-family phosphotransferase gene. The CPS locus of 19A- and 20-variants contained an inversion in the sugar-biosynthesis (rmlD) gene and a 717 bp deletion within the transferase (whaF) gene, respectively. CONCLUSIONS: The high multiple carriage in Malawian children provides opportunities for genetic exchange through horizontal gene transfer. This may potentially lead to CPS locus variants and vaccine escape. Variants reported here occurred naturally, however, PCV13 introduction could exacerbate the CPS genetic variations. Further studies are therefore recommended to assess the invasive potential of these variants and establish whether PCV13 would offer cross-protection. We have shown that younger children (0-2 years) are a reservoir of VT serotypes, which makes them an ideal target for vaccination. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/about/who-we-are/policies/open-access-science http://www.sanger.ac.uk/resources/downloads/bacteria/
Alias The sequencing of 84 isolates of Streptococcus pneumoniae to characterise antibiotic resistance.-sc-2010-04-06
External Id PRJEB2098