The following elements will have their visibility changed, please review the list before confirming the visibility change

Study

Study Name: Genetic diversity of Streptococcus pneumoniae strains from Malawi

Projects

Biosamples

Organisms

Biosamples: 0 Seq. Projects: 20
STUDY INFORMATION
GOLD Study ID Gs0121147
Study Name Genetic diversity of Streptococcus pneumoniae strains from Malawi
Other Names
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
SRA Studies
SRA Study Id ERP000152
Study Title Genetic diversity on Streptococcus pneumoniae in Malawi 2
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/
  
Legacy ER Study ID
Legacy GOLD ID
Added By JGI automated process on 2016-06-28
Last Modified By
PI
Description
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study No
Publication
Is GEBA
Is HMP
ECOSYSTEM CLASSIFICATION
Ecosystem
Ecosystem Category
Ecosystem Type
Ecosystem Subtype
Specific Ecosystem
STUDY COMPOSITION
Number of Biosamples 0
Number of Organisms 20
Number of Seq Projects 20
Number of Analysis Projects 20
Number of Related Studies 0

 

 

  You are going to add the following user to ALL Sequencing Projects, Biosamples and Analysis Projects that
sit under this study (a cascading permission update).

 

Contact Name/Email:

Do you want to continue?

 

 

  You are going to remove permissions for the following user to all Sequencing Projects,
Biosamples and Analysis Projects under this study.

 

Contact Name/Email:

Do you want to continue?