Journal article
Comparative Genomic Analyses of Seventeen Streptococcus pneumoniae Strains: Insights into the Pneumococcal Supragenome
Journal of bacteriology, v 189(22), pp 8186-8195
Nov 2007
PMID: 17675389
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
The distributed-genome hypothesis (DGH) states that pathogenic bacteria possess a supragenome that is much larger than the genome of any single bacterium and that these pathogens utilize genetic recombination and a large, noncore set of genes as a means of diversity generation. We sequenced the genomes of eight nasopharyngeal strains of S
treptococcus pneumoniae
isolated from pediatric patients with upper respiratory symptoms and performed quantitative genomic analyses among these and nine publicly available pneumococcal strains. Coding sequences from all strains were grouped into 3,170 orthologous gene clusters, of which 1,454 (46%) were conserved among all 17 strains. The majority of the gene clusters, 1,716 (54%), were not found in all strains. Genic differences per strain pair ranged from 35 to 629 orthologous clusters, with each strain's genome containing between 21 and 32% noncore genes. The distribution of the orthologous clusters per genome for the 17 strains was entered into the finite-supragenome model, which predicted that (i) the
S. pneumoniae
supragenome contains more than 5,000 orthologous clusters and (ii) 99% of the orthologous clusters (∼3,000) that are represented in the
S. pneumoniae
population at frequencies of ≥0.1 can be identified if 33 representative genomes are sequenced. These extensive genic diversity data support the DGH and provide a basis for understanding the great differences in clinical phenotype associated with various pneumococcal strains. When these findings are taken together with previous studies that demonstrated the presence of a supragenome for
Streptococcus agalactiae
and
Haemophilus influenzae
, it appears that the possession of a distributed genome is a common host interaction strategy.
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Details
- Title
- Comparative Genomic Analyses of Seventeen Streptococcus pneumoniae Strains: Insights into the Pneumococcal Supragenome
- Creators
- N. Luisa Hiller - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesBenjamin Janto - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesJustin S Hogg - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesRobert Boissy - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesSusan Yu - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesEvan Powell - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesRandy Keefe - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesNathan E Ehrlich - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesKai Shen - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesJay Hayes - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesKaren Barbadora - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesWilliam Klimke - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesDmitry Dernovoy - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesTatiana Tatusova - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesJulian Parkhill - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesStephen D Bentley - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesJ. Christopher Post - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesGarth D Ehrlich - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic SciencesFen Z Hu - Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences
- Publication Details
- Journal of bacteriology, v 189(22), pp 8186-8195
- Publisher
- American Society for Microbiology (ASM)
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Microbiology and Immunology
- Web of Science ID
- WOS:000250991300028
- Scopus ID
- 2-s2.0-36549020646
- Other Identifier
- 991014878056204721
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- Collaboration types
- Domestic collaboration
- International collaboration
- Web of Science research areas
- Microbiology