Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype

Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone... The Beijing genotype family is an epidemiologically important sub-group of Mycobacterium tuberculosis. It has been suggested that the high frequency of the Beijing isolates in some areas could be explained by selective advantages. Some evidence suggests that the emerging and most frequently isolated “Typical Beijing” lineage has the ability to circumvent BCG-induced immunity. To investigate the phylogeny of the Beijing genotype of M. tuberculosis , the genome of six Beijing strains from three different countries was sequenced with next-generation sequencing. The phylogeny of these strains was established using single nucleotide polymorphisms (SNPs). The three Typical Beijing strains clustered very tightly in the Beijing phylogeny suggesting that Typical Beijing strains represent a monophyletic lineage and resulted from recent diversification. Typing of 150 M . tuberculosis strains with a subset of the SNPs and comparison of the IS 6110 restriction-fragment length polymorphism (RFLP) patterns of these strains to a database of 1522 Beijing RFLP patterns revealed that about 80% of all Beijing strains belong to the Typical Beijing subclone, which indicates clonal expansion. To identify the genomic changes that are characteristic for all Typical Beijing strains and to reconstruct their most recent common ancestor, the presence of SNPs was assayed in other Beijing strains. We identified 51 SNPs that define the minimal set of polymorphisms for all Typical Beijing strains. Nonsynonymous polymorphisms in genes coding for the regulatory network were over-represented in this set of mutations. We suggest that alterations in the response to environmental signals may have enabled Typical Beijing strains to develop the emerging phenotype. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Infection, Genetics and Evolution Elsevier

Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype

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Publisher
Elsevier
Copyright
Copyright © 2011 Elsevier B.V.
ISSN
1567-1348
DOI
10.1016/j.meegid.2011.01.009
Publisher site
See Article on Publisher Site

Abstract

The Beijing genotype family is an epidemiologically important sub-group of Mycobacterium tuberculosis. It has been suggested that the high frequency of the Beijing isolates in some areas could be explained by selective advantages. Some evidence suggests that the emerging and most frequently isolated “Typical Beijing” lineage has the ability to circumvent BCG-induced immunity. To investigate the phylogeny of the Beijing genotype of M. tuberculosis , the genome of six Beijing strains from three different countries was sequenced with next-generation sequencing. The phylogeny of these strains was established using single nucleotide polymorphisms (SNPs). The three Typical Beijing strains clustered very tightly in the Beijing phylogeny suggesting that Typical Beijing strains represent a monophyletic lineage and resulted from recent diversification. Typing of 150 M . tuberculosis strains with a subset of the SNPs and comparison of the IS 6110 restriction-fragment length polymorphism (RFLP) patterns of these strains to a database of 1522 Beijing RFLP patterns revealed that about 80% of all Beijing strains belong to the Typical Beijing subclone, which indicates clonal expansion. To identify the genomic changes that are characteristic for all Typical Beijing strains and to reconstruct their most recent common ancestor, the presence of SNPs was assayed in other Beijing strains. We identified 51 SNPs that define the minimal set of polymorphisms for all Typical Beijing strains. Nonsynonymous polymorphisms in genes coding for the regulatory network were over-represented in this set of mutations. We suggest that alterations in the response to environmental signals may have enabled Typical Beijing strains to develop the emerging phenotype.

Journal

Infection, Genetics and EvolutionElsevier

Published: Apr 1, 2011

References

  • MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis
    Jacques, P.E.; Gervais, A.L.; Cantin, M.; Lucier, J.F.; Dallaire, G.; Drouin, G.; Gaudreau, L.; Goulet, J.; Brzezinski, R.
  • A marked difference in pathogenesis and immune response induced by different Mycobacterium tuberculosis genotypes
    Lopez, B.; Aguilar, D.; Orozco, H.; Burger, M.; Espitia, C.; Ritacco, V.; Barrera, L.; Kremer, K.; Hernandez-Pando, R.; Huygen, K.; van Soolingen, D.
  • The role of IS 6110 in the evolution of Mycobacterium tuberculosis
    McEvoy, C.R.; Falmer, A.A.; Gey van Pittius, N.C.; Victor, T.C.; van Helden, P.D.; Warren, R.M.
  • Phylogenetic understanding of clonal populations in an era of whole genome sequencing
    Pearson, T.; Okinaka, R.T.; Foster, J.T.; Keim, P.
  • Dynamics of bacterial colonisation in the respiratory tract of patients with cystic fibrosis
    Renders, N.; Verbrugh, H.; Van Belkum, A.
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    Rindi, L.; Lari, N.; Cuccu, B.; Garzelli, C.
  • Functional insights from the molecular modelling of a novel two-component system
    Shrivastava, R.; Das, D.R.; Wiker, H.G.; Das, A.K.
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    Wada, T.; Iwamoto, T.
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