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Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis
- Source :
- PLoS ONE, Vol 12, Iss 2, p e0171584 (2017), PLoS ONE, PLoS ONE, Public Library of Science, 2017, 12 (2), pp.e0171584. ⟨10.1371/journal.pone.0171584⟩, Plos One (1932-6203) (Public Library Science), 2017-02, Vol. 12, N. 2, P. e0171584 (13p.)
- Publication Year :
- 2017
- Publisher :
- Public Library of Science (PLoS), 2017.
-
Abstract
- International audience; Mycobacterium tuberculosis genetic structure, and evolutionary history have been studied for years by several genotyping approaches, but delineation of a few sublineages remains controversial and needs better characterization. This is particularly the case of T group within lineage 4 (L4) which was first described using spoligotyping to pool together a number of strains with ill-defined signatures. Although T strains were not traditionally considered as a real phylogenetic group, they did contain a few phylogenetically meaningful sublineages as shown using SNPs. We therefore decided to investigate if this observation could be corroborated using other robust genetic markers. We consequently made a first assessment of genetic structure using 24-loci MIRU-VNTRs data extracted from the SITVIT2 database (n = 607 clinical isolates collected in Russia, Albania, Turkey, Iraq, Brazil and China). Combining Minimum Spanning Trees and Bayesian population structure analyses (using STRUCTURE and TESS softwares), we distinctly identified eight tentative phylogenetic groups (T1-T8) with a remarkable correlation with geographical origin. We further compared the present structure observed with other L4 sublineages (n = 416 clinical isolates belonging to LAM, Haarlem, X, S sublineages), and showed that 5 out of 8 T groups seemed phylogeographi-cally well-defined as opposed to the remaining 3 groups that partially mixed with other L4 isolates. These results provide with novel evidence about phylogeographically specificity of a proportion of ill-defined T group of M. tuberculosis. The genetic structure observed will now be further validated on an enlarged worldwide dataset using Whole Genome Sequenc-ing (WGS).
- Subjects :
- Evolutionary Genetics
0301 basic medicine
MESH: Mycobacterium tuberculosis
Lineage (evolution)
Gene Dosage
lcsh:Medicine
Minisatellite Repeats
Plant Science
Plant Roots
MESH: Gene Dosage
Geographical Locations
MESH: Genotype
MESH: Phylogeny
lcsh:Science
Phylogeny
MESH: Evolution, Molecular
Data Management
Multidisciplinary
Geography
Phylogenetic tree
Plant Anatomy
3. Good health
Actinobacteria
Phylogenetics
Phylogeography
MESH: Multilocus Sequence Typing
Biogeography
MESH: Phylogeography
Genetic structure
Research Article
Computer and Information Sciences
China
Genotyping
Asia
Genotype
MESH: Bayes Theorem
030106 microbiology
Biology
Research and Analysis Methods
Evolution, Molecular
Computer Software
Mycobacterium tuberculosis
03 medical and health sciences
Genetics
Evolutionary Systematics
Molecular Biology Techniques
Molecular Biology
Alleles
Taxonomy
Whole genome sequencing
Evolutionary Biology
Bacteria
Population Biology
MESH: Alleles
Ecology and Environmental Sciences
lcsh:R
Organisms
Biology and Life Sciences
Bayes Theorem
biology.organism_classification
[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology
Root Structure
030104 developmental biology
Genetic marker
Evolutionary biology
People and Places
MESH: Minisatellite Repeats
Earth Sciences
lcsh:Q
Population Genetics
Multilocus Sequence Typing
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 12
- Issue :
- 2
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....dd20c8d29c58f581db13a0a5f8861dfa