Bayesian population structure analysis reveals presence of phylogeographically specific sublineages within previously ill-defined T group of Mycobacterium tuberculosis

Type Article
Date 2017-02
Language English
Author(s) Reynaud Yann1, Zheng Chao1, 2, Wu Guihui3, Sun Qun2, Rastogi Nalin1
Affiliation(s) 1 : Inst Pasteur Guadeloupe, TB & Mycobacteria Unit, WHO Supranat TB Reference Lab, Morne Joliviere Abymes, Guadeloupe, France.
2 : Sichuan Univ, Coll Life Sci, Chengdu, Sichuan, Peoples R China.
3 : Chengdu Publ Hlth Clin Ctr, Chengdu, Sichuan, Peoples R China.
Source Plos One (1932-6203) (Public Library Science), 2017-02 , Vol. 12 , N. 2 , P. e0171584 (13p.)
DOI 10.1371/journal.pone.0171584
WOS© Times Cited 4
Abstract 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 phylogeographically 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 Sequencing (WGS).
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S1 Fig. MST illustrating evolutionary reliationship between M. tuberculosis T sublineages using spoligotypes markers. 371 KB Open access
S2 Fig. Selection of appropriate K value by calculation of (A) ln P(D|K) and (B) delta K (Evanno method) for STRUCTURE analysis, and (C) DIC for TESS analysis. Congruent value is observed at ... 84 KB Open access
S3 Fig. TESS Ancestry coefficient (Q-matrix) of M. tuberculosis T sublineages displayed spatially by universal kriging. 622 KB Open access
S4 Fig. MST based on 24-loci MIRU-VNTR illustrating evolutionary relationships of the M. tuberculosis T sublineage isolates (n = 607) prelabeled as T1 to T8 based on previous TESS analysis. 276 KB Open access
S5 Fig. UPGMA based on 24-loci MIRU-VNTR of the M. tuberculosis T isolates (n = 607) compared to MIRU-VNTRplus database. 876 KB Open access
S1 Table. Global dataset used in this study for the 607 M. tuberculosis T isolates. Countries names are defined by ISO 3166–1 alpha-3 code. 153 KB Open access
S2 Table. Dunn’s test results. 11 KB Open access
S3 Table. Percentage of allele copy number of 24-loci MIRU-VNTR markers in T1 to T8 M. tuberculosis isolates. ND: not done. 23 KB Open access
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