Genetic Structuration, Demography and Evolutionary History of Mycobacterium tuberculosis LAM9 Sublineage in the Americas as Two Distinct Subpopulations Revealed by Bayesian Analyses

Type Article
Date 2015-10
Language English
Author(s) Reynaud YannORCID1, Millet Julie1, Rastogi Nalin1
Affiliation(s) 1 : WHO, Supranat TB Reference Lab, TB & Mycobacteria Unit, Inst Pasteur Guadeloupe, Abymes, Guadeloupe, France.
Source Plos One (1932-6203) (Public Library Science), 2015-10 , Vol. 10 , N. 10 , P. e0140911 (15p.)
DOI 10.1371/journal.pone.0140911
WOS© Times Cited 12
Abstract Tuberculosis (TB) remains broadly present in the Americas despite intense global efforts for its control and elimination. Starting from a large dataset comprising spoligotyping (n = 21183 isolates) and 12-loci MIRU-VNTRs data (n = 4022 isolates) from a total of 31 countries of the Americas (data extracted from the SITVIT2 database), this study aimed to get an overview of lineages circulating in the Americas. A total of 17119 (80.8%) strains belonged to the Euro-American lineage 4, among which the most predominant genotypic family belonged to the Latin American and Mediterranean (LAM) lineage (n = 6386, 30.1% of strains). By combining classical phylogenetic analyses and Bayesian approaches, this study revealed for the first time a clear genetic structuration of LAM9 sublineage into two subpopulations named LAM9C1 and LAM9C2, with distinct genetic characteristics. LAM9C1 was predominant in Chile, Colombia and USA, while LAM9C2 was predominant in Brazil, Dominican Republic, Guadeloupe and French Guiana. Globally, LAM9C2 was characterized by higher allelic richness as compared to LAM9C1 isolates. Moreover, LAM9C2 sublineage appeared to expand close to twenty times more than LAM9C1 and showed older traces of expansion. Interestingly, a significant proportion of LAM9C2 isolates presented typical signature of ancestral LAM-RDRio MIRU-VNTR type (224226153321). Further studies based on Whole Genome Sequencing of LAM strains will provide the needed resolution to decipher the biogeographical structure and evolutionary history of this successful family.
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S1 Fig. Geographic distribution of MTB lineages in various countries of Americas (when n>88). Country codes are shown as ISO 3166–1 alpha-3 cod 426 KB Open access
S2 Fig. Geographic distribution of T sublineages in various countries of Americas (when n>31). Country codes are shown as ISO 3166–1 alpha-3 code. 394 KB Open access
S3 Fig. Geographic distribution of H sublineages in various countries of Americas (when n>32). Country codes are shown as ISO 3166–1 alpha-3 code. 336 KB Open access
S4 Fig. Number of subpopulation among LAM9 sublineage by calculation of delta K using the Evanno method. The maximum value is observed at K = 2. 22 KB Open access
S5 Fig. Minimum Spanning Tree illustrating evolutionary relationship between (A) T lineage and (B) H lineage isolates. 515 KB Open access
S1 Table. Description of predominant SITs in this study. Only >3% of a given SIT as compared to their number in each lineage are presented. 12 KB Open access
S2 Table. Allelic richness ± standard deviation (SD) of main MTB lineages and sublineages. Allelic richness is evaluated for 12-loci MITU-VNTRs using a rarefaction procedure (when n>27 per lineage). 15 KB Open access
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