Local adaptive evolution of two distinct clades of Beijing and T families of Mycobacterium tuberculosis in Chongqing: a Bayesian population structure and phylogenetic study

Type Article
Date 2020-06
Language English
Author(s) Liang Peng-Kuan1, Zheng Chao1, 2, 3, Xu Xiao-Fang1, Zhao Zhe-Ze1, 4, 5, Zhao Chang-Song1, Li Chang-He1, Couvin DavidORCID6, Reynaud Yann6, Zozio Thierry6, Rastogi Nalin6, Sun Qun1
Affiliation(s) 1 : Sichuan Univ, Coll Life Sci, Minist Educ, Key Lab Bioresources & Ecoenvironm, Chengdu 610065, Sichuan, Peoples R China.
2 : SUSTC, Shenzhen Inst Resp Dis,Clin Med Coll 2, Jinan Univ,Shenzhen Peoples Hos,Affiliated Hosp 1, Bacteriol & Antibacterial Resistance Surveillance, Shenzhen 518020, Peoples R China.
3 : Jinan Univ, Integrated Chinese & Western Med Postdoctoral Res, Guangzhou 510632, Peoples R China.
4 : Chinese Univ Hong Kong, Sch Life Sci, Shatin, Hong Kong, Peoples R China.
5 : Chinese Univ Hong Kong, Sch Life Sci, State Key Lab Agrobiotechnol, Hong Kong, Peoples R China.
6 : Inst Pasteur Guadeloupe, Unite TB & Mycobacteries, WHO Supranatl TB Reference Lab, Abymes, Guadeloupe, France.
Source Infectious Diseases Of Poverty (2095-5162) (Bmc), 2020-06 , Vol. 9 , N. 1 , P. 59 (9p.)
DOI 10.1186/s40249-020-00674-7
WOS© Times Cited 2
Keyword(s) Mycobacterium tuberculosis, Local adaptive evolution, MIRU-VNTR, Bayesian population structure analysis, Phylogenetic analysis
Abstract Background Beijing sub-pedigree 2 (BSP2) and T sub-lineage 6 (TSL6) are two clades belonging to Beijing and T family of Mycobacterium tuberculosis (MTB), respectively, defined by Bayesian population structure analysis based on 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR). Globally, over 99% of BSP2 and 89% of TSL6 isolates were distributed in Chongqing, suggesting their possible local adaptive evolution. The objective of this paper is to explore whether BSP2 and TSL6 originated by their local adaptive evolution from the specific isolates of Beijing and T families in Chongqing. Methods The genotyping data of 16 090 MTB isolates were collected from laboratory collection, published literatures and SITVIT database before subjected to Bayesian population structure analysis based on 24-loci MIRU-VNTR. Spacer Oligonucleotide Forest (Spoligoforest) and 24-loci MIRU-VNTR-based minimum spanning tree (MST) were used to explore their phylogenetic pathways, with Bayesian demographic analysis for exploring the recent demographic change of TSL6. Results Phylogenetic analysis suggested that BSP2 and TSL6 in Chongqing may evolve from BSP4 and TSL5, respectively, which were locally predominant in Tibet and Jiangsu, respectively. Spoligoforest showed that Beijing and T families were genetically distant, while the convergence of the MIRU-VNTR pattern of BSP2 and TSL6 was revealed by WebLogo. The demographic analysis concluded that the recent demographic change of TSL6 might take 111.25 years. Conclusions BSP2 and TSL6 clades might originate from BSP4 and TSL5, respectively, by their local adaptive evolution in Chongqing. Our study suggests MIRU-VNTR be combined with other robust markers for a more comprehensive genotyping approach, especially for families of clades with the same MIRU-VNTR pattern.
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Publisher's official version 9 2 MB Open access
Table S1. The source of available data in this study. 67 KB Open access
Table S2. The Spoligotype International Type (SIT) information. 990 KB Open access
Table S3. The 24-loci MIRU-VNTR data of 2161 isolates for MST building. 2 MB Open access
Table S4. Dataset used in the MST of T and Beijing families for the 1742 MTB isolates. 1 MB Open access
Table S5. Repeat number of 24-loci MIRU-VNTR loci in MTB isolates of clades BSP2 and TSL6. 578 KB Open access
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Liang Peng-Kuan, Zheng Chao, Xu Xiao-Fang, Zhao Zhe-Ze, Zhao Chang-Song, Li Chang-He, Couvin David, Reynaud Yann, Zozio Thierry, Rastogi Nalin, Sun Qun (2020). Local adaptive evolution of two distinct clades of Beijing and T families of Mycobacterium tuberculosis in Chongqing: a Bayesian population structure and phylogenetic study. Infectious Diseases Of Poverty, 9(1), 59 (9p.). Publisher's official version : https://doi.org/10.1186/s40249-020-00674-7 , Open Access version : https://archimer.ifremer.fr/doc/00771/88284/