Local adaptive evolution of two distinct clades of Beijing and T families of Mycobacterium tuberculosis in Chongqing: a Bayesian population structure and phylogenetic study
|Author(s)||Liang Peng-Kuan1, Zheng Chao1, 2, 3, Xu Xiao-Fang1, Zhao Zhe-Ze1, 4, 5, Zhao Chang-Song1, Li Chang-He1, Couvin David6, 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.)|
|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.|