Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim

Abstract Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC), causing tuberculosis (TB) in humans. L1 and L3 are endemic to the Rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1...

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Published in:bioRxiv 2020-10
Main Authors: Menardo, Fabrizio, Rutaihwa, Liliana K, Zwyer, Michaela, Borrell, Sonia, Comas, Iñaki, Emilyn Costa Conceição, Coscolla, Mireia, Cox, Helen, Moses Joloba, Dou, Horng-Yunn, Feldmann, Julia, Fenner, Lukas, Fyfe, Janet, Gao, Qian, Darío García De Viedma, Garcia-Basteiro, Alberto L, Gygli, Sebastian M, Hella, Jerry, Hiza, Hellen, Levan Jugheli, Kamwela, Lujeko, Kato-Maeda, Midori, Liu, Qingyun, Ley, Serej D, Loiseau, Chloe, Mahasirimongkol, Surakameth, Malla, Bijaya, Palittapongarnpim, Prasit, Rakotosamimanana, Niaina, Rasolofo, Voahangy, Reinhard, Miriam, Reither, Klaus, Sasamalo, Mohamed, Rafael Silva Duarte, Sola, Christophe, Suffys, Philip, Batista Lima, Karla Valeria, Yeboah-Manu, Dorothy, Beisel, Christian, Brites, Daniela, Gagneux, Sebastien
Format: Article
Language:English
Subjects:
Genetic diversity
Genomes
Genomics
Mycobacterium tuberculosis
Tuberculosis
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Summary:Abstract Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC), causing tuberculosis (TB) in humans. L1 and L3 are endemic to the Rim of the Indian Ocean, the region that accounts for most of the world’s new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Here we analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We show that South Asia played a central role in the dispersion of these two lineages to neighboring regions. Moreover, we found that L1 exhibits signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://github.com/fmenardo/MTBC_L1_L3
ISSN:2692-8205
DOI:10.1101/2020.10.20.346866