F1000Research (Mar 2021)
Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim [version 2; peer review: 3 approved]
- Fabrizio Menardo,
- Liliana K. Rutaihwa,
- Michaela Zwyer,
- Sonia Borrell,
- Iñaki Comas,
- Emilyn Costa Conceição,
- Mireia Coscolla,
- Helen Cox,
- Moses Joloba,
- Horng-Yunn Dou,
- Julia Feldmann,
- Lukas Fenner,
- Janet Fyfe,
- Qian Gao,
- Darío García de Viedma,
- Alberto L. Garcia-Basteiro,
- Sebastian M. Gygli,
- Jerry Hella,
- Hellen Hiza,
- Levan Jugheli,
- Lujeko Kamwela,
- Midori Kato-Maeda,
- Qingyun Liu,
- Serej D. Ley,
- Chloe Loiseau,
- Surakameth Mahasirimongkol,
- Bijaya Malla,
- Prasit Palittapongarnpim,
- Niaina Rakotosamimanana,
- Voahangy Rasolofo,
- Miriam Reinhard,
- Klaus Reither,
- Mohamed Sasamalo,
- Rafael Silva Duarte,
- Christophe Sola,
- Philip Suffys,
- Karla Valeria Batista Lima,
- Dorothy Yeboah-Manu,
- Christian Beisel,
- Daniela Brites,
- Sebastien Gagneux
Affiliations
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Liliana K. Rutaihwa
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Michaela Zwyer
- University of Basel, Basel, Switzerland
- Sonia Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Iñaki Comas
- Institute of Biomedicine of Valencia, Valencia, Spain
- Emilyn Costa Conceição
- Instituto de Microbiologia, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Mireia Coscolla
- I2SysBio, University of Valencia, Valencia, Spain
- Helen Cox
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Moses Joloba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
- Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institute, Zhunan, Taiwan
- Julia Feldmann
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Lukas Fenner
- University of Basel, Basel, Switzerland
- Janet Fyfe
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia
- Qian Gao
- Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
- Darío García de Viedma
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Alberto L. Garcia-Basteiro
- Barcelona Institute for Global Health, Barcelona, Spain
- Sebastian M. Gygli
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Jerry Hella
- Ifakara Health Institute, Bagamoyo, Tanzania
- Hellen Hiza
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Levan Jugheli
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Lujeko Kamwela
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Midori Kato-Maeda
- School of Medicine, University of California, San Francisco, USA
- Qingyun Liu
- Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
- Serej D. Ley
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
- Chloe Loiseau
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Surakameth Mahasirimongkol
- Department of Microbiology, Mahidol University, Bangkok, Thailand
- Bijaya Malla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Prasit Palittapongarnpim
- Department of Microbiology, Mahidol University, Bangkok, Thailand
- Niaina Rakotosamimanana
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Voahangy Rasolofo
- Institut Pasteur de Madagascar, Antananarivo, Madagascar
- Miriam Reinhard
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Klaus Reither
- Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Mohamed Sasamalo
- University of Basel, Basel, Switzerland
- Rafael Silva Duarte
- Instituto de Microbiologia, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Christophe Sola
- Université Paris-Saclay, Paris, France
- Philip Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Karla Valeria Batista Lima
- Instituto Evandro Chagas, Ananindeua, Brazil
- Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- DOI
- https://doi.org/10.12688/f1000research.28318.2
- Journal volume & issue
-
Vol. 10
Abstract
Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around 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. Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics. For L1 we identified 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. Conclusions: 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.
