Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history

• DOI: 10.1099/mgen.0.000477
• Publication Date: 2021-02-08T23:19:24Z
• Authors: Mireia Coscolla; Sebastien Gagneux; Fabrizio Menardo; Chloé Loiseau; Paula Ruiz-Rodriguez; Sonia Borrell; Isaac Darko Otchere; Adwoa Asante-Poku; Prince Asare; Leonor Sánchez-Busó; Florian Gehre; C. N’Dira Sanoussi; Martin Antonio; Dissou Affolabi; Janet Fyfe; Patrick Beckert; Stefan Niemann; Abraham S. Alabi; Martin P. Grobusch; Robin Kobbe; Julian Parkhill; Christian Beisel; Lukas Fenner; Erik C. Böttger; Conor J. Meehan; Simon R. Harris; Bouke C. de Jong; Dorothy Yeboah-Manu; Daniela Brites
• Keywords: Phylogenomics; Lineage (genetic)

Human tuberculosis (TB) is caused by members of the Mycobacterium complex (MTBC). The MTBC comprises several human-adapted lineages known as M. sensu stricto, well two (L5 and L6) traditionally referred to africanum. Strains L5 L6 are largely limited West Africa for reasons unknown, little their genomic diversity, phylogeography evolution. Here, we analysed genomes 350 320 strains, isolated from patients 21 African countries, plus 5 related that had not been classified into any lineages. Our population phylogeographical analyses showed unclassified belonged a new group propose name lineage 9 (L9). While most likely ancestral distribution L9 was predicted be East Africa, both Eastern part Africa. Moreover, found important differences between strains with respect substructure genetic diversity. Finally, could confirm previous association drug-resistance markers sublineages. Instead, our results indicate drug resistance driven sample bias or geography. In conclusion, study sheds light onto diversity evolutionary history africanum, highlights need consider particularities each understanding ecology epidemiology TB in globally.