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

Mireia Coscolla, Sebastien Gagneux, Fabrizio Menardo, Chloe Loiseau, Paula Ruiz-Rodriguez, Sonia Borrell, Isaac Darko Otchere, Adwoa Asante-Poku, Prince Asare, Leonor Sanchez-Buso, Florian Gehre, C. N'Dira Sanoussi, Martin Antonio, Dissou Affolabi, Janet Fyfe, Patrick Beckert, Stefan Niemann, Abraham S. Alabi, Martin P. Grobusch, Robin KobbeJulian Parkhill, Christian Beisel, Lukas Fenner, Erik C. Bottger, Conor J. Meehan, Simon R. Harris, Bouke C. de Jong, Dorothy Yeboah-Manu, Daniela Brites

Research output: Contribution to journalA1: Web of Science-articlepeer-review

2 Downloads (Pure)


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

Original languageEnglish
Article number000477
JournalMicrobial Genomics
Issue number2
Number of pages14
Publication statusPublished - 2021


  • diversity
  • evolution
  • genome
  • mycobacteria
  • Mycobacterium africanum
  • Mycobacterium tuberculosis
  • TOOL
  • DNA


Dive into the research topics of 'Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history'. Together they form a unique fingerprint.

Cite this