Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests different ecological niches

Isaac Darko Otchere; Mireia Coscollá; Leonor Sánchez-Busó; Adwoa Asante-Poku; Daniela Brites; Chloé Loiseau; Conor Joseph Meehan; Stephen Osei-Wusu; Audrey G. Forson; Clement Laryea; Abdallah Iddrisu Yahayah; Akosua Baddoo; Gloria Akosua Ansa; Samuel Yaw Aboagye; Prince Philip Ankapong Asare; Sònia Borrell; Florian Gehre; Patrick Beckert; Thomas Andreas Kohl; N'Dira Sanoussi; Christian Beisel; Martín Antonio; Stefan Niemann; Bouke Catherine de Jong; Julian Parkhill; Simon R. Harris; Sébastien Gagneux; Dorothy Yeboah‐Manu

doi:10.1038/s41598-018-29620-2

GenomicsScientific ReportsJul 20, 2018

Peer-reviewed journal article

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests different ecological niches

Isaac Darko Otchere iD, Mireia Coscollá iD, Leonor Sánchez-Busó iD, Adwoa Asante-Poku iD, Daniela Brites iD, Chloé Loiseau iD, Conor Joseph Meehan iD, Stephen Osei-Wusu iD, Audrey G. Forson iD, Clement Laryea iD, Abdallah Iddrisu Yahayah, Akosua Baddoo, Gloria Akosua Ansa iD, Samuel Yaw Aboagye iD, Prince Philip Ankapong Asare iD, Sònia Borrell iD, Florian Gehre iD, Patrick Beckert, Thomas Andreas Kohl iD, N'Dira Sanoussi iD, Christian Beisel iD, Martín Antonio iD, Stefan Niemann iD, Bouke Catherine de Jong iD, Julian Parkhill iD, , Dorothy Yeboah‐Manu iD

Abstract

Mycobacterium africanum (Maf) causes up to half of human tuberculosis in West Africa, but little is known on this pathogen. We compared the genomes of 253 Maf clinical isolates from Ghana, including both L5 and L6. We found that the genomic diversity of L6 was higher than in L5, and the selection pressures differed between both groups. Regulatory proteins appeared to evolve neutrally in L5 but under purifying selection in L6. Conversely, human T cell epitopes were under purifying selection in L5, but under positive selection in L6. Although only 10% of the T cell epitopes were variable, mutations were mostly lineage-specific. Our findings indicate that Maf L5 and L6 are genomically distinct, possibly reflecting different ecological niches.

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