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Comparative Genomic Analysis of Mycobacterium Tuberculosis Complex Strains from Ghana: West Africa Is the Hot-Spot of Mycobacterium Tuberculosis Complex Diversity

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Description

Tuberculosis (TB), caused by the Mycobacterium tuberculosis complex (MTBC) has plagued mankind since recorded history and remains the leading cause of adult mortality globally yet treatable. Human TB is mainly caused by the globally distributed M. tuberculosis sensu stricto (Mtbss) and West Africa restricted M. africanum (Maf), but most global efforts for TB control largely concentrate on Mtbss. The reportedly high genetic homology of the MTBC and the observed relative attenuation of Maf compared to Mtbss have contributed to this neglect. However, Maf remains an important pathogen in West Africa especially Ghana (harbouring the two lineages (L) 5 and 6 in substantial numbers) where it causes about 20% of TB. This study sought to determine the genomic diversity among MTBC L4, L5 and L6 in Ghana and the potential functional implications of the observed genomic variability A collection of clinical MTBC genomes (L4, L5 and L6) from Ghana were analysed by phylogenetic analysis, average nucleotide identities (ANI) as well as pairwise nucleotide diversity (π) and averaged pairwise dN/dS among gene of 8 different functional categories. Furthermore, T cell antigenic variation was compared between L5 and L6 in addition to comparative lineage pan-genome analysis and core genome mutation. Lastly, drug resistance and mutation analysis of drug resistance associated targets were carried out. The MTBC L6 and L5 were found to be different bugs even though they do not qualify to be individual species of the MTBC. T cell epitopes of L5 were found to be relatively highly conserved and indication of adaptation to a specific host. The diverse T cell epitopes of L6 is reminiscent of a pathogen with wide host range indicating it may not be human-restricted pathogen. The L5 and L6 exhibited peculiar genomic features which can negatively impact the applicability of some control tools. It was also found that diversity of the MTBC has potential implications for epistatic interaction between drug resistance conferring and compensatory mutations, which could affect the emergence and transmission of drug resistance. Therefore, any future efforts towards effective control of TB must take into consideration the diversity within the entire MTBC

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