Deciphering the recent phylogenetic expansion of the originally deeply rooted Mycobacterium tuberculosis lineage 7. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Yimer, Solomon; Namouchi, Amine; Zegeye, Ephrem; Holm-Hansen, Carol; Norheim, Gunnstein; Abebe, Markos; Aseffa, Abraham; Tønjum, Tone
• Is Part Of: BMC evolutionary biology. Volume 16:Issue 1(2016)
• Page Start: 1
• Page End: 10
• Publication Date: 2016-12
• Subjects: Mycobacterium tuberculosis -- Lineage 7 -- Whole genome sequencing -- Single nucleotide polymorphism -- Mutations -- 3R genes -- Amhara Region -- Ethiopia; Evolution (Biology) -- Periodicals; 576.805
• DOI: 10.1186/s12862-016-0715-z
• Languages: English
• ISSNs: 1471-2148

Abstract

Abstract Background A deeply rooted phylogenetic lineage ofMycobacterium tuberculosis (M. tuberculosis ) termed lineage 7 was discovered in Ethiopia. Whole genome sequencing of 30 lineage 7 strains from patients in Ethiopia was performed. Intra-lineage genome variation was defined and unique characteristics identified with a focus on genes involved in DNA repair, recombination and replication (3R genes). Results More than 800 mutations specific toM. tuberculosis lineage 7 strains were identified. The proportion of non-synonymous single nucleotide polymorphisms (nsSNPs) in 3R genes was higher after the recent expansion ofM. tuberculosis lineage 7 strain started. The proportion of nsSNPs in genes involved in inorganic ion transport and metabolism was significantly higher before the expansion began. A total of 22346 bp deletions were observed. Lineage 7 strains also exhibited a high number of mutations in genes involved in carbohydrate transport and metabolism, transcription, energy production and conversion. Conclusions We have identified unique genomic signatures of the lineage 7 strains. The high frequency of nsSNP in 3R genes after the phylogenetic expansion may have contributed to recent variability and adaptation. The abundance of mutations in genes involved in inorganic ion transport and metabolism before the expansion period may indicate an adaptive response of lineage 7 strains to enable survival, potentially under environmental stress exposure. As lineage 7 strains originally were phylogenetically deeply rooted, this may indicate fundamental adaptive genomic pathways affecting the fitness ofM. tuberculosis as a species.