Whole genome sequence analysis of Mycobacterium suricattae

Anzaan Dippenaar,Sven David Charles Parsons,Samantha Leigh Sampson,Ruben Gerhard Van Der Merwe,Julian Ashley Drewe,Abdallah Musa Abdallah,Kabengele Keith Siame,Nicolaas Claudius Gey Van Pittius,Paul David Van Helden,Arnab Pain,Robin Mark Warren

doi:10.1016/j.tube.2015.10.001

Abstract

Tuberculosis occurs in various mammalian hosts and is caused by a range of different lineages of the Mycobacterium tuberculosis complex (MTBC). A recently described member, Mycobacterium suricattae, causes tuberculosis in meerkats (Suricata suricatta) in Southern Africa and preliminary genetic analysis showed this organism to be closely related to an MTBC pathogen of rock hyraxes (Procavia capensis), the dassie bacillus. Here we make use of whole genome sequencing to describe the evolution of the genome of M.suricattae, including known and novel regions of difference, SNPs and IS6110 insertion sites. We used genome-wide phylogenetic analysis to show that M.suricattae clusters with the chimpanzee bacillus, previously isolated from a chimpanzee (Pan troglodytes) in West Africa. We propose an evolutionary scenario for the Mycobacterium africanum lineage 6 complex, showing the evolutionary relationship of M.africanum and chimpanzee bacillus, and the closely related members M.suricattae, dassie bacillus and Mycobacterium mungi.

Highlights

60 The Mycobacterium tuberculosis complex (MTBC) comprises genotypically and phenotypically61 distinct lineages which have evolved through clonal expansion from a common progenitor [1].62 Much of this evolution has occurred through genomic loss and such genetic regions of difference63 (RDs) can be used to distinguish between these lineages [2]
We propose an evolutionary scenario for the M. africanum
163 with the dassie bacillus [6,8]. These markers were confirmed by the Whole genome sequencing (WGS) data analysed in our 164 study and includes a single nucleotide deletion (SND) in Rv0911 (Rv0911389), a single nucleotide polymorphisms (SNPs) in Rv1510

Summary

Introduction

60 The Mycobacterium tuberculosis complex (MTBC) comprises genotypically and phenotypically61 distinct lineages which have evolved through clonal expansion from a common progenitor [1].62 Much of this evolution has occurred through genomic loss and such genetic regions of difference63 (RDs) can be used to distinguish between these lineages [2]. 60 The Mycobacterium tuberculosis complex (MTBC) comprises genotypically and phenotypically. 64 1 to 4) is exquisitely adapted to the human host and despite infecting one third of the world’s human. In. contrast, a distinct MTBC clade, characterized by the loss of RD9, is unique in having given rise to lineages associated with both humans (M. africanum lineage 5 and 6) and a wide variety of animal. A group of strains which display remarkable phenotypic variation are those related to 69 lineage 6, i.e. M_africanum West African 2 (WA2), a lineage which circulates within human. 71 on the loss of RD7, RD8, RD9 and RD10, include the chimpanzee bacillus [1], the dassie bacillus. 72 [6], M. mungi [7], and M. suricattae [8], which have been isolated from a chimpanzee

Results

Discussion

Conclusion