Whole genome sequence analysis of Mycobacterium suricattae - 19/02/16

Doi : 10.1016/j.tube.2015.10.001

Anzaan Dippenaar ^a,^{^{1
Authors contributed equally.}} , Sven David Charles Parsons ^a,^{^{1
Authors contributed equally.}} , Samantha Leigh Sampson ^a , Ruben Gerhard van der Merwe ^a , Julian Ashley Drewe ^b , Abdallah Musa Abdallah ^c , Kabengele Keith Siame ^a , Nicolaas Claudius Gey van Pittius ^a , Paul David van Helden ^a , Arnab Pain ^c,^{^{2
Authors contributed equally.}} , Robin Mark Warren ^a,^⁎,^{^{2
Authors contributed equally.}}
^a DST-NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
^b Royal Veterinary College, London, UK
^c Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia

^∗Corresponding author. Tel.: +27 219389073; fax: +27 219389863.

Summary

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.

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Keywords : Meerkat, Mycobacterium suricattae, Tuberculosis, High-throughput nucleotide sequencing

Plan

Background

Material and methods

Whole genome sequencing (WGS)

WGS data analyses

PCR confirmation of genomic deletions

Phylogenomic analysis

Insertions/deletion (indels)

Regions of difference (RD)

Phylogeny

De novo assembly

Discussion

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Vol 95 - N° 6

P. 682-688 - décembre 2015 Retour au numéro

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Whole genome sequence analysis of Mycobacterium suricattae - 19/02/16

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