Mycobacterium riyadhense clinical isolates from Saudi Arabia provides insights into ancestry and adaptive evolution in tuberculosis

Mycobacterium riyadhense was first discovered in 2009 in Riyadh, Saudi Arabia. It causes tuberculosis (TB)-like symptoms and was originally misdiagnosed as such but subsequently classified as a novel species of Non-Tuberculous Mycobacteria (NTM). In order to define its phylogenetic relationship to other Mycobacteria species including members of the M. tuberculosis complex (MTBC), the genomes of eight clinical samples of M. riyadhense were sequenced and analyzed. We show that M. riyadhense shares a large number of conserved orthologs including the presence of 49 toxin/antitoxin pairs and a similar ESAT-6/CFP-10 secretions systems (ESX-1) as members of MTBC. A phylogenetic tree based on conserved marker genes places M. riyadhense closer to the MTBC than to other known environmental mycobacterial relatives such as M. kansasii and M. marinum. Using a K-mer-based comparative genomic approach, we have developed a PCR-based diagnostic marker for M. riyadhense suitable for rapid identification in a clinical setting. We conclude that M. riyadhense is the closest known environmental relative of M. tuberculosis before reductive genome evolution and host-adaptation. Our study suggests M. riyadhense is a good experimental model organism to study the tuberculosis pathogens belonging to the MTBC.