Retracing the Recent Emergence of Mycobacterium ulcerans.
It is more than 60 years since Mycobacterium ulcerans was shown to be the causative agent of Buruli ulcer yet it is still unclear where the bacterium resides in the environment and how it is transmitted to humans. Limited genome comparisons show that M. ulcerans has the characteristics of a niche-adapted microbe, having evolved recently from the fish-associated, opportunistic human pathogen, Mycobacterium marinum by horizontal gene transfer and reductive evolution. To further understand the relationship between these two species of pathogenic mycobacteria and to gain deeper insights into the evolution of M. ulcerans, we have used high throughput short-read DNA sequencing and compared the genomes of 30 strains of M. ulcerans and 5 strains of M. marinum, a strain collection that spans the known genetic diversity of these two species. We used a nucleotide read-mapping approach and objectively defined a 4,362,138 bp M. ulcerans-M. marinum core genome. Pairwise comparisons of every strain against this core revealed 129,416 variable nucleotide positions (3.0% nucleotide overall variation) across the two species and permitted the construction of a high resolution phylogeny for the complex, confirming that all M. ulcerans strains evolved from a common M. marinum progenitor and have diverged again into two distinct sub- lineages. In conjunction with de novo sequence assembly and gene ortholog clustering techniques, we used this phylogeny as a framework for reconstruction of a putative M. ulcerans most recent common ancestor (MRCA). We show that presence of the pMUM plasmid required for production of the polyketide toxin mycolactone (a potent immunosuppressor), high copy number of the insertion sequence IS2404, and loss/mutation of genes associated with, anaerobic respiration, lipid and cell-wall metabolism were all key attributes of the M. ulcerans MRCA before its global dispersal. Interestingly, intact genes involved with lipid metabolism and the cell wall showed evidence of positive selection with significantly higher dN/dS ratios than M. marinum strains. These data provide clues regarding the characteristics of the niche(s) M. ulcerans occupies and are guiding efforts to control the spread of Buruli ulcer.