Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans

Abstract

BackgroundComparative genomics has greatly improved our understanding of the evolution of pathogenic mycobacteria such as Mycobacterium tuberculosis. Here we have used data from a genome microarray analysis to explore insertion-deletion (InDel) polymorphism among a diverse strain collection of Mycobacterium ulcerans, the causative agent of the devastating skin disease, Buruli ulcer. Detailed analysis of large sequence polymorphisms in twelve regions of difference (RDs), comprising irreversible genetic markers, enabled us to refine the phylogenetic succession within M. ulcerans, to define features of a hypothetical M. ulcerans most recent common ancestor and to confirm its origin from Mycobacterium marinum.Results M. ulcerans has evolved into five InDel haplotypes that separate into two distinct lineages: (i) the "classical" lineage including the most pathogenic genotypes – those that come from Africa, Australia and South East Asia; and (ii) an "ancestral" M. ulcerans lineage comprising strains from Asia (China/Japan), South America and Mexico. The ancestral lineage is genetically closer to the progenitor M. marinum in both RD composition and DNA sequence identity, whereas the classical lineage has undergone major genomic rearrangements.ConclusionResults of the InDel analysis are in complete accord with recent multi-locus sequence analysis and indicate that M. ulcerans has passed through at least two major evolutionary bottlenecks since divergence from M. marinum. The classical lineage shows more pronounced reductive evolution than the ancestral lineage, suggesting that there may be differences in the ecology between the two lineages. These findings improve the understanding of the adaptive evolution and virulence of M. ulcerans and pathogenic mycobacteria in general and will facilitate the development of new tools for improved diagnostics and molecular epidemiology.

Lack of Insertional-Deletional Polymorphism in a Collection of Mycobacterium ulcerans Isolates from Ghanaian Buruli Ulcer Patients

“…The nature of some of the genomic changes speaks for an adaptation to an environment which is screened by immune effector mechanisms (14,26,28,41). Genetic monomorphism indicates that this lineage has been forged through a bottleneck situation (29,54,63). The genomic stability demonstrated here of this successful clone may be indicative of decreased selective pressure, rendering further genome shrinkage unnecessary.…”

“…Test hybridizations were performed with spotted DNA derived from regions of difference (RDs) identified in previous studies (29,47). Using DNA of strains differing in these target sequences, we established spotting and hybridization conditions that yielded the predicted hybridization signals in a reliable and reproducible manner (Fig.…”

“…The M. ulcerans classical lineage, responsible for the vast majority of BU cases worldwide, is thought to have undergone massive genome reduction while adapting to a relatively stable ecological niche (14,28,29,47,54). The nature of some of the genomic changes speaks for an adaptation to an environment which is screened by immune effector mechanisms (14,26,28,41).…”

“…An in-depth comparison of the recently published M. ulcerans genome of strain Agy99 to the progenitor species strain M. marinum M revealed LSPs, named M. ulcerans regions of difference (MURDs) (54). Analysis of large InDel polymorphisms allowed us to distinguish between two distinct lineages: (i) the "classical" lineage representing the most pathogenic genotypes, consisting of those that come from Africa, Australia, and Southeast Asia; and (ii) an "ancestral" lineage comprising strains from China and Japan, South America, and Mexico (29). A total of 209 copies of the insertion sequence (IS) IS2404 and 83 copies of IS2606 have been found interspersed in the genome of the M. ulcerans reference strain Agy99 from Ghana (54).…”

Defining mycobacteria: Shared and specific genome features for different lifestyles

“…This and a prior study with references to glycosylated PGL versions in M. ulcerans [86] are not compatible with the current genome information. Therefore, strain variants may reconcile these issues of the presence of phenolic glycolipids in M. ulcerans [86,87].…”