Genomic Diversity and Evolution of Mycobacterium ulcerans Revealed by Next-Generation Sequencing

Abstract

Mycobacterium ulcerans is the causative agent of Buruli ulcer, the third most common mycobacterial disease after tuberculosis and leprosy. It is an emerging infectious disease that afflicts mainly children and youths in West Africa. Little is known about the evolution and transmission mode of M. ulcerans, partially due to the lack of known genetic polymorphisms among isolates, limiting the application of genetic epidemiology. To systematically profile single nucleotide polymorphisms (SNPs), we sequenced the genomes of three M. ulcerans strains using 454 and Solexa technologies. Comparison with the reference genome of the Ghanaian classical lineage isolate Agy99 revealed 26,564 SNPs in a Japanese strain representing the ancestral lineage. Only 173 SNPs were found when comparing Agy99 with two other Ghanaian isolates, which belong to the two other types previously distinguished in Ghana by variable number tandem repeat typing. We further analyzed a collection of Ghanaian strains using the SNPs discovered. With 68 SNP loci, we were able to differentiate 54 strains into 13 distinct SNP haplotypes. The average SNP nucleotide diversity was low (average 0.06–0.09 across 68 SNP loci), and 96% of the SNP locus pairs were in complete linkage disequilibrium. We estimated that the divergence of the M. ulcerans Ghanaian clade from the Japanese strain occurred 394 to 529 thousand years ago. The Ghanaian subtypes diverged about 1000 to 3000 years ago, or even much more recently, because we found evidence that they evolved significantly faster than average. Our results offer significant insight into the evolution of M. ulcerans and provide a comprehensive report on genetic diversity within a highly clonal M. ulcerans population from a Buruli ulcer endemic region, which can facilitate further epidemiological studies of this pathogen through the development of high-resolution tools.

Insertion Sequence Element Single Nucleotide Polymorphism Typing Provides Insights into the Population Structure and Evolution of Mycobacterium ulcerans across Africa

“…Furthermore, given the comprehensive nature of full-genome data, sequences could also serve in large-scale microepidemiological studies that are focused on the elucidation of transmission pathways and relevant reservoirs of M. ulcerans. Indeed, different studies of mycobacterial genomics (18,49,56) have already shown that, at the whole-genome level, substantial genetic variation exists in African M. ulcerans, which can be exploited for phylogenetically robust strain classification. In order to capture as much diversity as possible and to minimize phylogenetic discovery bias (57) in such impending large sequencing endeavors, it will be desirable to select representative types from all the central and radial ISE-SNP types defined in this study.…”

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

“…Therefore, WGS might perhaps be used to develop new epidemiological tools, identifying novel hallmarks of mycobacterial variability, rather than as a genotyping method per se. To exemplify this, WGS allowed the mapping of several SNP loci in M. ulcerans isolates, some of which further served as the templates for the development of a novel epidemiological differentiation pattern for this species (429). It also allowed the typing of several SNPs in M. leprae (430).…”

Epidemiology and disease burden of Buruli ulcer: a review

“…Genetic analyses indicate that M. ulcerans has diverged from the ubiquitous waterborne organism Mycobacterium marinum 19 perhaps around a million years ago. 20 While M. marinum usually infects fish and frogs and only occasionally causes granulomatous skin lesions in humans, 21 emergence of the …”