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

Abstract

Mycobacterium ulcerans causes the devastating infectious skin disease Buruli ulcer and has a monomorphic population structure. The resolution of conventional genetic fingerprinting methods is therefore not sufficient for microepidemiological studies aiming to characterize transmission pathways. In a previous comparative genomic hybridization analysis with a microarray covering part of the M. ulcerans genome, we have found extensive insertional-deletional sequence polymorphisms among M. ulcerans isolates of diverse geographic origins that allowed us to distinguish between strains coming from different continents. Since large numbers of insertion sequences are spread over the genome of African M. ulcerans strains, we reasoned that these may drive large sequence polymorphisms in otherwise clonal local mycobacterial populations. In this study, we used a printed DNA microarray covering the whole genome of the Ghanaian M. ulcerans reference strain Agy99 for comparative genomic hybridization. The assay identified multiple regions of difference when DNA of a Japanese M. ulcerans strain was analyzed. In contrast, not a single insertional-deletional genomic variation was found within a panel of disease isolates coming from an area of Ghana where Buruli ulcer is endemic. These results indicate that, despite the expectations deduced from other mycobacterial pathogens, only analyses of single nucleotide polymorphisms will have the potential to differentiate local populations of M. ulcerans.

Serological Evaluation of Mycobacterium ulcerans Antigens Identified by Comparative Genomics

“…Only nine M. ulcerans specific sequences were conserved amongst all mycolactone producing mycobacterial strains tested. However, in agreement with previous findings that African M. ulcerans strains form a close genetic complex with relatively little variation at the whole genome level [38] , [39] , [40] , all selected chromosomal genes were present in all African M. ulcerans isolates that were examined. As pMUM plasmids are known to vary in size and gene content between M. ulcerans strains [11] , [33] , it is not surprising that only six of 33 non-PKS CDS were completely conserved.…”

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

“…A plasmid-based analysis allowed the identification of multiple DNA deletions among M. ulcerans clinical isolates (207). However, this method turned out to be impractical for studying genetic diversities within local populations (208).…”

Single Nucleotide Polymorphisms on the Road to Strain Differentiation in Mycobacterium ulcerans

“…Discrimination of genetic variants has become an indispensable tool to unravel the evolution, epidemiology, and transmission of pathogenic organisms and to gain insight into host-pathogen interactions (6,13,24). In M. ulcerans, such elucidation is impossible due to a remarkable lack of genetic diversity on a local geographic scale (22). Conventional genetic differentiation tools commonly used for phylogenetic profiling in Mycobacterium tuberculosis, such as restriction fragment length polymorphism, amplified fragment length polymorphism, variable-number tandem repeats (VNTR), and multilocus sequence typing, could distinguish between continental lineages only when applied to M. ulcerans (1-4, 7, 8, 15, 18, 29, 31, 34, 35).…”