Single Nucleotide Polymorphism Typing of Mycobacterium ulcerans Reveals Focal Transmission of Buruli Ulcer in a Highly Endemic Region of Ghana

Abstract

Buruli ulcer (BU) is an emerging necrotizing disease of the skin and subcutaneous tissue caused by Mycobacterium ulcerans. While proximity to stagnant or slow flowing water bodies is a risk factor for acquiring BU, the epidemiology and mode of M. ulcerans transmission is poorly understood. Here we have used high-throughput DNA sequencing and comparisons of the genomes of seven M. ulcerans isolates that appeared monomorphic by existing typing methods. We identified a limited number of single nucleotide polymorphisms (SNPs) and developed a real-time PCR SNP typing method based on these differences. We then investigated clinical isolates of M. ulcerans on which we had detailed information concerning patient location and time of diagnosis. Within the Densu river basin of Ghana we observed dominance of one clonal complex and local clustering of some of the variants belonging to this complex. These results reveal focal transmission and demonstrate, that micro-epidemiological analyses by SNP typing has great potential to help us understand how M. ulcerans is transmitted.

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

“…Hence, BU infections in these areas probably resulted from locally confined transmission of a single circulating clone, with only occasional transfer of clones between basins. Our findings confirm a study of Röltgen et al (49), in which a number of M. ulcerans haplotypes within the Densu hydrological basin of Ghana (with SNP typing based on whole-genome data) were differentiated, revealing similar focal transmission clusters within the basin itself. Hence, our findings provide additional evidence that both transmission and fine-grained evolutionary events play roles at the local level and we consequently hypothesize that potential reservoirs have limited mobility.…”

“…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.…”

Insights from genomic comparisons of genetically monomorphic bacterial pathogens

“…the causes of plague (Y. pestis [23]), anthrax (Bacillus anthracis [24]), glanders (Burkholderia mallei [25]) and tuberculosis (Mycobacterium tuberculosis [20]), although each of them corresponds to a lineage within a species of greater diversity (Yersinia pseudotuberculosis, Bacillus cereus, Burkholderia pseudomallei and the M. tuberculosis complex, respectively). Finally, still other species also have similar properties, except that a parental species has not been identified, such as the causes of leprosy (Mycobacterium leprae [14]) and Buruli ulcer (Mycobacterium ulcerans [26]). …”

Epidemiology and disease burden of Buruli ulcer: a review

“…In this regard, it has been hypothesized that humans with active BU lesions that are not treated appropriately may play a role in transmission by shedding the bacteria into the environment. [14][15][16] Transmission may thus be reduced by active case search followed by adequate treatment with the WHO-recommended antibiotic combination therapy of daily rifampicin and streptomycin for 8 weeks. 17,18 The mechanism by which M. ulcerans is transmitted from the environment to humans thereby remains inconclusive.…”