Unveiling the evolutionary history & molecular epidemiology of Mycobacterium ulcerans

Buruli ulcer is a neglected tropical disease of skin and subcutaneous tissue, caused by infection with Mycobacterium ulcerans. Cases are reported around the world, with rural wetlands of West- and Central African countries most affected. Prevention and control of the disease is complicated by limited understanding of the mode(s) of transmission of BU, probably involving inoculation directly by a vector, or from a contaminated skin surface. While direct human-to-human transmission does not occur, the potential environmental reservoir(s), and the role of the human reservoir in sustaining endemic BU, are controversial.
We redesigned a SNP-based (ISE-SNP) fingerprinting assay to gain fundamental insights into the population structure and evolutionary history of African M. ulcerans. Even though ISE-SNP genotyping resulted in higher geographical resolution than previously achieved, the resolution was still too limited to reconstruct evolutionary events on anything smaller than the continental scale. Therefore we used state-of-the-art second and third generation genome sequencing technologies and advanced statistical approaches to understand the detailed evolutionary and spatio-temporal history of African M. ulcerans. We also explored the use of the increased resolution offered by low-cost genomics to distinguish disease relapses from reinfections in patients with multiple BU episodes. African M. ulcerans was found to be evolving entirely through clonal expansion and its genetic diversity proved to be very restricted because of the pathogen’s slow genome-wide substitution rate coupled with its relative recent origin. Exploration of the genetic population structure revealed the existence of two specific lineages within the African continent. We used temporal associations and studied the past demographic history of M. ulcerans in a BU endemic region to implicate the role of humans as a major reservoir in BU transmission. In previous studies, M. ulcerans DNA has been detected in the environment, possibly originating from BU patients with active, openly discharging lesions. Transmission can then occur indirectly in the same community water source, when the superficial skin surface of a naïve individual is contaminated, and the bacilli present on the contaminated skin are subsequently inoculated subcutaneously through some form of penetrating (micro)trauma.
Our observations on the role of humans as maintenance reservoir to sustain new BU infections suggest that interventions in a region aimed at reducing the human BU burden will at the same time break the transmission chains within that region. Active case-finding programs and the early treatment of pre-ulcerative infections with specific antibiotics will decrease the amounts of mycobacteria shed into the environment, which may ultimately reduce disease transmission in Africa.