Comparative genomics reveals diversity and spatial clustering of Mycobacterium ulcerans in a small Buruli ulcer endemic area of West-Africa. Mycobacterium ulcerans

Past attempts to examine the ecology of Mycobacterium ulcerans through conventional genotyping techniques have been impaired due to the limited genetic diversity of its genome. However, the development of whole genome sequencing brought the opportunity to trace the evolutionary history of the bacteria more effectively but, so far, population structure inference were breaking down at the local village scale.To address this issue, we performed a phylogeographic analysis on 178 isolates obtained from human clinical specimens spanning 10 years and representing two endemic departments in the South of Benin and one neighboring department in Nigeria.Contrary to what was previously described, we were able to identify eight distinct genotypes at this scale. These genotypes were not evenly distributed over the area and we uncovered three discernible spatial clusters of genotypes associated with landscapes characteristics such as hydrological and pedological features. Our results were confirmed by a second set of sequencing 29 new bacterial isolates for which genotype distributions matched our expected results with an average accuracy of 90 %.