Locally Confined Clonal Complexes of <i>Mycobacterium ulcerans</i> in Two Buruli Ulcer Endemic Regions of Cameroon

<div><p>Background</p><p><i>Mycobacterium ulcerans</i> is the causative agent of the necrotizing skin disease Buruli ulcer (BU), which has been reported from over 30 countries worldwide. The majority of notified patients come from West African countries, such as Côte d’Ivoire, Ghana, Benin and Cameroon. All clinical isolates of <i>M</i>. <i>ulcerans</i> from these countries are closely related and their genomes differ only in a limited number of single nucleotide polymorphisms (SNPs).</p><p>Methodology/Principal Findings</p><p>We performed a molecular epidemiological study with clinical isolates from patients from two distinct BU endemic regions of Cameroon, the Nyong and the Mapé river basins. Whole genome sequencing of the <i>M</i>. <i>ulcerans</i> strains from these two BU endemic areas revealed the presence of two phylogenetically distinct clonal complexes. The strains from the Nyong river basin were genetically more diverse and less closely related to the <i>M</i>. <i>ulcerans</i> strain circulating in Ghana and Benin than the strains causing BU in the Mapé river basin.</p><p>Conclusions</p><p>Our comparative genomic analysis revealed that <i>M</i>. <i>ulcerans</i> clones diversify locally by the accumulation of SNPs. Case isolates coming from more recently emerging BU endemic areas, such as the Mapé river basin, may be less diverse than populations from longer standing disease foci, such as the Nyong river basin. Exchange of strains between distinct endemic areas seems to be rare and local clonal complexes can be easily distinguished by whole genome sequencing.</p>