Ancient DNA studies can provide new perspectives for evolutionary history of pathogens such as for Mycobacterium leprae, the causative agent of leprosy, one of the oldest recorded and most feared diseases in human history, which was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually.
Previously we observed an exceptional DNA preservation of M. leprae in medieval skeletons, that enabled us to successfully reconstruct a late medieval leprosy genome by de novo assembly, thus offering the prospect to retrace M. leprae’s pre-historic origin. Furthermore, the analysis of medieval M. leprae genomes pointed to a pre-medieval origin of most contemporary human and armadillo leprosy lineages and suggested a prevalence of two distinct lineages in medieval northwestern Europe.
Here we analyzed novel medieval M. leprae genomes from different time points and geographic locations including the so far oldest M. leprae genome derived from one of the earliest known cases of leprosy in the UK, a skeleton from the Great Chesterford cemetery dated to 415–545 AD, in order to reconstruct the last 1500 years of M. leprae’s evolutionary history. A phylogenetic comparison revealed the contemporary presence of at least 4 distinct lineages and suggests a high diversity of M. leprae strains in medieval Europe. In addition, the 1500-year-old Great Chesterford genome allowed us to trace one of the lineages, lineage 3, back to the 6th century.
These results develop and refine previous models for the geographic distribution of M. leprae lineages in the past indicating a higher complexity and point out the necessity of studying ancient M. leprae strains to understand the history of leprosy worldwide.