Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

BACKGROUND

Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.

RESULTS

Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.

CONCLUSIONS

Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

A possible Echinococcus granulosus calcified cyst found in a medieval adult female from the churchyard of Santo Domingo de Silos (Prádena del Rincón, Madrid, Spain)

Calcification, or mineralisation, can occur as part of a natural process, or by pathological processes. The purpose of this work is to examine an unidentified semi-spherical and perforate hollow mass, found near the pelvis of an adult female, dated 12th-13th century AD, exhumed of the Church of Santo Domingo de Silos (Prádena del Ricón, Madrid, Spain). The mass was examined by SEM and Energy Dispersive X-Ray Spectroscopy. These procedures revealed a heterogeneous inner surface with both smooth and irregular areas. A larger spherical and several smaller crescent-shaped perforations were noticed. X-ray microanalysis revealed the presence of the elements C, K, P, Ca, Al, Si, Fe, and Mg. The co-localisation of Ca and P suggests that they may be combined in a mineral matrix, likely formed in vivo. Other minerals probably came from the soil, although Fe could be related to the presence of blood. The macroscopic and microscopic appearances, chemical composition, and location of the calcified mass point to a possible hydatid cyst from Echinococcus granulosus, common in agricultural populations. This study used a suite of analytical techniques that are useful in the diagnosis of unknown calcified masses and can, therefore, be recommended for use in future analytical work.