Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes
Creators: name: Pfrengle, Saskia
name: Neukamm, Judith
name: Guellil, Meriam
name: Keller, Marcel
name: Molak, Martyna
name: Avanzi, Charlotte
name: Kushniarevich, Alena
name: Montes, Núria
name: Neumann, Gunnar U.
name: Reiter, Ella
name: Tukhbatova, Rezeda I.
name: Berezina, Nataliya Y.
name: Buzhilova, Alexandra P.
name: Korobov, Dmitry S.
name: Suppersberger Hamre, Stian
name: Matos, Vitor M. J.
name: Ferreira, Maria T.
name: González-Garrido, Laura
name: Wasterlain, Sofia N.
name: Lopes, Célia
name: Santos, Ana Luisa
name: Antunes-Ferreira, Nathalie
name: Duarte, Vitória
name: Silva, Ana Maria
name: Melo, Linda
name: Sarkic, Natasa
name: Saag, Lehti
name: Tambets, Kristiina
name: Busso, Philippe
name: Cole, Stewart T.
name: Avlasovich, Alexei
name: Roberts, Charlotte A.
name: Sheridan, Alison
name: Cessford, Craig
name: Robb, John
name: Krause, Johannes
name: Scheib, Christiana L.
name: Inskip, Sarah A.
name: Schuenemann, Verena J.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2021
Subjects: Research Article
Ancient DNA
Ancient pathogen genomics
Mycobacterium leprae
Pathogen diversity
Leprosaria
Pathogen population dynamics
Paleomicrobiology
Paleopathology

description: Funder: University of Zurich’s University Research Priority Program “Evolution in Action: From Genomes to Ecosystems”
description: Funder: the Senckenberg Centre for Human Evolution and Palaeoenvironment (S-HEP) at the University of Tübingen
description: Funder: Max-Planck Society
description: Funder: St John’s College, Cambridge
description: Funder: Fondation Raoul Follereau
description: Abstract: 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.