Oral Presentation Society for Molecular Biology and Evolution Conference 2016

Ancient leprosy genomics: Retracing the evolutionary history of Mycobacterium leprae from medieval genomes (#218)

Verena J Schuenemann 1 2 , Charlotte Avanzi 3 , Alexander Seitz 4 , Ben Krause-Kyora 5 , Alexander Herbig 6 , Andrej Benjak 3 , Jesper L Boldsen 7 , G. Michael Taylor 8 , Pushpendra Singh 3 , Sarah Inskip 9 , Simon Mays 10 , Helen D Donoghue 11 , Sonia Zakrzewski 12 , Kay Nieselt 4 , Stewart T Cole 3 , Johannes Krause 1 2 6
  1. Institute for Archaeological Sciences, University of Tuebingen, Tuebingen, BW, Germany
  2. Senckenberg Center for Human Evolution and Paleoenvironment, University of Tuebingen, Tuebingen, Germany
  3. Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
  4. Center for Bioinformatics, University of Tuebingen, Tuebingen, Germany
  5. Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
  6. Max Planck Institute for the Science of Human History, Jena, Germany
  7. Department of Anthropology (ADBOU), Institute of Forensic Medicine, University of Southern Denmark, Odense S, Denmark
  8. Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, UK
  9. Department of Archaeology, Leiden University, Leiden, The Netherlands
  10. Historic England, Portsmouth, UK
  11. Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London NW3 2PF, UK
  12. Department of Archaeology, University of Southampton, Southampton, UK

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.