Ancient Mycobacterium leprae genome reveals medieval English red squirrels as animal leprosy host

Leprosy, one of the oldest recorded diseases in human history, remains prevalent in Asia, Africa, and South America, with over 200,000 cases every year.1World Health Organization, Regional Office for South-East AsiaGlobal Leprosy Strategy 2016-2020: Accelerating towards a leprosy-free world (WHO Regional Office for South-East Asia).2016Google Scholar,2World Health Organization, Regional Office for South-East AsiaGlobal consultation of National Leprosy Programme managers, partners and affected persons on Global Leprosy Strategy 2021–2030: Report of the virtual meeting 26-30 October 2020.2020Google Scholar Although ancient DNA (aDNA) approaches on the major causative agent, Mycobacterium leprae, have elucidated the disease's evolutionary history,3Pfrengle S. Neukamm J. Guellil M. Keller M. Molak M. Avanzi C. Kushniarevich A. Montes N. Neumann G.U. Reiter E. et al.Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes.BMC Biol. 2021; 19: 220Crossref PubMed Scopus (14) Google Scholar,4Neukamm J. Pfrengle S. Molak M. Seitz A. Francken M. Eppenberger P. Avanzi C. Reiter E. Urban C. Welte B. et al.2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.BMC Biol. 2020; 18: 108Crossref PubMed Scopus (29) Google Scholar,5Schuenemann V.J. Singh P. Mendum T.A. Krause-Kyora B. Jäger G. Bos K.I. Herbig A. Economou C. Benjak A. Busso P. et al.Genome-wide comparison of medieval and modern Mycobacterium leprae.Science. 2013; 341: 179-183Crossref PubMed Scopus (258) Google Scholar the role of animal hosts and interspecies transmission in the past remains unexplored. Research has uncovered relationships between medieval strains isolated from archaeological human remains and modern animal hosts such as the red squirrel in England.6Avanzi C. Del-Pozo J. Benjak A. Stevenson K. Simpson V.R. Busso P. McLuckie J. Loiseau C. Lawton C. Schoening J. et al.Red squirrels in the British Isles are infected with leprosy bacilli.Science. 2016; 354: 744-747Crossref PubMed Scopus (122) Google Scholar,7Truman R.W. Singh P. Sharma R. Busso P. Rougemont J. Paniz-Mondolfi A. Kapopoulou A. Brisse S. Scollard D.M. Gillis T.P. Cole S.T. Probable zoonotic leprosy in the southern United States.N. Engl. J. Med. 2011; 364: 1626-1633Crossref PubMed Scopus (253) Google Scholar However, the time frame, distribution, and direction of transmissions remains unknown. Here, we studied 25 human and 12 squirrel samples from two archaeological sites in Winchester, a medieval English city well known for its leprosarium and connections to the fur trade. We reconstructed four medieval M. leprae genomes, including one from a red squirrel, at a 2.2-fold average coverage. Our analysis revealed a phylogenetic placement of all strains on branch 3 as well as a close relationship between the squirrel strain and one newly reconstructed medieval human strain. In particular, the medieval squirrel strain is more closely related to some medieval human strains from Winchester than to modern red squirrel strains from England, indicating a yet-undetected circulation of M. leprae in non-human hosts in the Middle Ages. Our study represents the first One Health approach for M. leprae in archaeology, which is centered around a medieval animal host strain, and highlights the future capability of such approaches to understand the disease's zoonotic past and current potential.