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.1,2 Although ancient DNA (aDNA) approaches on the major causative agent, Mycobacterium leprae, have elucidated the disease’s evolutionary history,3,4,5 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.6,7 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.</p

Immunohistochemical staining of armadillo spleen sections for the <i>M</i>. <i>leprae</i>-specific antigen, PGL-I, with a rabbit polyclonal antibody raised against this antigen.

<p>A) Wild infected armadillo B7 section stained with pre-immune rabbit serum, negative control; B) NHDP uninfected armadillo 13–02 stained with rabbit anti-PGL-I, negative control; C) NHDP infected armadillo 11K902 stained with anti-PGL-I showing diffuse brown staining, positive control; D) Higher magnification of NHDP infected armadillo 11K902 stained with anti-PGL-I, positive control; E) Wild infected armadillo A7 stained with anti-PGL-I, showing diffuse brown staining. F) Higher magnification of wild infected armadillo A7 stained with anti-PGL-I, showing diffuse brown staining with more intense clusters.</p

Map of study area.

<p>Municipality of Belterra in western Pará, and the villages of São Jorge at Km 92 and Corpus Christi at Km 135 on the Santarém-Cuiabá highway.</p

Risk factors associated with leprosy patients living in rural communities in the municipality of Belterra, Pará.

<p>Risk factors associated with leprosy patients living in rural communities in the municipality of Belterra, Pará.</p

Staining of mycobacteria <i>in situ</i> in <i>M</i>. <i>leprae</i> infected armadillo spleen sections.

<p>A) SYBR Gold staining (blue) of <i>M</i>. <i>leprae</i> in armadillo spleen A7, arrow denotes stained bacillus. Insert, enlarged area showing stained bacillus. B) SYBR Gold staining (green) of <i>M</i>. <i>leprae</i> in armadillo spleen B7. Arrow denotes stained cluster of bacilli, enlarged in insert. C) Auramine/rhodamine stained cluster (red) of bacilli (arrow) located within an apoptotic cell next to a cell-free necrotic zone (*) in armadillo spleen A7.</p

Hematoxylin and eosin (H&E) and Fite Faraco (acid fast) staining of non-infected and infected armadillo spleen sections.

<p>A) Non-infected control NHDP armadillo spleen (13–02) stained by H&E to show normal splenic architecture; B) <i>M</i>. <i>leprae</i> infected NHDP armadillo spleen (11I302) stained by H&E; C) Non-infected control NHDP armadillo spleen (12–70) stained by Fite Faraco method showing only counterstain; D) Many acid fast bacilli (red clusters) in <i>M</i>. <i>leprae</i> infected NHDP armadillo spleen (11I302) revealed by Fite Faraco stain; E) Wild armadillo (A2) spleen section stained with Fite Faraco, arrow pointing to acid fast bacilli at lower magnification and enlarged in insert; F) Wild armadillo (A2) spleen section stained with Fite Faraco revealing clusters of acid fast bacilli (arrows).</p

Analysis of anti-PGL-I ELISA titer of 146 individuals based on group behaviors.

<p>Behaviors were associated with the type of contact with armadillos, including A) hunting armadillos in the forest, B) handling or preparing armadillo meat for cooking or consumption, C) eating armadillo meat and D) frequency of consuming armadillos in the diet.</p

Detection of RLEP sequence by PCR in armadillo tissues.

<p>A) Analysis of PCR RLEP product from spleen samples from nine different armadillos. B) Analysis of RLEP from paired samples of liver (L) and spleen (S) from five different armadillos. The signal from positive samples is consistently stronger in the spleen for each individual. The positive control (+ve) reaction included purified <i>M</i>. <i>leprae</i> DNA, 2 ng, while the negative control (-ve) lacked DNA template.</p

Summary of the whole genome sequencing analysis (WGS) between the <i>M</i>. <i>leprae</i> strains investigated at the 1^st and 2^nd disease occurrences.

<p>Summary of the whole genome sequencing analysis (WGS) between the <i>M</i>. <i>leprae</i> strains investigated at the 1^st and 2^nd disease occurrences.</p

Main demographic and clinical features of recurrent cases from the U-MDT/CT-BR trial.

<p>Main demographic and clinical features of recurrent cases from the U-MDT/CT-BR trial.</p