Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus

Abstract

Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. Mycobacterium leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.

Keywords: Mycobacterium leprae; ancient DNA; dental calculus; leprosy; palaeoproteomics.

Figure 1.

(a) Location of Trondheim, Norway; (b) dental calculus found from SK92 (white arrows indicate location) (photo: Anna Fotakis); (c) evidence of rhinomaxillary syndrome, with possible loss of upper central incisors and resorption of the bone of the associated alveoli (indicated by black arrows); (d) concentric loss of bone from pedal phalanx. Photos (c,d): Åge Hojem, NTNU University Museum; arrows in (c) were added by the authors. (Online version in colour.)

Figure 2.

Maximum-likelihood tree of ancient and modern M. leprae strains. The tree is based on 3126 variant positions using 80% partial deletion and 1000 bootstrap replicates (bootstrap support for each node is shown). Mycobacterium lepromatosis was used as an outgroup. SK92 is coloured blue and previously published ancient genomes are coloured red. Radiocarbon dates and country of origin are provided for the ancient genomes where possible. The country of origin is provided for the modern genomes. Animal figures denote strains isolated from non-human primates, armadillos and squirrels. The primary branches are colour coded and the dotted lines indicate established SNP types (1–4) and subtypes (A–P). (Online version in colour.)