Human leprosy is primarily caused by Mycobacterium leprae, but also by the related

‘M. lepromatosis’. Ancient leprosy can be recognised in archaeological materials by the

paleopathology associated with multi-bacillary or lepromatous forms of the disease. Whole

M. leprae genomes have been obtained from human skeletons, and diagnostic aDNA frag-

ments have been recovered. The derived M. leprae phylogenies, based on single nucleotide

polymorphisms, mirror past human migrations, as M. leprae is usually an obligate pathogen.

The detection of M. leprae in historical leprosy cases is assisted by the hydrophobic M. leprae

cell envelope, which is composed of unusual lipids that can be used as specific biomarkers.

Lipid biomarkers are more stable than aDNA and can be detected directly without amplifi-

cation. Indigenous human leprosy is extinct in Western Europe, but recently, both M. leprae

and ‘M. lepromatosis’ were found in British red squirrels. Leprosy may also be found in nine-

banded armadillos (Dasypus novemcinctus) where it can cause a zoonotic human infection.

Certain leprosy-like diseases, caused by uncultivable species in cats, for example, may be

related to M. leprae. The closest extant relatives of leprosy bacilli are probably members of the

M. haemophilum taxon, emerging pathogens with genomic and lipid biomarker similarities.