Leprosy , a disfiguring mycobacterial infection, was a feared illness in biblical and medieval times (the biblical term may have been a catchall for several skin diseases), and remains very persistent in the developing world. Like TB, leprosy is making a comeback in areas with high rates of HIV infection.
The genomic effort to sequence leprosy shows that leprosy worldwide is the result of an almost clonal population of mycobacteria (about 1/10th the number of SNPs compared to M. tuberculosis), so homogeneous that SNP analysis can reveal the human migrations which spread the disease. Specifically, the disease in the New World is West African in origin and almost certainly was brought by slave traders. The European variant is divergent from the India strain, so Alexander the Great brought the disease from a lot closer to home than previously thought.
In western Europe, the once common leprosy nearly vanished by the 16th century, even as tuberculosis, another mycobacterial disease, persisted. An old hypothesis suggested that cross-immunity to tuberculosis contributed to the disappearance of leprosy in Western Europe. However, a paper from February in PRSL-B suggests that the relationship between TB and leprosy is more complicated than previously thought, with co-infection historically being actually very common. PCR detection of the two microbes' DNAs revealed that co-infections with TB and leprosy occured in about 42% of human remains stretching from 100-1000 A.D. TB may thus historically have acted as the killing blow to people already suffering from leprosy.
So rather than cross-immunity within human hosts, it must be that social changes in the middle ages favored the persistence of TB and the demise of leprosy (and the rise of Foucault ).