A newly sequenced genome of the bacterium that causes syphilis, Treponema pallidum, highlights the deep antiquity of treponemal diseases in the Americas. The findings, based on a 5,500-year-old specimen from Colombia, suggest syphilis’s emergence was not dependent on the agricultural intensification and population crowding often linked to the spread of infectious disease. Instead, it was dependent on social and ecological conditions of hunter-gatherer societies. “Reframing syphilis, alongside other infectious diseases, as products of both localized and highly specific evolutionary, ecological, and biosocial conditions and globalization may represent critical steps toward reducing stigma and improving public health,” write Molly Zuckerman and Lydia Ball in a related perspective. Treponemal diseases, such as syphilis, yaws, bejel, and pinta, have afflicted human populations across much of the world for thousands of years. However, much about the global antiquity and distribution of these diseases, as well as the evolutionary history of the bacteria that cause them, remains unknown. Among the most debated questions is the geographic origin and global spread of syphilis, which is caused by the bacterium T. pallidum . Some argue that the disease originated in the Americas and was brought to the Eastern Hemisphere following European contact in the late 15 th century. Others maintain that Treponema was already present in Europe before contact. Yet the rarity and ambiguity of skeletal evidence of these diseases and the technical difficulty of recovering ancient bacterial DNA from affected remains has made addressing these questions difficult.
David Bozzi and colleagues present a 5,500-year-old Treponema genome recovered from Middle Holocene-age human hunter-gatherer remains from Colombia. The new evidence extends the known genetic record of this pathogen by roughly 3,000 years. According to Bozzi et al. , phylogenetic analysis shows that this genome (TE1-3) represents a previously unknown branch of T. pallidum that split off before all other known subspecies emerged. Although it falls clearly within the T. pallidum species, TE1-3 is genetically diverse and distinct from modern strains. Notably, the authors found that TE1-3 also carries the full suite of genetic features associated with virulence in modern T. pallidum . Moreover, the findings suggest that T. pallidum predates the rise of agriculture in the Americas, indicating that the pathogen’s emergence was not dependent on the agricultural intensification and population crowding often linked to the spread of infectious disease. Instead, the TE1-3 lineage is associated with the social and ecological conditions of hunter-gatherer societies, including high mobility, small community interactions, and close contact with wild animals. According to Bozzi et al., the study’s findings expand the temporal, ecological, and social framework for understanding treponemal disease worldwide.
Science
A 5,500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia
22-Jan-2026