An international team recovered a 5,500-year-old genome of Treponema pallidum from a human shin bone containing what is believed to be the earliest sample of syphilis-linked bacteria, as published in the peer-reviewed journal Science in late January.
The ancient lineage, dubbed TE1-3, is the oldest treponemal genome yet identified and diverged far earlier than known strains, the study noted. The sample was found at the Tequendama rock shelter on the Sabana de Bogotá, Colombia.
The genome does not match those of modern syphilis, yaws, or bejel, indicating a previously unknown branch of the pathogen group, and the skeleton lacked the classic bone lesions of advanced treponemal disease, even though sufficient pathogen DNA was preserved to reconstruct the genome.
Lead author Davide Bozzi said the findings “push back the association of T. pallidum with humans by thousands of years,” adding that the split from other lineages may reach “more than 10,000 years ago.” The team’s modeling places TE1-3’s divergence at roughly 13,700 years ago, while the three modern T. pallidum subspecies likely diverged around 6,000 years ago.
Co-author Elizabeth Nelson cautioned that, while the genome deepens the historical record, it does not settle the question of where today’s distinct disease syndromes originated: “Current genomic evidence… does not resolve the long-standing debate… but it does show there’s this long evolutionary history of treponemal pathogens,” she said.
The researchers emphasized that TE1-3 sits outside known disease-causing subspecies, with Anna-Sapfo Malaspinas noting one possibility is “an ancient form of the pathogen that causes pinta,” a skin-limited treponematosis still endemic in parts of Central and South America, though she stressed this cannot yet be proven.
Syphilis became evident in Europe around 15th century
According to the study, documentary evidence of syphilis in Europe becomes clear in the late 15th century; the Colombian genome strengthens the American-origin hypothesis by anchoring treponemal diversity in the Americas thousands of years earlier, while not confirming sexual transmission in this individual.
The project’s unusually deep sequencing, originally undertaken for human population history, generated about 1.5 billion genetic fragments and enabled the detection of scarce bacterial reads without specialized pathogen-enrichment techniques, the team said. “Our findings show the unique potential of paleogenomics to contribute to our understanding of the evolution of species, and potential health risks for past and present communities,” said Lars Fehren-Schmitz.
The skeleton was sampled from the tibia, a bone not typically used for ancient pathogen work. This success suggests that even remains without visible lesions can harbor recoverable pathogen DNA, broadening the range of contexts in which such infections might be detected in the archaeological record.
Before publication, the researchers shared results with communities in Colombia and obtained the necessary permits, according to the statement. “Engaging scholars, students, and Indigenous and non-Indigenous community members ensures the results are ethically communicated,” archaeologist Miguel Delgado said.