The oldest known genome of the bacterium responsible for syphilis and related diseases has been discovered in the remains of a 5,500-year-old hunter-gatherer buried near Bogotá, Colombia. The finding, published in the journal Science, pushes back the known history of treponemal diseases in the Americas by over 3,000 years and reveals a previously unknown lineage of Treponema pallidum.
Researchers from the University of Lausanne, in collaboration with an international team, reconstructed the bacterium’s genetic blueprint from DNA recovered from a tibia bone. The individual, a middle-aged man who lived around 3500 BCE, showed no visible signs of bone damage typically associated with treponemal infections, suggesting the disease can remain undetected in skeletal remains. This discovery challenges previous assumptions about the prevalence and visibility of these diseases in ancient populations.
The analysis revealed that the ancient strain represents a distinct branch within the Treponema pallidum species, diverging from all known subspecies approximately 13,700 years ago. This divergence occurred around the time the first humans were migrating across the Americas, suggesting the pathogen may have been present on the continent since its earliest peopling. The research team utilized novel bioinformatics methods, developed by SIB’s Population Genetics Group at the University of Lausanne, to analyze the ancient pathogen DNA, overcoming the challenges of recovering scarce bacterial DNA from ancient bones.
Treponema pallidum causes a range of diseases, including syphilis, yaws, and bejel, which continue to be public health concerns globally. The evolutionary origins of these diseases have been a subject of ongoing debate, with questions surrounding whether syphilis originated in the Americas and spread to Europe with Christopher Columbus, or if it originated elsewhere. This new evidence supports the theory that treponemal diseases were already circulating in the Americas long before European contact.
The discovery also highlights the potential for paleogenomics – the study of ancient DNA – to reveal previously unknown information about the history of infectious diseases. The successful recovery of T. Pallidum DNA from a healthy-looking bone demonstrates that many more ancient cases of these infections may have gone undetected, and that further research could uncover a more complete picture of their evolution and spread. Researchers are continuing to analyze ancient genomes to trace the origins and diversification of Treponema pallidum and related pathogens.
