Ancient DNA pushes back record of syphilis-causing bacteria by 3,000 years
The archeological site of Tequendama I at the border of the Sabana de Bogotá, Cundinamarca, Colombia. Photo credit: Angélica Triana
Scientists have recovered the oldest known genome of Treponema pallidum — the bacterium responsible today for several treponemal diseases, including syphilis — from 5,500-year-old human remains in present-day Colombia.
The findings, published in Science, push the genetic record of this pathogen back more than 3,000 years and demonstrate that treponemal infections were circulating in the Americas long before European contact.
The individual was excavated from a rock shelter in the Sabana de Bogotá region and dated to approximately 5,500 years ago. While earlier archaeological evidence suggested treponemal disease may have been present in ancient populations, this study provides the earliest direct genetic confirmation.
“My role in this study was to evaluate the disease-altered bone and assess the impact of infection on the individual,” said Jane Buikstra, Regents Professor in Arizona State University’s School of Human Evolution and Social Change. Notably, Buikstra and colleagues found no visible skeletal signs of treponemal disease in the remains.
Because skeletal lesions appear in only a portion of infected individuals and often only at later stages of disease, the absence of visible pathology does not rule out infection. Instead, researchers turned to deep DNA sequencing data, demonstrating the power of paleogenomics to identify pathogens even when disease is not suspected.
“This study highlights the unique potential of paleogenomics to illuminate the long-term evolution of infectious diseases and their risks for past and present populations,” said Lars Fehren-Schmitz, a geneticist at the University of California, Santa Cruz.
In a first for ancient disease research, Treponema DNA was recovered from a non-pathological section of cortical bone from the tibia, rather than from visibly diseased bone or dental pulp, which is typically used for detecting systemic infections. The unexpected result underscores the value of metagenomic screening of sequencing data generated for other purposes, such as studies of human population history.
Treponemal diseases today are caused by closely related forms of Treponema pallidum, including syphilis, yaws and bejel. A fourth disease, pinta, is caused by Treponema carateum or a closely related subspecies, though no genome has yet been recovered.
“Not having disease-altered bone would fit the pinta model,” Buikstra said. “While these results about the disease very important, we must not forget the people who carried the bacterium and how they and their communities were affected.”
Although these pathogens are nearly identical genetically, they differ in transmission routes and clinical presentation, and their evolutionary origins remain poorly understood.
The ancient genome recovered in this study belongs to T. pallidum but does not match any known modern subspecies. Instead, it represents an early-diverging lineage, suggesting a previously unknown diversity of treponemal pathogens in the past.
“One possibility is that we uncovered an ancient form related to the pathogen that causes pinta, which is endemic to Central and South America,” said Anna-Sapfo Malaspinas of the University of Lausanne and the SIB Swiss Institute of Bioinformatics. “While we cannot confirm this yet, it is an important lead for future research.”
Researchers estimate that this ancient lineage split from other T. pallidum strains about 13,700 years ago, while the modern disease-causing subspecies diverged much more recently, around 6,000 years ago. Together, the findings reveal a long and complex evolutionary history of treponemal pathogens in the Americas.
The discovery was made unexpectedly while researchers were analyzing extensive DNA data generated to study ancient human population history. Although bacterial DNA represented only a tiny fraction of the genetic material, unusually deep sequencing enabled reconstruction of the pathogen’s genome without specialized enrichment techniques.
Before publication, the research team shared their findings with scholars, students and community members in Colombia, and obtained all necessary permits for study and export.
“Engaging with local communities is essential when research touches on cultural and medical history,” archaeologist Miguel Delgado said. “This collaborative approach supports ethical stewardship and shared ownership of knowledge.”
Understanding how infectious diseases emerged and evolved in the past, researchers say, may help scientists better anticipate how pathogens could change in the future.
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