A groundbreaking discovery in Colombia has unveiled a previously unknown strain of syphilis bacteria in human remains dating back 5,500 years. This ancient sample predates the earliest known record of Treponema pallidum, the bacterium responsible for syphilis, by over 3,000 years. The findings, published in the journal Science, could significantly alter our understanding of the disease’s history and spread.
The sample was recovered from a hunter-gatherer buried in a rock shelter in Sabana de Bogotá, Colombia. Led by Davide Bozzi from the Swiss Institute of Bioinformatics at the University of Lausanne, the international study extends the genomic record of treponematoses by more than three millennia. It also raises new questions about the timing, routes, and drivers of treponemal spread.
Unveiling the Past: Ancient DNA Analysis
The remains were found in Tequendama I, a rock shelter dating to the Middle Holocene, approximately 7,000 to 5,000 years ago. This site is known for its stratified sequence of burials spanning 10,000 to 2,300 calendar years before present. The hunter-gatherer’s remains, though incomplete, were estimated to belong to an individual who died between 45 to 60+ years of age.
Remarkably, there were no outward signs of syphilis on the skeleton. According to Bastien Llamas, an associate professor in Molecular Anthropology at the Australian Centre for Ancient DNA, this highlights the potential of metagenomic screening to find pathogens in bone even when no visible disease is present. This method could increase the chances of discovering “archaeologically invisible” cases.
The ‘Shotgun’ Method: A New Approach to Ancient Pathogen DNA
From a long fragment of tibia, researchers extracted sections of the Treponema genome using “shotgun-sequencing”. This method, as explained by the National Human Genome Research Institute, involves randomly breaking up the genome into DNA fragments. When reassembled, researchers identified a previously unknown subspecies, TE1-3, which split from other lines of Treponema pallidum more than 13,700 years ago.
“Our findings extend the genomic record of treponematoses by more than three millennia,” the report stated. “In contrast to more recent examples, TE1-3 reveals a deeper evolutionary history for this treponemal pathogen from cultural contexts not yet examined by ancient DNA and paleomicrobiology.”
Tracing the Controversial History of Syphilis
The origin of syphilis has been a long-standing debate among scientists. Some researchers suggest that syphilis and other treponemal diseases were widespread in Europe, Asia, and the Americas, with sexually transmitted syphilis emerging in South-Western Asia around 3000 BC. A more popular theory posits that Christopher Columbus’s crew brought the disease from the Americas to Europe in 1493.
Dr. George Taiaroa, an honorary research fellow at the University of Melbourne’s Doherty Institute, emphasized the value of the ancient treponeme genome as a rare calibration point for reconstructing the early evolution of syphilis and related diseases. “Having an ancient reference like this improves confidence in our evolutionary estimates and helps anchor when major evolutionary events occur,” noted Dr. Mona Taouk, a Doherty Institute research fellow.
“Historical records, such as descriptions of outbreaks in travel accounts, are largely inscrutable. Pathological lesions from Treponema on the human skeleton are uncommon and rarely distinctive,” anthropologists Molly Zuckerman and Lydia Bailey commented in a related commentary.
Modern Implications: Rising Syphilis Rates Today
Despite the insights into the ancient past, the study does not explain the current rise in syphilis rates globally. In Australia, syphilis diagnoses have more than doubled over the past decade, reaching 5,866 diagnoses in 2024, according to the Kirby Institute’s latest sexual health report. The World Health Organization estimated that about 8 million adults acquired syphilis globally in 2022.
Dr. Taiaroa pointed out that these trends are driven by social, behavioral, and healthcare factors rather than changes in the bacterium itself. “What this study gives us is a deep-time perspective. The research shows syphilis and related diseases are ancient, with deep evolutionary roots, but preventing their impact today is very much a modern responsibility,” he concluded.
The discovery in Colombia not only sheds light on the ancient origins of syphilis but also underscores the ongoing challenge of combating the disease in contemporary society. As researchers continue to explore the evolutionary history of syphilis, the findings may provide critical insights into preventing its spread in the future.
