A previously unknown strain of the syphilis-causing bacterium has been discovered in ancient human remains in Colombia, dating back 5,500 years. This groundbreaking find is more than 3,000 years older than the earliest known record of Treponema pallidum, the bacterium responsible for syphilis, and may provide crucial insights into the origins and spread of the disease.
The sample, recovered from a hunter-gatherer buried in a rock shelter in Sabana de Bogota, Colombia, represents a significant extension of the genomic record of treponematoses by over three millennia. The international study, led by Davide Bozzi from the Swiss Institute of Bioinformatics at the University of Lausanne, has been published in the peer-reviewed journal Science.
Uncovering Ancient Pathogens
According to the report, only a small percentage of people who contract syphilis exhibit “skeletal signs,” making ancient examples of the disease rare. The remains were found in Tequendama I, a rock shelter dating to the Middle Holocene, a period approximately 7,000 to 5,000 years ago. This area contains a “stratified sequence of burials spanning 10,000 to 2,300 calendar years before present,” the report noted.
The hunter-gatherer’s remains, though incomplete, were estimated to belong to an individual who died between the ages of 45 and 60+. Remarkably, there were no outward signs of syphilis. Bastien Llamas, an associate professor in Molecular Anthropology at the Australian Centre for Ancient DNA (ACAD), highlighted the significance of this discovery, stating that it demonstrates the potential of metagenomic screening to identify pathogens in bone even when no visible disease is present.
The ‘Shotgun’ Method
The researchers employed a “shotgun-sequencing” method to extract sections of the Treponema genome from a long fragment of tibia. This method, as explained by the National Human Genome Research Institute, involves randomly breaking up the genome into DNA fragments. Upon reassembly, the researchers identified what they termed TE1-3, a “previously unknown subspecies” that split off from other lines of Treponema pallidum over 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 subject of long-standing debate among scientists. Some researchers propose 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 suggests that syphilis was brought to Europe from the Americas by those traveling with Christopher Columbus in 1493.
Dr. George Taiaroa, an honorary research fellow at the University of Melbourne’s Doherty Institute, emphasized the value of the ancient Treponema 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,” said Dr. Mona Taouk, a Doherty Institute research fellow.
“Historical records, such as descriptions of outbreaks in travel accounts, are largely inscrutable,” noted anthropologists Molly Zuckerman and Lydia Bailey in a commentary published alongside the research. “Pathological lesions from Treponema on the human skeleton are uncommon and rarely distinctive.”
Modern Implications and Rising Syphilis Rates
Despite the historical insights provided by this discovery, the findings do not explain the current global rise in syphilis rates. In Australia, for example, 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. Notably, while 80 percent of diagnoses were among men, the rate of women being diagnosed has quadrupled in the same timeframe.
The World Health Organization estimated that about 8 million adults acquired syphilis globally in 2022.
Dr. Taiaroa attributes these trends to social, behavioral, and healthcare factors rather than changes in the bacterium itself. “What this study gives us is a deep-time perspective,” he stated. “The research shows syphilis and related diseases are ancient, with deep evolutionary roots, but preventing their impact today is very much a modern responsibility.”
As researchers continue to explore the ancient origins of syphilis, the challenge remains to address its modern resurgence, emphasizing the importance of public health initiatives and education in combating this age-old disease.
