A previously unknown strain of syphilis has been discovered in a 5,500-year-old remains in Colombia.
This ancient sample is more than 3,000 years older than the earliest record of Treponema pallidum, the bacterium that causes syphilis.
According to the report, only a small percentage of people with the disease experience “skeletal signs.” This means that ancient examples of the disease are rare.
This sample was recovered from a hunter-gatherer buried in a rock cave in Sabana de Bogota, Colombia, South America.
The discovery extends the “genomic record of treponemal infections” by more than 3,000 years and raises “new questions about the timing, routes, and drivers of treponemal epidemics,” according to the researchers’ paper.
Dr George Taiaroa, honorary research fellow at the Doherty Institute at the University of Melbourne, said the ancient Treponema genome was similar to the modern genome.
“The origin of Treponema pallidum in human populations has been the focus of research for hundreds of years,” he told the ABC.
“We have collected evidence of treponemal disease in pre-Columbian populations, and these signs often overlap with other symptoms.
“And some treponemal diseases are ‘archaeologically invisible.'”
‘Shotgun’ method to test DNA for ancient pathogens
The remains were discovered in Tekendama I, a mid-Holocene rock cave dating from about 7,000 to 5,000 years ago.
The area is home to what the report calls “a series of layered burials ranging from 10,000 to 2,300 calendar years before the present.”
Other bodies in the area showed “treponematosis-like lesions,” or damage similar to those caused by diseases such as syphilis, the report said.
Although the hunter-gatherer’s remains were incomplete, it is estimated that he died between 45 and over 60 years of age.
There were no outward signs of syphilis.
Bastian Lamas, associate professor of molecular anthropology at the Australian Center for Ancient DNA (ACAD), said this was “remarkable”.
“This highlights that metagenomic screening can detect pathogens in bone even in the absence of visible disease, potentially increasing the likelihood of future discoveries in ‘archaeologically invisible’ cases,” he said.
According to Professor Lamas, it was rare for this specimen to even be found in Colombia.
“Temperature plays an important role in preserving DNA,” he said.
“DNA can survive for up to hundreds of thousands of years if stored permanently in a frozen environment.
“Sabana de Bogota is located in the highlands of eastern Colombia.
“This region is blessed with a cool, warm high-altitude climate, which could help preserve ancient DNA for thousands of years.
Samples for ancient DNA analysis and radiocarbon dating were taken from the right tibia. (Provided by: Colombian Institute of Anthropology and History, Institute of Natural Sciences, National University of Colombia)
“So while it is possible to find a well-preserved microbial genome that is 5,500 years old, it is extremely rare in this part of the world.”
They extracted part of the treponemal genome from a long fragment of the tibia using “shotgun sequencing.”
According to the National Human Genome Research Institute, this “shotgun” method randomly splits the genome into DNA fragments.
When these fragments were reassembled, the researchers discovered what they called TE1-3, a “previously unknown variant.”
They estimated that TE1-3 diverged from other lineages of Treponema pallidum over 13,700 years ago.
“Our findings extend the genomic record of treponematosis by more than 3000 years,” the report said.
“In contrast, [more recent examples]TE1-3 reveals a deeper evolutionary history of this treponemal pathogen from ancient DNA and cultural contexts not yet explored in paleomicrobiology. ”
Their report did not list any potential limitations.
‘Rare’ chance to trace the controversial history of syphilis
Dr Taiaroa co-led research into modern syphilis in Australia with Doherty Institute Research Fellow Dr Mona Taouk.
Researchers, who were not involved in the study published today in Science, said the study provided a “rare” opportunity to trace the history of the disease.
“This ancient treponeme genome is valuable because it provides a rare calibration point for reconstructing the early evolution of syphilis and related diseases,” said Dr. Taouk.
“Having ancient references like this increases confidence in our evolutionary estimates and helps anchor major evolutionary events as they occur.”
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The origin of syphilis has been a long-standing debate among scientists.
Syphilis is a sexually transmitted disease that usually starts with one or more small wounds and progresses in stages.
If untreated, it can spread to the brain, nervous system, eyes, and other parts of the body, causing long-term damage.
Some researchers believe that syphilis and other treponemal diseases were widespread in Europe, Asia, and the Americas.
Their theory is that the sexually transmitted disease syphilis emerged in Southwest Asia around 3000 BC.
A more common theory suggests that people traveling with Christopher Columbus brought the disease from the Americas to Europe in 1493.
Anthropologists Molly Zuckerman and Lydia Bailey say researchers have often relied on “very limited and ambiguous evidence” to resolve the controversy.
The two wrote a commentary on the new research, which was published in a parallel journal.
“This discovery indicates that syphilis originated in the Americas rather than Europe.”
they said.
“Historical records, such as descriptions of outbreaks in travelogues, are mostly incomprehensible.
“Treponemal pathological lesions in the human skeleton are rare and have few distinctive features.”
However, the researchers added that DNA did not reveal when the disease evolved to be transmitted sexually.
To answer that question, researchers need to continue investigating.
Modern syphilis incidence rises in Australia
However, Dr Taiaroa said the new findings did not explain why syphilis rates are rising worldwide today.
The number of syphilis diagnoses in Australia has more than doubled in the past decade, to 5,866 in 2024, according to the Kirby Institute’s latest sexual health report.
Although 80% of diagnoses were in men, the rate of diagnoses in women increased even more rapidly, with the number of diagnoses increasing fourfold over the same period.
The World Health Organization estimates that approximately 8 million adults worldwide will be infected with syphilis in 2022.
“These trends are driven by social, behavioral and medical factors, rather than changes in the bacteria themselves,” Dr. Taiaroa said.
“What this research gives us is a deep time perspective.
“Research shows that syphilis and related diseases are ancient and have deep evolutionary roots, but preventing its effects today is a very modern responsibility.”