A previously unknown strain of syphilis bacteria has been discovered in human remains in Colombia, dating back 5,500 years.
The ancient sample is more than 3,000 years older than the earliest known record of Treponema pallidum, the bacterium responsible for syphilis.
Only a small percentage of people who contract the disease experience "skeletal signs", according to the report — meaning ancient examples of the disease are rare.
The sample was recovered from a hunter-gatherer, who was buried in a rock shelter in Sabana de Bogota in Colombia, South America.
The international study, led by Davide Bozzi from the Swiss Institute of Bioinformatics at the University of Lausanne. has been published today in the peer-reviewed journal Science.
The findings extended the "genomic record of treponematoses by more than three millennia" and opened "new questions about the timing, routes, and drivers of treponemal spread", according to the researchers' paper.
Dr George Taiaroa, an honorary research fellow at the University of Melbourne's Doherty Institute, said the ancient Treponema genome was similar to its modern counterpart.
"The origins of Treponema pallidum in human populations have been the focus of study for hundreds of years," he told the ABC.
"Although we have gathered evidence for treponemal disease in pre-Colombian populations … these signatures often overlap with other conditions.
"And some treponemal diseases are 'archaeologically invisible'."
The 'shotgun' method testing ancient pathogen DNA
The remains were found in Tequendama I, a rock shelter dated to the Middle Holocene, a period about 7,000 to 5,000 years ago.
The area is home to what the report called a "stratified sequence of burials spanning 10,000 to 2,300 calendar years before present".
Other remains in the area, the report said, showed "treponematosis-like lesions", or damage similar to that caused by diseases like syphilis.
The hunter-gatherer's remains were incomplete, however it was estimated he died somewhere between 45 to 60+ years of age.
There were no outward signs of syphilis.
This, according to Bastien Llamas, an associate professor in Molecular Anthropology at the Australian Centre for Ancient DNA (ACAD), was "remarkable".
"This highlights that metagenomic screening can find pathogens in bone even when no visible disease is present, potentially increasing the chances of future discoveries in "archaeologically invisible" cases," he said.
Even finding the specimen in Colombia, according to Professor Llamas, was rare.
"Temperature plays a significant role in the preservation of DNA," he said.
"DNA can survive for up to hundreds of thousands of years if permanently preserved in a frozen environment.
"The Sabana de Bogota is located in the eastern highlands of Colombia.
"The region has a cool, temperate highland climate that could help preserve ancient DNA for a few thousand years.
"Therefore, finding a 5,500-year-old well-preserved microbial genome is possible but highly unusual in this part of the world."
From a long fragment of tibia, they extracted sections of the Treponema genome via "shotgun-sequencing".
This "shotgun" method, according to the National Human Genome Research Institute, randomly breaks up the genome into DNA fragments.
When those fragments were reassembled, researchers found what they called TE1-3 — a "previously unknown subspecies".
They estimated TE1-3 split off 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 said.
"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."
Their report did not note any potential limitations.
'Rare' chance to trace the controversial history of syphilis
Dr Taiaroa co-led a study on modern-day syphilis in Australia, alongside Dr Mona Taouk, a Doherty Institute research fellow.
The researchers, who were not involved in the study published in Science today, said it provided a "rare" chance to trace the history of the disease.
"This ancient treponeme genome is valuable as it provides a rare calibration point for reconstructing the early evolution of syphilis and related diseases," Dr Taouk said.
"Having an ancient reference like this improves confidence in our evolutionary estimates and helps anchor when major evolutionary events occur."
The origin of syphilis has been a long-running debate among scientists.
Syphilis is a sexually transmitted infection, typically beginning as one or multiple small sores and progressing in stages.
If untreated, it can spread to the brain and nervous system, the eye and other parts of the body, causing long-term damage.
Some researchers believe syphilis and other treponemal diseases were widespread in Europe, Asia and the Americas.
In their theory, sexually transmitted syphilis emerged in South-Western Asia about 3000 BC.
A more popular theory suggests that those travelling with Christopher Columbus brought the disease from the Americas to Europe in 1493.
To resolve this debate, researchers have often relied on "highly limited and ambiguous evidence", according to anthropologists Molly Zuckerman and Lydia Bailey.
The pair penned a commentary on the new research, published alongside it in the journal.
"The finding points to an origin for syphilis in the Americas rather than in Europe," they said.
"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."
But the DNA didn't show when the disease evolved to be transmitted sexually, they added.
To answer that question, researchers will need to keep digging.
Rates of modern syphilis on the rise in Australia
But the new findings, according to Dr Taiaroa, did not explain why syphilis rates were on the rise globally today.
Syphilis diagnoses in Australia have more than doubled over the past decade to 5,866 diagnoses in 2024, according to the Kirby Institute's latest sexual health report.
While 80 per cent of diagnoses were men, the rate of women being diagnosed was increasing even faster, with the number of diagnoses quadrupling in the same time frame.
The World Health Organisation estimated that about 8 million adults had acquired syphilis globally in 2022.
"Those trends are driven by social, behavioural and healthcare factors rather than changes in the bacterium itself," Dr Taiaroa said.
"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."
