Friday, January 23, 2026

Ancient DNA pushes back record of treponemal disease-causing bacteria by 3,000 years

Discovery adds to evidence of extensive pathogen diversity in the Americas long before European contact

University of Lausanne

image:
The archeological site of Tequendama I at the border of the Sabana de Bogotá, Cundinamarca, Colombia.
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Credit: Angélica Triana

Scientists have recovered a genome of Treponema pallidum – the bacterium whose subspecies today are responsible for four treponemal diseases, including syphilis – from 5,500-year-old human remains in Sabana de Bogotá, Colombia. The research expands knowledge about the history of this infectious disease and its occurrence in human populations, with findings now published in the journal Science.

The individual was archaeologically recovered from a rock shelter near Bogotá, Colombia, dating back roughly 5,500 years. The discovery pushes the genetic record of this pathogenic species back by more than 3,000 years, strengthening evidence that these infections have circulated in the Americas far longer than previously known.

“Our findings show the unique potential of paleogenomics to contribute to our understanding of the evolution of species, and potential health risks for past and present communities” said geneticist Lars Fehren-Schmitz at the University of California, Santa Cruz.

What are treponemal diseases?

Treponema pallidum is a spiral-shaped bacterium that exists in three closely related forms today, each responsible for a different disease: syphilis, yaws and bejel. A fourth treponemal disease, pinta, is caused by Treponema carateum or Treponema pallidum subsp. carateum, but no genome for this pathogen has yet been recovered, casting doubts about its phylogenetic relationships and taxonomic classification.

Although the three T. pallidum subspecies are nearly identical genetically, scientists do not know when or how the different disease forms emerged. Some data exists about the evolutionary history of pathogens, but there remain significant gaps between what skeletal remains reveal and what genetics can confirm.

For the study, the research team demonstrated that the ancient DNA recovered belongs to the Treponema pallidum species, but it does not match any of the genetically known forms that cause disease today. The scientists showed that while it is closely related, it diverged early in the evolutionary tree.

“One possibility is that we uncovered an ancient form of the pathogen that causes pinta, which we know little about, but is known to be endemic in Central to South America and causes symptoms localized to the skin,” said Anna-Sapfo Malaspinas at the University of Lausanne and group leader at the SIB Swiss Institute of Bioinformatics. “At this time, we cannot prove this is the case, but it is a lead worth investigating further.”

Scientists estimate this ancient strain split from other T. pallidum lineages about 13,700 years ago. The three modern subspecies, by comparison, diverged much more recently, about 6,000 years ago, which aligns with previous research. These findings shed new light on how diverse these pathogens were in the past and serve as a reference point for understanding when they began branching into different forms.

"Current genomic evidence, along with our genome presented here, does not resolve the long-standing debate about where the disease syndromes themselves originated, but it does show there's this long evolutionary history of treponemal pathogens that was already diversifying in the Americas thousands of years earlier than previously known,” said Elizabeth Nelson, a molecular anthropologist and paleopathologist at SMU.

A genetic puzzle

Understanding how treponemal diseases emerged and how treponemal pathogens evolved is surprisingly complicated because the bacteria are almost identical genetically, yet they get transmitted differently and can vary in clinical presentation.

“Our results push back the association of T. pallidum with humans by thousands of years, possibly more than 10,000 years ago in the Late Pleistocene,” said researcher Davide Bozzi at the University of Lausanne and SIB Swiss Institute of Bioinformatics.

This discovery builds on years of collaborative archaeological and genomic research at the Tequendama 1 site. Archaeologist Miguel Delgado at the Universidad Nacional de La Plata in Argentina and Fehren-Schmitz had previously published work offering detailed context about the skeleton.

The finding emerged unexpectedly. Researchers originally sequenced the individual’s DNA to study human population history, generating 1.5 billion fragments of genetic data—far more than typical studies. While screening the data, teams at the University of California, Santa Cruz and the University of Lausanne independently detected T. pallidum and joined forces to investigate. The bacterial DNA made up only a tiny fraction of the genetic material, but the unusually deep sequencing allowed researchers to reconstruct the genome without the specialized techniques normally required.

The three diseases caused by T. pallidum (bejel, yaws, and syphilis) can leave marks on bones, but only at certain stages and not in every infected person. Most ancient T. pallidum genomes have been recovered from teeth or bones of people with clear signs of infection, but this skeleton showed none. Researchers sampled a tibia, or shin bone, a skeletal element not typically used for ancient DNA extraction. The approach paid off, suggesting that even bones without visible signs of disease could be valuable sources of pathogen DNA.

Researchers believe understanding how infectious diseases emerged and evolved in the past could help scientists predict how they may change in the future and help societies prepare for what lies ahead.

Before publishing, the researchers shared their findings with communities in Colombia, recognizing the discovery's significance to the country's medical history. They consulted with local scholars, students and community members, and connected with stakeholders through presentations and interviews. The team also obtained all necessary permits for exportation and study.

"This process was essential because the findings are deeply connected to Colombia's medical and cultural history," said Delgado. "Engaging scholars, students, and Indigenous and non-Indigenous community members ensures the results are ethically communicated and interpreted in partnership with local communities. This approach builds trust, supports responsible stewardship of sensitive discoveries, and reinforces local ownership of knowledge."

In addition to Nelson, Bozzi, Malaspinas, Delgado and Fehren-Schmitz, Nasreen Broomandkhoshbacht, now at the University of Vermont, also co-led the research, working with Kalina Kassadjikova of the University of California, Santa Cruz; Jane Buikstra of Arizona State University; Carlos Eduardo G. Amorim of California State University, Northridge; Melissa Estrada Pratt of the Instituto Colombiano de Antropología e Historia in Bogotá, Colombia; Gilbert Greub of the University of Lausanne and Lausanne University Hospital in Switzerland; Nicolas Rascovan of the Institut Pasteur in Paris; and David Šmajs of Masaryk University in the Czech Republic.

The archeological site of Tequendama I at the border of the Sabana de Bogotá, Cundinamarca, Colombia.

Credit

Angélica Triana

Journal

Science

DOI

10.1126/science.adw3020

Article Title

A 5,500-year-old Treponema pallidum genome from Sabana de Bogotá, Colombia

Article Publication Date

22-Jan-2026

Illinois study: How a potential antibiotics ban could affect apple growers

University of Illinois College of Agricultural, Consumer and Environmental Sciences

close-up of apple blooms infected with fire blight — image:
Apple blossoms infected with fire blight.
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Credit: Tianna DuPont, WSU Extension

URBANA, Ill. – Antibiotic resistance in human and animal health is on the forefront of public debate, but it’s a less well-known issue in plant agriculture. However, antibiotics are important tools in fruit production, and their efficacy hinges on avoiding resistance in disease-causing bacteria.

The U.S. does not currently restrict antibiotics use in fruit orchards, but regulatory measures could occur in the future. A new study from the University of Illinois Urbana-Champaign examines how apple growers might respond to a potential ban on antibiotics and how those responses could affect management decisions and profitability.

“The majority of antibiotics in plant agriculture are used on fire blight in pear and apple orchards. Growers face a dilemma, because they must treat their trees to protect them, but they run the risk of overusing the pesticides, so the disease develops resistance,” said lead author Khashi Ghorbani, doctoral candidate in the Department of Agricultural and Consumer Economics, part of the College of Agricultural, Consumer and Environmental Sciences at Illinois.

Fire blight is a devastating bacterial disease that causes flowers, leaves, and fruit to wilt and die, and it can severely damage affected orchards. Treatment options are limited, but spraying blossoms with an antibiotic such as streptomycin can protect against the disease. Controlling for fire blight is a significant expense; for example, growers spent an average of $250 per acre on preventative sprays during a 2017-18 disease outbreak in Washington State, the country’s premier apple producing state.

“The U.S. already has numerous federal and state restrictions on other pesticides and fungicides, so a ban on streptomycin is quite possible,” said co-author Shadi Atallah, associate professor in ACE.

The researchers developed a dynamic model that evaluates growers’ management decisions regarding antibiotic use when there is uncertainty about whether a ban will be enforced.

Their modeling scenario assumed two types of growers, representing opposite ends of a spectrum. The researchers note that these are extreme positions, and most grower strategies would fall somewhere in the middle.

At one end of the spectrum is the “business as usual” grower, who continues to apply antibiotics at the optimal levels based on a long time horizon, without planning for a future ban.

At the other end of the spectrum is the proactive grower, who would adjust their spraying schedule according to the looming ban. They would increase their antibiotic use to ensure maximum efficiency before the product is no longer available.

Ghorbani and Atallah find that the proactive grower is going to benefit from this strategy if the government does enforce the ban. However, if the ban does not happen, the business-as-usual grower will be better off.

“Imagine that 10 years from now you have adjusted your application according to a potential ban, but it does not materialize. You will be in a situation where you still have access to the pesticide, but the efficacy is not there anymore because you have depleted the resource,” Ghorbani said.

They also looked at whether the value of the crop influences the outcome, as antibiotic efficacy can be considered a non-renewable resource that derives its value from the crop it protects, rather than having intrinsic value.

Indeed, they find that growers of lower-value apple varieties such as Fuji and Gala are more vulnerable to regulatory uncertainty and suffer the most damage from it, while those who grow higher-value varieties such as Honeycrisp are less affected.

“We found that the negative impact for proactive growers diminished as the crop value increased. It underscores that crop choices can have a long-term impact on the economics of the farm, and that higher value crops can help mitigate the uncertainty that comes from policy shifts,” Ghorbani said.

The study presents a hypothetical scenario, but it’s not far from reality, Atallah noted.

“As U.S. administrations come and go, regulatory priorities change, and there is considerable uncertainty regarding policies towards herbicides and pesticides,” he said. “Our model is a planning tool that tells you what would happen under different circumstances.”

The study demonstrates to policymakers how uncertainty affects the decisions of farmers and what the economic and ecological consequences might be. The findings can also illustrate how growers of different apple varieties would need to be compensated for production losses considering their management decisions and possible incentives for their actions.

Ghorbani adds that the study also provides a broader perspective.

“Bringing the issue to the surface will hopefully get people to think about how to ensure optimal antibiotic use for plant agriculture, in addition to human medicine or animal agriculture,” he said.

The paper, “Strategic responses to ban enforcement uncertainty: Antibiotic application decisions in plant agriculture,” is published in the European Review of Agricultural Economics [DOI:10.1093/erae/jbaf068].

Research in the College of ACES is made possible in part by Hatch funding from USDA’s National Institute of Food and Agriculture. This study was also supported by USDA-NIFA under grant number 1023572.

"Shepherd's crook" is a symptom of fire blight.