Ancient Syphilis Genome Rewrites Disease History in the Americas

A 5,500-year-old skeleton discovered in Colombia has yielded the oldest known genome of the bacterium responsible for syphilis and related diseases, revealing a previously unknown lineage that challenges existing understandings of the infection’s history and spread. The discovery, detailed in a recent January 22, 2026 publication in Science, pushes back the known timeline of treponemal diseases in the Americas by over 3,000 years.

The bacterium, Treponema pallidum, is the causative agent of syphilis, a sexually transmitted infection that can cause serious health complications if left untreated. However, T. Pallidum is also responsible for a group of related diseases, including yaws, bejel, and pinta, which exhibit varying symptoms and modes of transmission. Understanding the evolutionary relationships between these diseases is crucial for tracing their origins and developing effective prevention and treatment strategies.

Researchers, led by Anna-Sapfo Malaspinas at the University of Lausanne, extracted DNA from the tibia (shin bone) of a Middle Holocene hunter-gatherer found near Bogota. Despite the lack of visible bone damage typically associated with treponemal infections, the team successfully reconstructed a significant portion of the bacterium’s genome. The analysis revealed that this ancient strain diverged early from all known subspecies of T. Pallidum, representing a distinct and previously unrecognized lineage.

“This discovery extends the genetic record of these bacteria by more than 3,000 years,” explains Malaspinas, “and provides valuable clues about where these diseases came from and how they evolved.” The finding suggests that treponemal diseases were present in the Americas much earlier than previously thought, potentially predating the arrival of Europeans.

For decades, a prevailing theory suggested that syphilis was brought to Europe by sailors returning from the Americas in the 15th century. However, the discovery of ancient T. Pallidum strains in European remains, and now this new genome from Colombia, complicates that narrative. The possibility that European explorers may have actually acquired the infection in the Americas, and then spread it across the globe, is gaining traction.

The bacterium’s ability to cause disease – its virulence – appears to have been present in this ancient strain, suggesting it was capable of infecting people thousands of years ago. However, determining the exact mode of transmission – whether through sexual contact or skin-to-skin contact – remains challenging. Genetic markers that reliably distinguish between these transmission routes are limited.

Interestingly, the absence of obvious bone lesions in the ancient skeleton raises questions about the manifestation of the disease in the past. Not all infections leave detectable marks on bones, particularly in the early stages. The researchers speculate that the ancient strain may have caused a form of the disease similar to pinta, which primarily affects the skin and doesn’t typically cause skeletal damage.

The successful recovery of the ancient genome was a technical achievement, relying on advanced DNA sequencing techniques and careful analysis of a large dataset containing approximately 1.5 billion DNA fragments. The team at the University of Lausanne collaborated with researchers in California to confirm the findings and reconstruct the genome.

The implications of this discovery extend beyond historical understanding. Syphilis remains a significant public health concern globally, with an estimated 5.6 million cases occurring annually. While readily treatable with antibiotics like penicillin, access to healthcare and timely diagnosis remain challenges, particularly in underserved populations. The recent shortages of benzathine penicillin G, a key antibiotic used to treat syphilis, have further exacerbated the situation.

the resurgence of sexually transmitted infections, coupled with cuts to public health funding – such as the dismantling of the United States Agency for International Development (USAID) – has raised concerns about a potential increase in syphilis cases. A deeper understanding of the bacterium’s evolution could help identify changes that might affect its virulence or response to antibiotics.

Future research will focus on recovering genomes from additional ancient remains to determine whether the newly discovered lineage was widespread or confined to a specific geographic area. Analyzing DNA from both human and animal remains could also shed light on potential host-switching events, where the bacterium jumped between species. Recovering the genome of the organism responsible for pinta would further clarify its relationship to T. Pallidum.

The researchers emphasize the importance of ethical considerations in this type of research, sharing their findings with local communities in Colombia and incorporating their perspectives into the interpretation and dissemination of the results. This collaborative approach ensures that the research is conducted responsibly and respects the cultural heritage of the communities involved.

This study underscores the power of ancient DNA analysis to rewrite our understanding of infectious disease history. As more ancient genomes are recovered and analyzed, One can expect further insights into the origins and evolution of pathogens, ultimately informing our efforts to prevent and treat these diseases in the future.