Ancient syphilis genome traces the bacterium’s origins to the Americas

A 5,500-year-old genome of Treponema pallidum recovered from Colombia has revealed that syphilis-causing bacteria circulated in the Americas millennia before agriculture, undermining the disease’s previously presumed European origins

A newly sequenced ancient genome of the bacterium that causes syphilis – Treponema pallidum – has provided compelling evidence for the deep antiquity of treponemal diseases in the Americas. The findings, derived from a 5,500-year-old human specimen recovered in Colombia, have indicated that the emergence of syphilis was not dependent on agricultural intensification or sustained population crowding, factors often linked to the spread of infectious disease.

The data, instead, points towards social and ecological conditions associated with hunter-gatherer societies as sufficient to support the evolution and persistence of the pathogen and not European colonisation which has long been presumed as the origin of the pathogen.

Some scholars have argued that the disease originated in the Americas and was introduced to the Eastern Hemisphere following European contact in the late fifteenth century, while others have maintained that treponemal disease already existed in Europe before transatlantic contact. Progress in resolving this debate has remained limited because skeletal evidence is rare and often ambiguous and because recovery of ancient bacterial DNA from archaeological remains has posed major technical challenges.

Dr. David Bozzi and colleagues have now reported the recovery of a 5,500-year-old Treponema genome from Middle Holocene-age human hunter-gatherer remains in Colombia. This discovery has extended the known genetic record of T. pallidum by roughly 3,000 years. Phylogenetic analysis demonstrated that the genome – designated TE1-3 – represented a previously unrecognised lineage of T. pallidum that diverged before the emergence of all other known subspecies. While clearly belonging to the T. pallidum species, TE1-3 showed substantial genetic diversity and remained distinct from modern strains.

Notably, the researchers found that TE1-3 carried the full complement of genetic features associated with virulence in contemporary T. pallidum. This observation has suggested that key pathogenic traits evolved early in the history of the species. The results have also indicated that T. pallidum predated the rise of agriculture in the Americas, undermining models that have tied its emergence primarily to sedentary farming populations and dense settlements.

Instead, the TE1-3 lineage appeared to align with the social and ecological contexts of hunter-gatherer life, including high mobility, small and interconnected communities, and frequent close contact with wild animals.

According to Bozzi et al, the study has broadened the temporal, ecological and social framework through which treponemal disease can be understood on a global scale. By demonstrating that syphilis-causing bacteria thrived long before agriculture and urbanisation, the findings have challenged long-standing assumptions about how and when complex human pathogens emerged and have underscored the importance of considering diverse human lives in the evolutionary history of infectious disease.

“Reframing syphilis, alongside other infectious diseases, as products of both localised and highly specific evolutionary, ecological and biosocial conditions – [as well as] globalisation – may represent critical steps toward reducing stigma and improving public health,” wrote Dr. Molly Zuckerman seperately.

Treponemal diseases, including syphilis, yaws, bejel and pinta, have affected human populations across much of the world for thousands of years. Despite their long history, substantial uncertainty has persisted around their global antiquity, geographic distribution and the evolutionary trajectories of the bacteria responsible.

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