A 5500-year-old <i>Treponema pallidum</i> genome from Sabana de Bogotá, Colombia.

Bozzi, Davide; Broomandkhoshbacht, Nasreen Z; Delgado, Miguel; Buikstra, Jane E; Amorim, Carlos Eduardo G; Kassadjikova, Kalina; Estrada, Melissa Pratt; Greub, Gilbert et al. · Science · 2026

basic_science · Level V

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Abstract

Treponematosis, a bacterial infection caused by <i>Treponema pallidum</i> subspecies and <i>T. carateum</i> (yaws, bejel, syphilis, pinta), has afflicted humans for millennia. Despite paleopathological evidence and emerging genomic data, little is known about the evolutionary history of these pathogens. We report a 5500-year-old <i>Treponema</i> genome (TE1-3) from Middle Holocene hunter-gatherer contexts of the rock shelter Tequendama I in Colombia. Our analyses place TE1-3 as a sister lineage to all known <i>T. pallidum</i> subspecies, positioning this pathogen in the Americas millennia before European contact and before diversification of the subspecies causing syphilis, yaws, and bejel. This discovery broadens the known diversity of <i>T. pallidum</i> while extending the genomic record of treponemal pathogens by millennia, providing molecular support for a deep history of <i>T. pallidum</i> in the Americas.

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