5,500-year-old Treponema pallidum genome

Treponematosis (yaws, bejel, syphilis, pinta) caused by Treponema pallidum subspecies and T. carateum has afflicted humans worldwide for millennia. Despite paleopathological evidence and emerging genomic data, little is known about the evolutionary history of these pathogens. In this study, we report a 5,500-year-old Treponema genome (TE1-3) from Middle Holocene hunter-gatherer contexts of the rock shelter Tequendama I, Colombia. Our analyses place TE1-3 as a sister lineage to all known T. pallidum subspecies, positioning this pathogen in the Americas millennia before European contact and before diversification of the syphilis-, yaws-, and bejel-causing subspecies. This discovery broadens the known diversity of T. pallidum while extending the genomic record of treponemal pathogens by millennia, providing molecular support for a deep history of T. pallidum in the Americas.