Historic <i>Treponema pallidum</i> genomes from Colonial Mexico retrieved from archaeological remains

<div><p><i>Treponema pallidum</i> infections occur worldwide causing, among other diseases, syphilis and yaws. In particular sexually transmitted syphilis is regarded as a re-emerging infectious disease with millions of new infections annually. Here we present three historic <i>T</i>. <i>pallidum</i> genomes (two from <i>T</i>. <i>pallidum</i> ssp. <i>pallidum</i> and one from <i>T</i>. <i>pallidum</i> ssp. <i>pertenue</i>) that have been reconstructed from skeletons recovered from the Convent of Santa Isabel in Mexico City, operational between the 17^th and 19^th century. Our analyses indicate that different <i>T</i>. <i>pallidum</i> subspecies caused similar diagnostic presentations that are normally associated with syphilis in infants, and potential evidence of a congenital infection of <i>T</i>. <i>pallidum</i> ssp. <i>pertenue</i>, the causative agent of yaws. This first reconstruction of <i>T</i>. <i>pallidum</i> genomes from archaeological material opens the possibility of studying its evolutionary history at a resolution previously assumed to be out of reach.</p></div

Summary statistics of the three positive historic samples.

<p>Summary statistics of the three positive historic samples.</p

Examples for bone lesions for the three positive individuals.

<p>(A) The right tibia of individual 94A displays reactive periosteal bone on the anterior aspect of the diaphysis accompanied by progressive layering of the reactive bone. (B) The <i>pars basilaris</i> portion of the cranium of individual 94A showing pathological reactive bone in the endocranial surface, active at time of death. (C) An unidentified long bone from individual 94B displays fulminating periosteal reaction involving the whole of the diaphysis fragment. (D) The left femur of individual 133 presenting periosteal bone formation and expansion with cortical resorption characteristic of treponemal diseases. Source of the pictures: skeletal collection from Santa Isabel Convent, Mexico City, in custody of the Laboratory of Osteology, Post Graduate Studies Division, National School of Anthropology and History (ENAH), Mexico.</p

Phylogenetic trees and Circos plot [90] of the three ancient strains in comparison to modern strains.

<p>(A) Maximum Likelihood tree with bootstrap support for 39 modern strains and the three ancient strains. The strains 94A (magenta) and 94B (orange) branch with the syphilis SS14 clade while strain 133 (brown) branches with Fribourg-Blanc and other yaws strains. The scale represents the mean number of substitutions per site according to the GTR+GAMMA. Colored bars highlight the three subspecies <i>Treponema pallidum</i> ssp <i>pallidum</i> (TPA), <i>pertenue</i> (TPE) and <i>endemicum</i> (TEN). Strains of subspecies <i>pallidum</i> cause syphilis, subspecies <i>pertenue</i> cause yaws and subspecies <i>endemicum</i> causes bejel. (B) Bayesian trees visualized in Densitree overlaying phylogenetic trees based on the most probable topologies. Blue colored trees represent the most probable topology followed by red colored trees. For the ancient strains 94A and 94B two conflicting topologies are visible. The bars represent the 95% highest probability density intervals of the heights of the clades. The support value given at each clade is the fraction of trees in the tree-set that contain the clade. (C) Circos plot showing the shared SNP positions with specific clades and the coverage of the three ancient strains. From outer circle to the inner circle regions of possible recombination detected by ClonalFrameML are denoted on the outermost circle (purple). ‘ORI’ refers to the origin of replication. The genome coverages of the ancient strains 94B, 94A and 133 are represented in orange magenta and brown respectively from outward to inwards. Based on the SNPs that are specifically shared with different clades, colored bars are shown for strains 94B and 94A respectively in the innermost circles. Red bars highlight the SNP positions specifically shared with Fribourg-Blanc (supporting a phylogenetic position ancestral to the two syphilis clades). The green bars highlight the SNP positions shared with the SS14 clade while the blue bars highlight the SNP positions shared with the Nichols clade.</p