Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains

Abstract

Treponema pallidum 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 T. pallidum genomes (two from T. pallidum ssp. pallidum and one from T. pallidum ssp. pertenue) that have been reconstructed from skeletons recovered from the Convent of Santa Isabel in Mexico City, operational between the 17th and 19th century. Our analyses indicate that different T. pallidum subspecies caused similar diagnostic presentations that are normally associated with syphilis in infants, and potential evidence of a congenital infection of T. pallidum ssp. pertenue, the causative agent of yaws. This first reconstruction of T. pallidum genomes from archaeological material opens the possibility of studying its evolutionary history at a resolution previously assumed to be out of reach.

Ancient pathogen genomics as an emerging tool for infectious disease research

“…The evaluation of genetic relationships between ancient and modern pathogens is often conducted by direct whole genome or genome wide SNP compari sons of bacteria 20,27,29,36,48 , viruses 43,44,50,53 or mito chondrial genomes and nuclear genome data from eukaryotic microorganisms 56,59,60 . Hence, accurate variant calling is critical for drawing reliable evolutionary inferences, although this process is often a challenge when handling data sets derived from samples with high rates of DNA fragmentation (resulting in ultrashort read data), low endogenous DNA content and high levels of DNA dam age.…”

Ancient bacterial genomes reveal a formerly unknown diversity ofTreponema pallidumstrains in early modern Europe

“…Midpoint-rooted ML trees of our historical European genomes, previously published colonial Mexican genomes 45 and 26 modern treponemal genomes 34,[67][68][69][70][71][72][73][74][75] were constructed for the alignment. The four ancient European genomes are placed at three distinct positions in the phylogenetic tree.…”

“…Most notably, the bones that likely contain a large amount of treponemal agents belong to congenitally infected neonates. These fragile remains rarely survive and are, even when present, often overlooked in the archaeological record 44,45 . Previously, it would not have been feasible to use samples with low bacterial loads to detect pathogen DNA; however, recent advances in target-enrichment, high-throughput sequencing and sensitive screening methods for aDNA have aided overcoming this issue 46 .…”

“…pallidum and one ancient T. pallidum ssp. pertenue genome were described 45 . However, attempts to retrieve T. pallidum DNA from historical adult individuals have so far been unsuccessful.…”

Clinical round-up

“…We know syphilis has been around for centuries, but this paper from Schuenemann et al 2 describes finding three T pallidum genomes (two T pallidum pallidum and one T pallidum pertenue) in skeletons in a convent in Mexico City, which was known to be in use from the 17th to 19th centuries. They describe notable features consistent with congenital syphilis and yaws, and they conclude that this technique opens up the possibility of studying the evolutionary history of syphilis at greater depth.…”