The age-old question remains: whether European colonists dragged syphilis back to the Old World in their blood after forays in the Americas, or whether the dreaded disease was already spread across the breadth of humanity by the 15th century.

A new breakthrough by European scientists has still not solved the riddle, but they may have laid the groundwork for finally understanding the whole history of a centuries-old scourge on humanity.

Three genomes sequenced from the bones of babies buried at a convent in colonial-era Mexico have provided the latest answers, according to the paper, in the journal PLOS Neglected Tropical Diseases

They isolated the genomes of Treponema pallidum, including ancient samples of the bacterial subspecies that causes syphilis, the researchers report.

“The ancient T. pallidum genomes presented here allow us, for the first time, to perform genome-wide comparative analyses and to assess a connection between osteological manifestations of past treponemal cases and specific T. pallidum species,” the scientists write.

The specimens were all ancient babies, buried at the Convent of Santa Isabel in Mexico City. The Convent had been run by Franciscan nuns from 1681 to 1861. A group of 239 sets of bones were unearthed in the 1990s. About 90 percent of the remains were from fetuses, newborns, and infants, according to the paper.

Five of the skeletons were selected because the bones seemed to show the evidence of bone lesions and other trace evidence of syphilis. From the long bones, approximately 50 mg of bone powder was extracted, and purified. The DNA was amplified, according to the paper.

Three tested positive for T. pallidum DNA. Those sets of remains, which were dated generally from the last 350 years, yielded another 50mg extraction of bone powder.

Next-generation sequencing was employed in the full run of the bacterial DNA.

The scientists also used whole-genome array capture to reduce background and environmental DNA. Mitochondrial sequencing was also run through high-throughput sequencing, to gauge the extent of DNA damage over the centuries of burial.

One of the three babies had a subspecies called T. pallidum ssp. pertenue that causes a skin disease called yaws. But the other two carried T. pallidum ssp. pallidum that causes syphilis.

“Our study demonstrates the possibility of retrieving ancient T. pallidum genomes from archaeological material, and thereby establishes a new method that could greatly contribute to uncover the mystery regarding the origins of treponemal diseases,” the authors said.

But so far, that exact family tree of the deadly germ remains elusive, according to a statement from Alexander Herbig, a corresponding author from the Max Planck Institute for the Science of Human History.

“Previous research that found the presence of T. pallidum ssp. pertenue in Old World monkey, and our finding that two T. pallidum subspecies likely caused similar skeletal manifestations in the past, may suggest a more complex evolutionary history of T. pallidum than previously assumed,” Gerbig said in a statement.