For years the scene seemed simple enough: certain infections would arrive in the Americas together with the Europeans. Then a tooth, preserved for centuries in a museum in La Paz, was enough to call everything into question. From that find, which belonged to a young man who lived on the Bolivian Altiplano between 1283 and 1383, a group of researchers has reconstructed an almost complete ancient genome of Streptococcus pyogenesthe bacterium that we now associate with pharyngitis, invasive infections and, in some strains, even with scarlet fever. The discovery pushes back its documented presence in the Americas by centuries.
The find comes from MUNARQthe National Museum of Archeology of La Paz. The individual analyzed had Native American ancestry, confirmed by mitochondrial DNA, and the preservation of the remains was favored by the cold and dry climate of the Altiplano. These are details that matter, because they explain how it was possible to recover genetic material intact enough to allow such a precise reconstruction.
The ancient genome of Streptococcus pyogenes
The study, published on Nature Communicationswas based on shotgun metagenomic sequencing and a technique called new assemblywhich recomposes a genome starting from many small fragments of DNA without using a ready-made modern map. It is an important step, because it reduces the risk of forcing ancient data into patterns built on the present. From this work emerged an ancient strain close to contemporary lines of S. pyogenes mainly linked to pharyngitis.
Here, however, caution is needed which the easy title tends to overlook. Saying that this discovery “rewrites the history of scarlet fever” works well, but the paper tells a more precise nuance. The authors explain that the ancient genome preserves central virulence genes, while the reconstructed prophages include streptococcal pyrogenic exotoxins. The CDC reminds us that scarlet fever is caused by strains of Streptococcus pyogenes producers of pyrogenic exotoxins. The really solid part, then, concerns the pre-Columbian presence of the bacterium in the Americas. The direct link with an ancient case of scarlet fever remains closer, more cautious, more technical.
This does not reduce the weight of the discovery. It changes its tone, which is a different thing. There Bolivian mummy he does not give the clinical diagnosis of that young man and does not say what he died from. However, it delivers very strong genetic evidence: S. pyogenes it circulated among indigenous South American populations before European contact. At that point the idea of a simple “importation” after 1492 narrows considerably.
The value of the discovery also lies in the present
In fact, the bacterium remains anything but a dusty textbook name. The WHO considers it an important pathogen globally, while the European agency of the World Health Organization had already reported an increase in invasive group A streptococcus infections in 2022 and, in some countries, also in cases of scarlet fever, especially in children. In the United States, the CDC continues to monitor the most relevant clinical forms related to S. pyogenes. Looking back this way, therefore, also helps to better understand a problem that continues to evolve in the present.
The study also adds an interesting evolutionary piece. Phylogenetic analyzes place the Bolivian lineage at the basis of the modern diversity of Streptococcus pyogeneswhile temporal reconstructions indicate that most modern lineages have diverged globally over the last approximately 5,500 years. The authors link this expansion to increasingly sedentary and dense human communities, where close contact has offered the pathogen favorable terrain to spread and diversify.
There is also an element that makes this story even more interesting. The researchers weren’t specifically looking for that bacterium. They were analyzing the genetic material present in the remains with an open eye, and from there came one of the clearest data in recent years on the ancient history of this microorganism. Sometimes research works like this: it doesn’t open a door, it just moves a tile. Except that that tile changes the whole design.
