Long considered a disease introduced to America by European colonizers, leprosy may in fact have a much older history on the American continent.
Scientists reveal that a second species of bacteria responsible for leprosy, recently identified as
Mycobacterium lepromatosis, has been infecting humans in America for at least 1,000 years—several centuries before the arrival of Europeans. These findings are published in the journal
Science on May 29, 2025.
Leprosy is a neglected disease, primarily caused by the bacterium
Mycobacterium leprae, which affects thousands of people worldwide: approximately 200,000 new cases of leprosy are reported each year. Although
M. leprae remains the primary cause, this study focused on another species,
Mycobacterium lepromatosis, discovered in 2008 in a patient in the United States and later in 2016 in red squirrels in the British Isles.
Led by scientists from the Microbial Paleogenomics Laboratory at the Institut Pasteur, in collaboration with the CNRS, the University of Colorado, Indigenous communities, and over 40 scientists from international institutions—including archaeologists—this study analyzed the DNA of nearly 800 samples, including ancient human remains (from archaeological excavations) and recent clinical cases showing leprosy symptoms. The results confirm that
M. lepromatosis was already widespread in North and South America long before European colonization and provide a better understanding of the current genetic diversity of pathogens in the
Mycobacterium genus.
"
This discovery transforms our understanding of the history of leprosy in America," said Dr. Maria Lopopolo, the study's lead author and a researcher at the Microbial Paleogenomics Laboratory at the Institut Pasteur. "
It shows that a form of the disease was already endemic among Indigenous populations long before the arrival of Europeans."
The team used cutting-edge genetic techniques to reconstruct the genomes of
M. lepromatosis from ancient individuals found in Canada and Argentina. Despite being separated by thousands of miles (kilometers), these ancient strains, dating from similar periods (around 1,000 years ago), turned out to be surprisingly close genetically. Although they belong to two distinct branches in the evolutionary tree of the
Mycobacterium genus, they are genetically closer to each other than to any other known strain. This genetic proximity, combined with their geographic distance, implies a rapid spread of the pathogen across the continent, likely within just a few centuries.
The scientists also identified several new lineages, including an ancestral lineage that emerged more than 9,000 years ago but continues to infect humans today in North America—a discovery that suggests an ancient and enduring diversification on the continent, as well as a largely unexplored diversity.
Notably, the analyses also suggest that the strains found in red squirrels in the UK in 2016 belong to an American lineage that may have been introduced to the British Isles in the 19th century, where it subsequently spread. This finding highlights the pathogen's recent ability to cross continents, likely through human or commercial exchanges.
"
We are only beginning to uncover the diversity and global movements of this recently identified pathogen. The study allows us to hypothesize that there may still be unknown animal reservoirs," said Nicolás Rascovan, the study's senior author and head of the Microbial Paleogenomics Laboratory at the Institut Pasteur. "
This study clearly illustrates how ancient and modern DNA can rewrite the history of a human pathogen and help us better understand the epidemiology of contemporary infectious diseases."
The project was conducted in close collaboration with Indigenous communities, who were involved in decisions regarding the use of ancestral remains and the interpretation of results. Ancient DNA and remaining materials were repatriated when requested, and the generated data were shared through ethical and adaptable platforms designed to facilitate data sharing in line with the specific expectations of Indigenous communities.