The goal of this project was to expand our knowledge about the history of tuberculosis (TB) before and after the Age of Exploration and Colonization in the Americas. TB is a disease caused by pathogens in the genus Mycobacterium. These pathogens, the Mycobacterium tuberculosis complex (MTBC), includes M. tuberculosis that causes most cases of TB in humans today as well as strains that cause disease in humans and other animals. Worldwide, TB is the leading cause of death by a single infectious agent, responsible for ~1.3 million deaths according to WHO in 2017. Our previous research reported MTBC genomes from 1000-year old skeletal TB cases from coastal Peru and showed that these strains are closely related to strains found in Southern Hemisphere pinnipeds including seals and sea lions. These strains, traditionally classified as M. pinnipedii, are among the animal strains in the MTBC. We also found that, surprisingly, the extant lineages of TB date only to the last 6000 years.

For this project, we extracted DNA from over 200 ancient individuals with characteristic bone lesions of TB to investigate whether zoonotic M. pinnipedii strains jumped into human populations more than once and whether they spread via trade routes to Central and North America, perhaps becoming adapted to humans along the way. We also investigated whether there is evidence of additional TB strains reaching the Americans before 1492. Over the course of this project, we have produced evidence that M. pinnipedii strains were, indeed, transmitted inland and further north. Approximately one third of the bone samples tested positive using quantitative PCR assays but only a few contained enough pathogen DNA to reconstruct full genomes. We recovered two genomes from individuals buried at pre-contact and contact period archaeological sites in highland Columbia, and we have preliminary genome data from pre-contact individuals from the Valley of Mexico. We also reconstructed a MTBC genome from a precontact site in Moquegua, Peru. All of these individuals were infected with M. pinnipedii strains, and while zoonotic pinniped transmission remains possible for the Peruvian case, it does not easily account for its presence in the other locations. We explored different scenarios for disease transmission, including the potential of human adaptation and/or animal mediated dissemination. The phylogenetic analysis of the relationships among strains suggests that there were multiple “jumps” of M. pinnipedii from seals to humans, likely through butchering affected seals and/or consuming undercooked meat. Together these data demonstrate the ability of ancient M. pinnipedii strains to cause human infection in the past and point to likely human-to-human transmission. Analyses of these strains also suggest some mutations may have aided M. pinnipedii in adapting to the new human host, including changes in genes associated with metabolism, ion transport and DNA repair, but further research is needed to understand the functional effects of these changes. We find that samples from burials directly in the soil/water environment show greater amounts of environmental mycobacteria. This makes bioinformatics analyses and reconstruction of the ancient TB genome more difficult.

We also examined DNA from individuals who died with TB after contact to understand the pattern of replacement by European strains. We recovered a TB genome from an individual buried at a poorhouse in Rochester, NY dating to 1826-1863 and find that it is closely related to H37Rv, the type strain of TB that was isolated in upstate New York ~50-80 years later. These strains are related to others present today commonly in the Eastern US and Canada, and their presence likely reflects the colonization history of this region. Further research is needed to understand the pattern and pace of change in TB strain distribution after European contact in the Americas. In sum, the intellectual merit of this research was to increase our understanding of the evolutionary history of the pathogen that causes TB, with a focus on discerning the process of adaption after a host jump, followed by replacement after European contact.

The broader impacts of this work included the training of ten graduate students and five undergraduate students in laboratory methods and analyses over the course of this project. In addition, it fostered collaboration and consultation with multiple tribal and First Nations Communities as well as international scientific institutions and scholars. This research was presented in a Leakey Foundation “Origin Stories” podcast, public lectures to museums, tribal, and community groups, scholarly conferences, university lectures and colloquia, and multiple publications. Researchers working on this project also participated in other public science outreach activities including Comic-con in Phoenix and March Mammal Madness (a science education mock mammal competition on twitter followed by 250,000 schoolkids in 2019).

Last Modified: 07/18/2019
Modified by: Anne C Stone