Genomic insights into the ancient spread of Lyme disease across North America

Lyme disease is the most prevalent vector-borne disease in North America and continues to spread. The disease was first clinically described in the 1970s in Lyme, Connecticut, but the origins and history of spread of the Lyme disease bacteria, Borrelia burgdorferi sensu stricto, are unknown. To explore the evolutionary history of B. burgdorferi in North America, we collected ticks from across the United States and southern Canada from 1984 to 2013 and sequenced the largest ever collection of 146 B. burgdorferi s.s. genomes. Here, we show that B. burgdorferi s.s. has a complex evolutionary history with previously undocumented levels of migration. Diversity is ancient and geographically widespread, well predating the Lyme disease epidemic of the last ~40 years, as well as the Last Glacial Maximum ~20,000 years ago. This means the recent emergence of human Lyme disease likely reflects ecological change—climate change and land use changes over the last century—rather than evolutionary change of the bacterium.