Locally persistent lineages are an important component of zoonotic foodborne pathogen Shiga toxin-producing Escherichia coli O157:H7 disease ecology

The control of zoonotic foodborne pathogens, including Shiga toxin-producing Escherichia coli (STEC), has proven difficult, in part because we know remarkably little about how these pathogens are maintained in an ecosystem. In response to this gap, we have developed a method for identifying pathogen strains that persistently infect defined human populations, which we call locally persistent lineages (LPLs). Using STEC O157:H7 in Minnesota as a model, we show that LPLs are widespread across the O157 phylogenetic tree, contribute significantly to local disease burden, and can persist for several years. They are also spatially clustered in an area with large populations of cattle, considered O157 STEC's primary reservoir. Our results suggest that STEC O157:H7 LPLs are established in ecological niches that support persistence. Identifying LPLs, and ultimately their reservoirs, can advance understanding of their disease ecology and provide opportunities for disease control at both local and national levels.