Emergence of Potentially Disinfection Resistant, Naturalized Escherichia coli Populations Across Food- and Water-Associated Engineered Environments

Abstract

The Escherichia coli species is comprised of several ‘ecotypes’ inhabiting a wide range of host and natural environmental niches. Recent studies have suggested that novel naturalized ecotypes have emerged across wastewater treatment plants and meat processing facilities. Phylogenetic and typing analyses clustered 37 previously described naturalized wastewater and meat plant strains into two main sequence types, ST635 and ST399, and several serotypes, representing independent lineages that have each naturalized within their respective engineered niches. Reflecting this, pan-genomic analyses revealed that the naturalized strains possessed an abundance of genes related to biofilm formation, defense, and disinfection-related stress resistance, but lacked genes associated with virulence and colonization, indicating that their naturalization may have come at the cost of fitness in the original host environment. Indeed, ecotype prediction analyses reliably distinguished the naturalized strains from the rest of the E. coli species, suggesting they represent a novel, disinfection-resistant ecotype that has recently emerged across food- and water-associated engineered environments.