Using source-associated mobile genetic elements to identify zoonotic extraintestinal E. coli infections

Abstract

A one-health perspective may provide new and actionable information about <i>Escherichia coli</i> transmission. <i>E. coli</i> colonizes a broad range of vertebrates, including humans and food-production animals, and is a leading cause of bladder, kidney, and bloodstream infections in humans. Substantial evidence supports foodborne transmission of pathogenic <i>E. coli</i> strains from food animals to humans. However, the relative contribution of foodborne zoonotic <i>E. coli</i> (FZEC) to the human extraintestinal disease burden and the distinguishing characteristics of such strains remain undefined. Using a comparative genomic analysis of a large collection of contemporaneous, geographically-matched clinical and meat-source <i>E. coli</i> isolates (<i>n</i> = 3111), we identified 17 source-associated mobile genetic elements - predominantly plasmids and bacteriophages - and integrated them into a novel Bayesian latent class model to predict the origins of clinical <i>E. coli</i> isolates. We estimated that approximately 8 % of human extraintestinal <i>E. coli</i> infections (mostly urinary tract infections) in our study population were caused by FZEC. FZEC strains were equally likely to cause symptomatic disease as non-FZEC strains. Two FZEC lineages, ST131-<i>H</i>22 and ST58, appeared to have particularly high virulence potential. Our findings imply that FZEC strains collectively cause more urinary tract infections than does any single non-<i>E. coli</i> uropathogenic species (e.g., <i>Klebsiella pneumoniae</i>). Our novel approach can be applied in other settings to identify the highest-risk FZEC strains, determine their sources, and inform new one-health strategies to decrease the heavy public health burden imposed by extraintestinal <i>E. coli</i> infections.