Zoonotic Escherichia coli and urinary tract infections in Southern California

Abstract

Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of urinary tract infections (UTIs) worldwide and may be transmitted from food animals to humans via contaminated meat. However, the contribution of zoonotic ExPEC strains to UTIs in metropolitan areas remains unclear. We estimated the proportion of UTIs attributable to zoonotic ExPEC across eight Southern California counties. Between 2017 and 2021, we collected 12,616 E. coli isolates from retail meat and 23,483 from UTI patients, sequencing a representative subset of 5,728 isolates. Using a Bayesian latent class model trained with 17 host-associated genetic markers, we inferred the host origin of each isolate. Demographic, clinical, and antimicrobial resistance profiles were compared between meat isolates and clinical isolates inferred to be of human or food-animal origin. Most UTI patients were female (88%), with a median age of 50 years; 37% were Hispanic and 31% non-Hispanic white. Zoonotic ExPEC strains accounted for 18% of UTIs overall, rising to 21.5% in high-poverty neighborhoods. Women had a higher zoonotic proportion than men (19.7% vs 8.5%, P < 0.001). Among men, those with zoonotic infections were older than those with non-zoonotic infections (median 73.0 vs 65.0 years, P = 0.028). These findings underscore the contribution of zoonotic ExPEC to the UTI burden in Southern California and the need for targeted interventions to reduce risk in vulnerable communities.IMPORTANCEUrinary tract infections (UTIs) are among the most common bacterial infections worldwide and are primarily caused by Escherichia coli. While E. coli is known to colonize both humans and food-producing animals, the extent to which zoonotic strains impact human disease remains poorly understood. Emerging evidence suggests that food animals may serve as an underrecognized reservoir for extraintestinal pathogenic E. coli (ExPEC). In this study, we used a genomic attribution model to quantify the contribution of zoonotic strains to UTIs in Southern California. We found that approximately 18% of E. coli UTIs were likely attributable to food animals. Individuals living in high-poverty neighborhoods had a 1.6-fold increased risk of zoonotic UTIs compared to those in low-poverty areas. These findings highlight zoonotic transmission as an important driver of UTIs and suggest that reducing ExPEC in food-animal reservoirs could help lower disease burden and address health disparities.

Keywords: Bayesian latent class model; Escherichia coli; antimicrobial resistance; extraintestinal pathogenic E. coli; genomic attribution model; urinary tract infection; zoonotic infections.

Fig 1

Host origin predictions for E. coli isolates from urinary tract infections and meat. The probability that isolates were derived from a food-animal host was estimated using a Bayesian latent class model based on core-genome mutations and 17 host-associated mobile genetic elements. (A) Probabilities for urinary tract infection isolates. Isolates with probabilities ≥0.8 (right of the dashed line at 0.8) were categorized as zoonotic ExPEC. (B) Probabilities for meat isolates.

Fig 2

Tree maps of E. coli phylogroups and sequence types. (A) Non-zoonotic urinary tract infection isolates; (B) zoonotic urinary tract infection isolates; and (C) meat isolates. Rare sequence types are represented by a scaled box but non-individually named. The full list of sequence types can be found in Table S3.

Fig 3

Association between family poverty rate and zoonotic urinary tract infection rates in Southern California. (A) Geospatial distributions of zoonotic urinary tract infections in each three-digit ZIP code tabulation area overlaying the family poverty rate category. The size of each circle is proportional to the sample size of urinary tract infection isolates from each respective region, ranging from 7 to 277. (B) Dose response between poverty rate category and proportion of urinary tract infections inferred to be zoonotic.