Pediatric urinary tract infections caused by poultry-associated Escherichia coli

Abstract

Escherichia coli is the leading cause of urinary tract infections (UTIs) in children and adults. The gastrointestinal tract is the primary reservoir of uropathogenic E. coli, which can be acquired from a variety of environmental exposures, including retail meat. In the current study, we used a novel statistical-genomic approach to estimate the proportion of pediatric UTIs caused by foodborne zoonotic E. coli strains. E. coli urine isolates were collected from DC residents aged 2 months to 17 years from the Children's National Medical Center Laboratory, 2013-2014. During the same period, E. coli isolates were collected from retail poultry products purchased from 15 sites throughout DC. A total of 52 urine and 56 poultry isolates underwent whole-genome sequencing, core genome phylogenetic analysis, and host-origin prediction by a Bayesian latent class model that incorporated data on the presence of mobile genetic elements (MGEs) among E. coli isolates from multiple vertebrate hosts. A total of 56 multilocus sequence types were identified among the isolates. Five sequence types-ST10, ST38, ST69, ST117, and ST131-were observed among both urine and poultry isolates. Using the Bayesian latent class model, we estimated that 19% (10/52) of the clinical E. coli isolates in our population were foodborne zoonotic strains. These data suggest that a substantial portion of pediatric UTIs in the Washington DC region may be caused by E. coli strains originating in food animals and likely transmitted via contaminated poultry meat.IMPORTANCEEscherichia coli UTIs are a heavy public health burden and can have long-term negative health consequences for pediatric patients. E. coli has an extremely broad host range, including humans, chickens, turkeys, pigs, and cattle. E. coli derived from food animals is a frequent contaminant of retail meat products, but little is known about the risk these strains pose to pediatric populations. Quantifying the proportion of pediatric UTIs caused by food-animal-derived E. coli, characterizing the highest-risk strains, and identifying their primary reservoir species could inform novel intervention strategies to reduce UTI burden in this vulnerable population. Our results suggest that retail poultry meat may be an important vehicle for pediatric exposure to zoonotic E. coli strains capable of causing UTIs. Vaccinating poultry against the highest-risk strains could potentially reduce poultry colonization, poultry meat contamination, and downstream pediatric infections.

Keywords: Bayesian latent class model; Escherichia coli; foodborne; pediatric; poultry; urinary tract infection.

Fig 1

Rooted maximum-likelihood phylogeny for 108 E. coli isolates. The inferred phylogeny is based on 224,315 non-recombinant core-genome single nucleotide polymorphisms. Isolates are coded by multilocus sequence type (ST), sample type, and model prediction (i.e., inferred source). Clinical isolates with ≥80% probability of being from a meat source are marked by red triangles, indicating putative spillover. The scale bar reflects genetic distance, reported as the expected number of nucleotide changes per site. Black dots on branches represent bootstrap values of ≥80 (based on 100 replicates). Note: There were two ST58 isolates—recovered from duplicate packages of ground turkey—that were 100% identical at the nucleotide level; therefore, only one of the isolates was included in the phylogenetic analysis.