Similarities Between Antibiotic-Resistant Escherichia coli from Raw Meat, Commercial Raw Dog Food and Those Causing Extraintestinal Human Infections: A Contemporaneous Geographically Focussed Genomic Epidemiology Study

Abstract

ObjectivesThere is strong evidence linking raw meat or raw dog food (RDF) feeding with dogs shedding antibiotic-resistant (ABR) Escherichia coli. As well as potential risks of ingesting ABR E. coli when handling/consuming meat, therefore, people who raw-feed pets may face additional risks. However, phylogenetic evidence closely linking E. coli found on raw meat/RDF with those causing opportunistic human infections is lacking, partly due to non-contemporaneous sampling. Here, we monitored ABR E. coli in meat/RDF in Bristol, UK in 2022/23, and compared E. coli isolates with E. coli causing human urinary tract and bloodstream infections in Bristol in 2023. MethodsWe monitored ABR E. coli positivity in raw chicken, beef, pork and lamb meat from 15 large-chain stores and chicken-based RDF from 15 pet stores and selected 200 ABR E. coli for Illumina WGS. E. coli causing 1182 human infections were sequenced, irrespective of resistance phenotype. ResultsChicken/RDF were most likely to carry amoxicillin-, spectinomycin-, streptomycin-, cefotaxime-, and ciprofloxacin-resistant E. coli. Phylogroup A/B1 and B2 E. coli dominated meat/RDF and human isolates, respectively. Resistance to antibiotics used predominantly in farmed animals dominated meat/RDF isolates; resistance to antibiotics extensively used in humans dominated human isolates. Nineteen meat/RDF-infection E. coli pairs differed by <50 SNPs across the core-genome, with four pairs (three ST69 and one ST117) differing by <20 SNPs and carrying identical resistance genes, suggestive of recent sharing. ConclusionsUsing contemporaneous, geographically focussed sampling, we have confirmed close phylogenetic relationships between meat/RDF and human infection-causing ABR E. coli. Despite representing a small number of infections, these findings support the consideration of tighter microbiological standards for RDF given that it is explicitly sold to be fed uncooked. Improved risk communication to pet owners and the inclusion of RDF within integrated ABR surveillance is warranted.