Extensive Overlap in Avian and Extraintestinal Pathogenic Escherichia coli Strains Between Backyard Poultry, Humans, and Dogs in Ecuador

Escherichia coli is a ubiquitous organism that colonizes a variety of animal hosts and has the ability to persist within the environment. As such, it is not surprising that animals frequently share E. coli strains and contribute to environmental E. coli ecology. It has been well documented that poultry meat can serve as a reservoir of avian pathogenic E. coli (APEC) with the potential to cause human disease. However, the impact of backyard poultry rearing on household and community APEC sharing is less clear. In this study, we examined 1348 E. coli isolates from children, dogs, and chickens in 222 households in peri-urban communities of Quito, Ecuador, sampled across five timepoints. Extensive overlap between isolates from all three host sources were identified using Clermont phylotyping and multilocus sequence typing. Human and dog isolates also had a high rate of carriage (37% and 49%, respectively) of genes indicative of APEC. Phylogenetic analyses of dominant sequence types (ST10, ST155, ST117, ST2847, ST162, ST38, and ST354) provided examples of highly related clones found between host sources and households, and spanning timepoints. Overall, this study illustrates the apparent extensive sharing of E. coli that occurs across peri-urban communities. The high rates of carriage of APEC by humans and dogs in this study contrasts with previous work examining the carriage of APEC in mammalian hosts and suggests that widespread rearing of, and frequent contact with, backyard chickens may influence the dissemination of APEC within households and communities.