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Background:

There is a significant gap in our understanding of the sources of multidrug-resistant bacteria and resistance genes in community settings where human–animal interfaces exist.

Objectives:

This study characterized the relationship of third-generation cephalosporin-resistant Escherichia coli (3GCR-EC) isolated from animal feces in the environment and child feces based on phenotypic antimicrobial resistance (AMR) and whole genome sequencing (WGS).

Methods:

We examined 3GCR-EC isolated from environmental fecal samples of domestic animals and child fecal samples in Ecuador. We analyzed phenotypic and genotypic AMR, as well as clonal relationships (CRs) based on pairwise single-nucleotide polymorphisms (SNPs) analysis of 3GCR-EC core genomes. CRs were defined as isolates with fewer than 100 different SNPs.

Results:

A total of 264 3GCR-EC isolates from children ($n=21$), dogs ($n=20$), and chickens ($n=18$) living in the same region of Quito, Ecuador, were identified. We detected 16 CRs total, which were found between 7 children and 5 domestic animals (5 CRs) and between 19 domestic animals (11 CRs). We observed that several clonally related 3GCR-EC isolates had acquired different plasmids and AMR genes. Most CRs were observed in different homes ($n=14$) at relatively large distances. Isolates from children and domestic animals shared the same $bl{a}_{\text{CTX}\text{-M}}$ allelic variants, and the most prevalent were $bl{a}_{\text{CTX}\text{-M-}55}$ and $bl{a}_{\text{CTX}\text{-M-}65}$, which were found in isolates from children, dogs, and chickens.

Discussion:

This study provides evidence of highly dynamic horizontal transfer of AMR genes and mobile genetic elements (MGEs) in the E. coli community and shows that some 3GCR-EC and (extended-spectrum $\mathrm{\beta }\text{-lactamase}$) ESBL genes may have moved relatively large distances among domestic animals and children in semirural communities near Quito, Ecuador. Child–animal contact and the presence of domestic animal feces in the environment potentially serve as important sources of drug-resistant bacteria and ESBL genes. https://doi.org/10.1289/EHP7729