Environmental Spread of Extended Spectrum Beta-Lactamase (ESBL) Producing Escherichia coli and ESBL Genes among Children and Domestic Animals in Ecuador


Liseth Salinas 1Fernanda Loayza 1Paúl Cárdenas 1Carlos Saraiva 1Timothy J Johnson 2 3Heather Amato 4Jay P Graham 4Gabriel Trueba 1



1Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador.

2Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA.

3Mid Central Research & Outreach Center, Willmar, Minnesota, USA.

4Environmental Health Sciences Division, University of California, Berkeley, California, USA.

PMID: 33617318       PMCID: PMC7899495     DOI: 10.1289/EHP7729


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=21n=21), dogs (n=20n=20), and chickens (n=18n=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=14n=14) at relatively large distances. Isolates from children and domestic animals shared the same blaCTX-MblaCTX-M allelic variants, and the most prevalent were blaCTX-M-55 blaCTX-M-55 and blaCTX-M-65blaCTX-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 β-lactamaseβ-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.