Risk factors for extended-spectrum beta-lactamase (ESBL) producing E. coli carriage among children in a food animal producing region of Quito, Ecuador

Background The spread of antibiotic-resistant bacteria may be driven by human-animal-environment interactions, especially in regions with limited restrictions on antibiotic use, widespread food animal production, and free-roaming domestic animals. In this study, we aimed to identify risk factors related to domestic animals, backyard food animals, and commercial food animal production in Ecuadorian communities. Methods & Findings We conducted a repeated-measures study from 2018-2021 in 7 semi-rural parishes of Quito, Ecuador to identify determinants of third-generation cephalosporin-resistant E. coli (3GCR-EC) and extended-spectrum beta-lactamase E. coli (ESBL-EC) in children and domestic animals. We used multivariable log-binomial regression models to estimate relative risks (RR) of 3GCR-EC and ESBL-EC carriage. We collected 1,699 child fecal samples from 600 households and 1,871 animal fecal samples from 376 of the same households. Risk factors for 3GCR-EC included living within 5 km of more than 5 commercial food animal operations (RR: 1.36; 95% Confidence Interval: 1.16, 1.59), household pig ownership (1.23; 1.02, 1.48), child pet contact (1.23; 1.09, 1.39), and rarely/never washing hands after contact with animals (1.15; 0.98, 1.34). Risk factors for ESBL-EC were dog ownership (1.43; 1.00, 2.04), child pet contact (1.54; 1.10, 2.16), placing animal feces on household land/crops (1.63; 1.09, 2.46), and combined exposures to both household food animals and commercial food animal operation drainage paths (1.80; 0.94, 3.45). Conclusions Policies and interventions that improve the safety of animal waste management in communities and in commercial food animal production operations may be necessary to curb the spread of resistant bacteria. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was supported by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (NIH) under Award Number R01AI135118. The funding institution had no involvement in study design, data collection, interpretation of results, or submission for publication. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Office for Protection of Human Subjects (OPHS) of the University of California, Berkeley gave ethical approval for this work (IRB# 2019-02-11803). The Bioethics Committee of the Universidad San Francisco de Quito gave ethical approval for this work (#2017-178M). The Ecuadorian Health Ministry gave ethical approval for this work (#MSPCURI000243-3). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Raw reads from isolates sequenced in this study are available at the NCBI Short Read Archive(SRA) under BioProject accession no. PRJNA861272. All data used to perform analyses in the present study are currently available upon reasonable request to the authors.