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.