Amato, Heather K., Loayza, Fernanda, Salinas, Liseth, Paredes, Diana, Garcia, Daniela, Sarzosa, Soledad, Saraiva-Garcia, Carlos, Johnson, Timothy J., Pickering, Amy J., Riley, Lee W., Trueba, Gabriel, and Graham, Jay P.
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 commercial food animal production, small-scale or "backyard" food animal production, domestic animal ownership, and practices related to animal handling, waste disposal, and antibiotic use in Ecuadorian communities. Methods and findings: We conducted a repeated measures study from 2018 to 2021 in 7 semirural 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. We collected 1,699 fecal samples from 600 children and 1,871 domestic animal fecal samples from 376 of the same households at up to 5 time points per household over the 3-year study period. We used multivariable log-binomial regression models to estimate relative risks (RR) of 3GCR-EC and ESBL-EC carriage, adjusting for child sex and age, caregiver education, household wealth, and recent child antibiotic use. Risk factors for 3GCR-EC included living within 5 km of more than 5 commercial food animal operations (RR: 1.26; 95% confidence interval (CI): 1.10, 1.45; p-value: 0.001), household pig ownership (RR: 1.23; 95% CI: 1.02, 1.48; p-value: 0.030) and child pet contact (RR: 1.23; 95% CI: 1.09, 1.39; p-value: 0.001). Risk factors for ESBL-EC were dog ownership (RR: 1.35; 95% CI: 1.00, 1.83; p-value: 0.053), child pet contact (RR: 1.54; 95% CI: 1.10, 2.16; p-value: 0.012), and placing animal feces on household land/crops (RR: 1.63; 95% CI: 1.09, 2.46; p-value: 0.019). The primary limitations of this study are the use of proxy and self-reported exposure measures and the use of a single beta-lactamase drug (ceftazidime with clavulanic acid) in combination disk diffusion tests for ESBL confirmation, potentially underestimating phenotypic ESBL production among cephalosporin-resistant E. coli isolates. To improve ESBL determination, it is recommended to use 2 combination disk diffusion tests (ceftazidime with clavulanic acid and cefotaxime with clavulanic acid) for ESBL confirmatory testing. Future studies should also characterize transmission pathways by assessing antibiotic resistance in commercial food animals and environmental reservoirs. Conclusions: In this study, we observed an increase in enteric colonization of antibiotic-resistant bacteria among children with exposures to domestic animals and their waste in the household environment and children living in areas with a higher density of commercial food animal production operations. In a repeated-measures study conducted between 2018-2021 in 7 semi-rural parishes of Quito, Ecuador, Heather Kathleen Amato and colleagues aim to identify determinants of antibiotic resistant E.coli infection in children. Author summary: Why was this study done?: An estimated 1.27 million deaths in 2019 were attributable to bacterial antibiotic-resistant infections, 89% of which occurred in low- and middle-income countries (LMICs). Small-scale and commercial-scale food animal production is expanding rapidly in middle-income countries like Ecuador and antibiotic use in food animals is increasing at the fastest rate in these settings, fueling the emergence and selection of multidrug-resistant bacteria. Evidence is needed to inform action against the spread of antibiotic resistance in communities with varying degrees of both small-scale or "backyard" and commercial food animal production, especially in South America where research on community-acquired antibiotic resistance is lacking. What did the researchers do and find?: We conducted a repeated measures study in a food animal-producing region in Ecuador to compare the risk of antibiotic-resistant bacterial (ARB) carriage among children with varying degrees of exposure to backyard and commercial food animals. We used multivariable log-binomial regression models to estimate relative risks (RR) of ARB carriage, adjusting for child sex and age, caregiver education, household wealth, and recent child antibiotic use. Living within 5 km of >5 commercial food animal operations, household pig or dog ownership, child contact with pets, and placing animal feces on household crops were identified as significant risk factors for ARB carriage in children. What do these findings mean?: This study underscores the need for improved waste management and surveillance of antibiotic resistance in LMICs with widespread food animal production. A significant challenge remains: There is a lack of available data on antibiotic usage and resistance in commercial food animal operations and their effluent, in Ecuador and globally, due to limited oversight and surveillance. In future studies, researchers should work with local and national governments to monitor antibiotic use and resistance in food animals, food animal production waste, nearby environmental reservoirs, and food animal products in order to more accurately characterize sources of exposure and transmission routes of community-acquired ARB. The primary limitations of this study are the use of proxy and self-reported exposure measures and the use of a single beta-lactamase drug (ceftazidime with clavulanic acid) in combination disk diffusion tests for ESBL confirmation, potentially underestimating phenotypic ESBL production among cephalosporin-resistant E. coli isolates. [ABSTRACT FROM AUTHOR]