Risk factors for extended-spectrum beta-lactamase (ESBL)-producing E. coli carriage among children in a food animal-producing region of Ecuador: A repeated measures observational study

Abstract

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.

Fig 1. Map of active commercial food animal production operations (n = 130) and their drainage flow paths in the study area, east of Quito, Ecuador.

The inset is an aerial photograph of commercial poultry production facilities in the study area (image credit: Jay P. Graham). Map created in QGIS; contains information from OpenStreetMap and OpenStreetMap Foundation, which is made available under the Open Database License.

Fig 2. Map of distribution of CTX-M-type genes from a subset of 571 3GCR-EC isolated from children in 7 parishes east of Quito, Ecuador.

Pie chart sections represent the proportion of isolates with a specific CTX-M-type gene detected, among those represented in the plot legend. Shaded areas represent parishes, where darker shading indicates a higher number of commercial food animal operations in a given parish. Map created in RStudio; Ecuador parish boundary shapefiles are made publicly available by the INEC and the United Nations OCHA. Data and license information are available at https://data.humdata.org/dataset/cod-ab-ecu?. 3GCR-EC, third-generation cephalosporin-resistant E. coli; INEC, Instituto Nacional de Estadística y Censos; OCHA, Office for the Coordination of Humanitarian Affairs.

Fig 3. Bar plot of distribution of 3GCR-EC and ESBL-EC carriage stratified by exposures to HH food animals and CFOs.

Number of observations includes fecal samples that were negative for 3GCR-EC (light gray bars for 3GCR-EC), isolates from fecal samples that were 3GCR-EC (orange bars), or ESBL-EC (purple bars) based on phenotypic susceptibility testing, and isolates plus fecal samples negative for both 3GCR-EC and ESBL-EC (light gray bars for ESBL-EC). Percent of observations positive for each outcome are listed above each bar. 3GCR-EC, third-generation cephalosporin-resistant E. coli; CFO, commercial food animal operation; ESBL-EC, extended-spectrum beta-lactamase E. coli; HH, household.

Fig 4. Additional risk factors for 3GCR-EC and ESBL-EC carriage among children in semirural parishes of Quito, Ecuador.

Points are adjusted RR and error bars are 95% CIs; asterisks (*) indicate significance given alpha = 0.05 (corresponding data including sample sizes and P-values in Tables K and J in S1 Files). RR are adjusted for repeated measures and controlled for the following covariates: caregiver education, asset score, child age and sex, and child antibiotic use in the last 3 months. 3GCR-EC, third-generation cephalosporin-resistant E. coli; CI, confidence interval; ESBL-EC, extended-spectrum beta-lactamase E. coli; RR, relative risk.