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

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 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.

Genomic insights into ESBL-producing Escherichia coli isolated from non-human primates in the Peruvian Amazon

“…This genetic similarity is noteworthy, as both strains were sampled from two different monkey species, S. mystax and S. labiatus , located 26.5 km apart. The phylogenetic analysis also revealed that two CTX-M-15-producing E. coli from Quito, Ecuador ( 33 ), were, on average, 18 SNP distant from our strains. Several studies have demonstrated clonal expansion as a key mechanism for understanding the spread of MDR E. coli in diverse hosts and environments.…”

“…Furthermore, within the subclade (highlighted in red) that includes monkey strains, there are two additional closely related strains: one from a human and one from a dog isolated in Quito, Ecuador, in 2021 ( 33 ). The SNP distance between our strains and Ecuadorian strains ranged from 16 to 19 SNPs, respectively, ( Figure 2C ).…”

“…Maximum likelihood phylogenetic reconstruction was carried out using IQ-TREE v 2.0 (30) with GTR + G + I model and 1,000 bootstrap replicates. The resulting tree was visualized using the ggtree package (31) in the R environment v4.3 (32). Additionally, the pairwise SNP distance between genomes, derived from the free-recombination core genome alignment was calculated using SNP-dists v0.6 (see text footnote 1).…”