Background: There is a significant gap in our understanding of the sources of multidrug-resistant bacteria and resistance genes in community settings where human–animal interfaces exist. Objectives: This study characterized the relationship of third-generation cephalosporin-resistant Escherichia coli (3GCR-EC) isolated from animal feces in the environment and child feces based on phenotypic antimicrobial resistance (AMR) and whole genome sequencing (WGS). Methods: We examined 3GCR-EC isolated from environmental fecal samples of domestic animals and child fecal samples in Ecuador. We analyzed phenotypic and genotypic AMR, as well as clonal relationships (CRs) based on pairwise single-nucleotide polymorphisms (SNPs) analysis of 3GCR-EC core genomes. CRs were defined as isolates with fewer than 100 different SNPs. Results: A total of 264 3GCR-EC isolates from children ( ), dogs ( ), and chickens ( ) living in the same region of Quito, Ecuador, were identified. We detected 16 CRs total, which were found between 7 children and 5 domestic animals (5 CRs) and between 19 domestic animals (11 CRs). We observed that several clonally related 3GCR-EC isolates had acquired different plasmids and AMR genes. Most CRs were observed in different homes ( ) at relatively large distances. Isolates from children and domestic animals shared the same allelic variants, and the most prevalent were and , which were found in isolates from children, dogs, and chickens. Discussion: This study provides evidence of highly dynamic horizontal transfer of AMR genes and mobile genetic elements (MGEs) in the E. coli community and shows that some 3GCR-EC and (extended-spectrum ) ESBL genes may have moved relatively large distances among domestic animals and children in semirural communities near Quito, Ecuador. Child–animal contact and the presence of domestic animal feces in the environment potentially serve as important sources of drug-resistant bacteria and ESBL genes. https://doi.org/10.1289/EHP7729

Recent studies have found limited associations between antimicrobial resistance (AMR) in domestic animals (and animal products), and AMR in human clinical settings. These studies have primarily used Escherichia coli, a critically important bacterial species associated with significant human morbidity and mortality. E. coli is found in domestic animals and the environment, and it can be easily transmitted between these compartments. Additionally, the World Health Organization has highlighted E. coli as a “highly relevant and representative indicator of the magnitude and the leading edge of the global antimicrobial resistance (AMR) problem”. In this paper, we discuss the weaknesses of current research that aims to link E. coli from domestic animals to the current AMR crisis in humans. Fundamental gaps remain in our understanding the complexities of E. coli population genetics and the magnitude of phenomena such as horizontal gene transfer (HGT) or DNA rearrangements (transposition and recombination). The dynamic and intricate interplay between bacterial clones, plasmids, transposons, and genes likely blur the evidence of AMR transmission from E. coli in domestic animals to human microbiota and vice versa. We describe key factors that are frequently neglected when carrying out studies of AMR sources and transmission dynamics.

No abstract

Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL), a family of bacteria that includes Escherichia coli, have emerged as a global health threat. This study examined risks associated with carriage of third-generation cephalosporin-resistant (3GC-R) E. coli, including ESBL-producing, multidrug-resistant, and extensively drug-resistant (XDR) strains in children living in semirural parishes of Quito, Ecuador. We conducted a longitudinal study with two cycles of sampling (N = 374, N = 366) that included an analysis of child fecal samples and survey questions relating to water, sanitation, and hygiene, socioeconomic status, household crowding, and animal ownership. We used multivariate regression models to assess risk factors associated with a child being colonized. Across the two cycles, 18.4% (n = 516) of the 3GC-R isolates were ESBL-producing E. coli, and 40.3% (n = 516) were XDR E. coli. Children living in households that owned between 11 and 20 backyard animals had an increased odds of being colonized with XDR E. coli (odds ratio [OR] = 1.94, 95% confidence interval [CI]: 1.05–3.60) compared with those with no animals. Households that reported smelling odors from commercial poultry had increased odds of having a child positive for XDR E. coli (OR = 1.72, 95% CI: 1.11–2.66). Our results suggest that colonization of children with antimicrobial-resistant E. coli is influenced by exposure to backyard and commercial livestock and poultry. Future studies should consider community-level risk factors because child exposures to drug-resistant bacteria are likely influenced by neighborhood and regional risk factors.

Background The rapid spread of extended-spectrum beta-lactamase-producing E. coli (ESBL-EC) is an urgent global health threat. We examined child caretaker knowledge, attitudes, and practices (KAP) towards proper antimicrobial agent use and whether certain KAP were associated with ESBL-EC colonization of their children. Methods Child caretakers living in semi-rural neighborhoods in peri-urban Quito, Ecuador were visited and surveyed about their KAP towards antibiotics. Fecal samples from one child (less than 5 years of age) per household were collected at two time points between July 2018 and May 2019 and screened for ESBL-EC. A repeated measures analysis with logistic regression was used to assess the relationship between KAP levels and child colonization with ESBL-EC. Results We analyzed 740 stool samples from 444 children living in households representing a range of environmental conditions. Of 374 children who provided fecal samples at the first household visit, 44 children were colonized with ESBL-EC (11.8%) and 161 were colonized with multidrug-resistant E. coli (43%). The prevalences of ESBL-EC and multidrug-resistant E. coli were similar at the second visit (11.2% and 41.3%, respectively; N = 366). Only 8% of caretakers knew that antibiotics killed bacteria but not viruses, and over a third reported that they “always” give their children antibiotics when the child’s throat hurts (35%). Few associations were observed between KAP variables and ESBL-EC carriage among children. The odds of ESBL-EC carriage were 2.17 times greater (95% CI: 1.18–3.99) among children whose caregivers incorrectly stated that antibiotics do not kill bacteria compared to children whose caregivers correctly stated that antibiotics kill bacteria. Children from households where the caretaker answered the question “When your child’s throat hurts, do you give them antibiotics?” with “sometimes” had lower odds of ESBL-EC carriage than those with a caretaker response of “never” (OR 0.48, 95% CI 0.27–0.87). Conclusion Caregivers in our study population generally demonstrated low knowledge regarding appropriate use of antibiotics. Our findings suggest that misinformation about the types of infections (i.e. bacterial or viral) antibiotics should be used for may be associated with elevated odds of carriage of ESBL-EC. Understanding that using antibiotics is appropriate to treat infections some of the time may reduce the odds of ESBL-EC carriage. Overall, however, KAP measures of appropriate use of antibiotics were not strongly associated with ESBL-EC carriage. Other individual- and community-level environmental factors may overshadow the effect of KAP on ESBL-EC colonization. Intervention studies are needed to assess the true effect of improving KAP on laboratory-confirmed carriage of antimicrobial resistant bacteria, and should consider community-level studies for more effective management.

Extended-spectrum β-lactamase (ESBL)-producing and other antimicrobial resistant (AR) Escherichia coli threaten human and animal health worldwide. This study examined risk factors for domestic animal colonization with ceftriaxone-resistant (CR) and ESBL-producing E. coli in semirural parishes east of Quito, Ecuador, where small-scale food animal production is common. Survey data regarding household characteristics, animal care, and antimicrobial use were collected from 304 households over three sampling cycles, and 1195 environmental animal fecal samples were assessed for E. coli presence and antimicrobial susceptibility. Multivariable regression analyses were used to assess potential risk factors for CR and ESBL-producing E. coli carriage. Overall, CR and ESBL-producing E. coli were detected in 56% and 10% of all fecal samples, respectively. The odds of CR E. coli carriage were greater among dogs at households that lived within a 5 km radius of more than 5 commercial food animal facilities (OR 1.72, 95% CI 1.15–2.58) and lower among dogs living at households that used antimicrobials for their animal(s) based on veterinary/pharmacy recommendation (OR 0.18, 95% CI 0.04–0.96). Increased odds of canine ESBL-producing E. coli carriage were associated with recent antimicrobial use in any household animal (OR 2.69, 95% CI 1.02–7.10) and purchase of antimicrobials from pet food stores (OR 6.83, 95% CI 1.32–35.35). Food animals at households that owned more than 3 species (OR 0.64, 95% CI 0.42–0.97), that used antimicrobials for growth promotion (OR 0.41, 95% CI 0.19–0.89), and that obtained antimicrobials from pet food stores (OR 0.47, 95% CI 0.25–0.89) had decreased odds of CR E. coli carriage, while food animals at households with more than 5 people (OR 2.22, 95% CI 1.23–3.99) and located within 1 km of a commercial food animal facility (OR 2.57, 95% CI 1.08–6.12) had increased odds of ESBL-producing E. coli carriage. Together, these results highlight the complexity of antimicrobial resistance among domestic animals in this setting.

No abstract

23The aim of this study was to investigate the presence of Escherichia coli carrying mcr-1 gene 24 in domestic animals close to a child who suffered a peritoneal infection by a mcr-1 positive 25 E. coli. Rectal or cloacal swabs and fecal samples from domestic animals were plated on 26 selective media to isolate colistin-resistant E. coli and isolates were submitted to detection of 27 mcr-1 gene, pulsed field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), 28 replicon typing and S1-PFGE. Four mcr-1 positive E. coli isolates (from chicken, turkey and 29 dog) were recovered. No shared PFGE pattern or MLST sequence type were observed among 30 isolates. A 60Kb IncI1 mcr-1-carrying plasmid was detected in all isolates. Our results 31 suggest that mcr-1 gene was horizontally disseminated amongst different lineages of E. coli 32 from domestic animals in the child's household. 33 Importance 34Horizontally transferable colistin resistance (mcr-1 gene) is thought to have originated in 35 domestic animals and transferred to humans through meat and dairy products. In the present 36 report we show evidence that the mcr-1 gene could be transferred to different E. coli strains 37 colonizing different hosts (humans and pets) in the same household. 38 42 different bacterial genera colonizing different animal species (2, 3).43 3The first report of a colistin resistance (CR) gene carried by plasmids (mcr-1) came from China in 44 2015 (4). This gene codes for a phosphoethanolamine transferase (MCR-1), which modifies the 45 lipid A moiety in the outer membrane of Gram negative bacteria and confers resistance to 46 polymyxins (4, 5). Among Enterobacteriacea different mcr gen groups (1-5) could be transferred by 47 PCR was performed to detect mcr gene (4); amplicons were sequence and aligned using mcr-1 130 (NG_055582.1), mcr-2 (NG_051171.1), mcr-3 ( NG_056184.1), mcr-4( MG822665.1), mcr-5 131 (MG384740.1) accession numbers with Geneius software. Pulsed field gel electrophoresis (PFGE) 132 (25) and multilocus sequence typing (MLST) was performed on seven housekeeping genes to 133 define clonal relatedness (26). Replicon typing was performed using a commercial kit (PBRT KIT, 134 DIATHE, Fano, Italy) (20, 27, 28). -lactamase genes (blaCTX-M-1, blaTEM, blaSHV) were detected 135 using primers previously described (29). Briefly, 12,5mL of GoTaq ® Green Master Mix 136 (Promega, Madison, USA) were mixed with 1L of upstream primer, 10M, 1L of downstream 137 primer, 10 L of DNA template and 9,5 L of Nuclease-free water to complete a 25L of 138 reaction volume. The reaction mix were amplified using 2-minute of initial denaturation at 94°C 139 followed by 40 cycles of DNA denaturation at 94°C (40 sec), annealing at 60°C (40sec) and 140 extension at 72°C (1min). The final elongation step at 72°C for 5 min. Amplicons were detected by 141 electrophoresis in a 2% agarose gel. For complete amplification and sequencing of the detected 142resistance genes, primers and conditions previously described were used (30). 143 S1-PFG...