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.

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.

Leveraging the COVID-19 pandemic as a natural experiment to assess changes in antibiotic use and antibiotic-resistant E. coli carriage in semi-rural Ecuador.

The coronavirus 2019 (COVID-19) pandemic has had significant impacts on health systems, population dynamics, public health awareness, and antibiotic stewardship, which could affect antibiotic resistant bacteria (ARB) emergence and transmission. In this study, we aimed to compare knowledge, attitudes, and practices (KAP) of antibiotic use and ARB carriage in Ecuadorian communities before versus after the COVID-19 pandemic began. We leveraged data collected for a repeated measures observational study of third-generation cephalosporin-resistant E. coli (3GCR-EC) carriage among children in semi-rural communities in Quito, Ecuador between July 2018 and September 2021. We included 241 households that participated in surveys and child stool sample collection in 2019, before the pandemic, and in 2021, after the pandemic began. We estimated adjusted Prevalence Ratios (aPR) and 95% Confidence Intervals (CI) using logistic and Poisson regression models. Child antibiotic use in the last 3 months declined from 17% pre-pandemic to 5% in 2021 (aPR: 0.30; 95% CI 0.15, 0.61) and 3GCR-EC carriage among children declined from 40 to 23% (aPR: 0.48; 95% CI 0.32, 0.73). Multi-drug resistance declined from 86 to 70% (aPR: 0.32; 95% CI 0.13; 0.79), the average number of antibiotic resistance genes (ARGs) per 3GCR-EC isolate declined from 9.9 to 7.8 (aPR of 0.79; 95% CI 0.65, 0.96), and the diversity of ARGs was lower in 2021. In the context of Ecuador, where COVID-19 prevention and control measures were strictly enforced after its major cities experienced some of the world's the highest mortality rates from SARS-CoV-2 infections, antibiotic use and ARB carriage declined in semi-rural communities of Quito from 2019 to 2021.

The role of plasmids in carbapenem resistant E. coli in Alameda County, California.

BACKGROUND: Antimicrobial resistant infections continue to be a leading global public health crisis. Mobile genetic elements, such as plasmids, have been shown to play a major role in the dissemination of antimicrobial resistance (AMR) genes. Despite its ongoing threat to human health, surveillance of AMR in the United States is often limited to phenotypic resistance. Genomic analyses are important to better understand the underlying resistance mechanisms, assess risk, and implement appropriate prevention strategies. This study aimed to investigate the extent of plasmid mediated antimicrobial resistance that can be inferred from short read sequences of carbapenem resistant E. coli (CR-Ec) in Alameda County, California. E. coli isolates from healthcare locations in Alameda County were sequenced using an Illumina MiSeq and assembled with Unicycler. Genomes were categorized according to predefined multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) schemes. Resistance genes were identified and corresponding contigs were predicted to be plasmid-borne or chromosome-borne using two bioinformatic tools (MOB-suite and mlplasmids). RESULTS: Among 82 of CR-Ec identified between 2017 and 2019, twenty-five sequence types (STs) were detected. ST131 was the most prominent (n = 17) followed closely by ST405 (n = 12). blaCTX-M were the most common ESBL genes and just over half (18/30) of these genes were predicted to be plasmid-borne by both MOB-suite and mlplasmids. Three genetically related groups of E. coli isolates were identified with cgMLST. One of the groups contained an isolate with a chromosome-borne blaCTX-M-15 gene and an isolate with a plasmid-borne blaCTX-M-15 gene. CONCLUSIONS: This study provides insights into the dominant clonal groups driving carbapenem resistant E. coli infections in Alameda County, CA, USA clinical sites and highlights the relevance of whole-genome sequencing in routine local genomic surveillance. The finding of multi-drug resistant plasmids harboring high-risk resistance genes is of concern as it indicates a risk of dissemination to previously susceptible clonal groups, potentially complicating clinical and public health intervention.

Weaning U.S. food-animals off antimicrobials: What can we learn from state- and city-level policies?

Antimicrobials are widely used worldwide in food animal production for controlling and preventing disease and for improving feed conversion efficiency and growth promotion. Inappropriate use of antimicrobials in animal agriculture has the potential to promote antimicrobial resistance, which represents a threat to human, animal, and environmental health. State and municipal policies in the United States have recently been implemented to improve antimicrobial use and reporting in this sector. This study analyzed the implementation of two state-level policies (California (CA) and Maryland (MD)) and a city-level policy in San Francisco (SF), California that aimed to reduce the use of antimicrobials in food-animals and increase transparency of antimicrobial use. A qualitative analysis was based on in-depth interviews with key informants (KIs) (n = 19) who had direct experience implementing or working in the context of these sub-national policies. Interviews were recorded and transcriptions were analyzed independently by two researchers using a three-stage, grounded theory coding procedure. This study identified four major findings, including 1) vague language on antimicrobial use within policies reduces policy effectiveness; 2) the lack of reporting by producers challenges the ability to evaluate the impact of the policies on actual use; 3) diverse stakeholders need to be involved in order to develop a more effective policy; and 4) funding should be linked to the policy to provide for reporting and data analysis. This analysis provides insights on the successes and failures of existing policies and serves to inform future sub-national policies aiming to improve the judicious use of antimicrobials in food-animals.

Clonal Lineages and Virulence Factors of Carbapenem Resistant E. coli in Alameda County, California, 2017-2019.

The prevalence of carbapenem-resistant Enterobacterales (CRE) has been increasing since the year 2000 and is considered a serious public health threat according to the Centers for Disease Control and Prevention. Limited studies have genotyped Carbapenem-resistant Escherichia coli using whole genome sequencing to characterize the most common lineages and resistance and virulence genes. The aim of this study was to characterize sequence data from carbapenem-resistant E. coli isolates (n = 82) collected longitudinally by the Alameda County Public Health Laboratory (ACPHL) between 2017 and 2019. E. coli genomes were screened for antibiotic resistance genes (ARGs) and extraintestinal pathogenic E. coli virulence factor genes (VFGs). The carbapenem-resistant E. coli lineages were diverse, with 24 distinct sequence types (STs) represented, including clinically important STs: ST131, ST69, ST95, and ST73. All Ambler classes of Carbapenemases were present, with NDM-5 being most the frequently detected. Nearly all isolates (90%) contained genes encoding resistance to third-generation cephalosporins; blaCTX-M genes were most common. The number of virulence genes present within pandemic STs was significantly higher than the number in non-pandemic lineages (p = 0.035). Virulence genes fimA (92%), trat (71%), kpsM (54%), and iutA (46%) were the most prevalent within the isolates. Considering the public health risk associated with CRE, these data enhance our understanding of the diversity of clinically important E. coli that are circulating in Alameda County, California.

Somewhere to go: assessing the impact of public restroom interventions on reports of open defecation in San Francisco, California from 2014 to 2020.

BACKGROUND: Open defecation due to a lack of access to sanitation facilities remains a public health issue in the United States. People experiencing homelessness face barriers to accessing sanitation facilities, and are often forced to practice open defecation on streets and sidewalks. Exposed feces may contain harmful pathogens posing a significant threat to public health, especially among unhoused persons living near open defecation sites. The City of San Francisco's Department of Public Works implemented the Pit Stop Program to provide the unhoused and the general public with improved access to sanitation with the goal of reducing fecal contamination on streets and sidewalks. The objective of this study was to assess the impact of these public restroom interventions on reports of exposed feces in San Francisco, California. METHODS: We evaluated the impact of various public restroom interventions implemented from January 1, 2014 to January 1, 2020 on reports of exposed feces, captured through a 311 municipal service. Publicly available 311 reports of exposed feces were spatially and temporally matched to 31 Pit Stop restroom interventions at 27 locations across 10 San Francisco neighborhoods. We conducted an interrupted time-series analysis to compare pre- versus post-intervention rates of feces reports near the restrooms. RESULTS: Feces reports declined by 12.47 reports per week after the installation of 13 Pit Stop restrooms (p-value = 0.0002). In the same restrooms, the rate of reports per week declined from the six-month pre-intervention period to the post-intervention period (slope change = -0.024 [95% CI = -0.033, -0.014]). In a subset of restrooms, where new installations were made (Mission and Golden Gate Park), and in another subset of restrooms where restroom attendants were provided (Mission, Castro/Upper Market, and Financial District/South Beach), feces reports also declined. CONCLUSIONS: Increased access to public toilets reduced feces reports in San Francisco, especially in neighborhoods with people experiencing homelessness. The addition of restroom attendants also appeared to have reduced feces reports in some neighborhoods with PEH. These interventions should be audited for implementation quality, observed utilization data, and user experience at the neighborhood level in order to tailor sanitation interventions to neighborhood-specific needs.

Biodigester Cookstove Interventions and Child Diarrhea in Semirural Nepal: A Causal Analysis of Daily Observations.

BACKGROUND: Hundreds of thousands of biodigesters have been constructed in Nepal. These household-level systems use human and animal waste to produce clean-burning biogas used for cooking, which can reduce household air pollution from woodburning cookstoves and prevent respiratory illnesses. The biodigesters, typically operated by female caregivers, require the handling of animal waste, which may increase domestic fecal contamination, exposure to diarrheal pathogens, and the risk of enteric infections, especially among young children. OBJECTIVE: We estimated the effect of daily reported biogas cookstove use on incident diarrhea among children <5y old in the Kavrepalanchok District of Nepal. Secondarily, we assessed effect measure modification and statistical interaction of individual- and household-level covariates (child sex, child age, birth order, exclusive breastfeeding, proof of vaccination, roof type, sanitation, drinking water treatment, food insecurity) as well as recent 14-d acute lower respiratory infection (ALRI) and season. METHODS: We analyzed 300,133 person-days for 539 children in an observational prospective cohort study to estimate the average effect of biogas stove use on incident diarrhea using cross-validated targeted maximum likelihood estimation (CV-TMLE). RESULTS: Households reported using biogas cookstoves in the past 3 d for 23% of observed person-days. The adjusted relative risk of diarrhea for children exposed to biogas cookstove use was 1.31 (95% confidence interval (CI): 1.00, 1.71) compared to unexposed children. The estimated effect of biogas stove use on diarrhea was stronger among breastfed children (2.09; 95% CI: 1.35, 3.25) than for nonbreastfed children and stronger during the dry season (2.03; 95% CI: 1.17, 3.53) than in the wet season. Among children exposed to biogas cookstove use, those with a recent ALRI had the highest mean risk of diarrhea, estimated at 4.53 events (95% CI: 1.03, 8.04) per 1,000 person-days. DISCUSSION: This analysis provides new evidence that child diarrhea may be an unintended health risk of biogas cookstove use. Additional studies are needed to identify exposure pathways of fecal pathogen contamination associated with biodigesters to improve the safety of these widely distributed public health interventions. https://doi.org/10.1289/EHP9468.

Risk factors for third-generation cephalosporin-resistant and extended-spectrum ß-lactamase-producing Escherichia coli carriage in domestic animals of semirural parishes east of Quito, Ecuador.

Extended-spectrum ß-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.

Social and Environmental Determinants of Community-Acquired Antimicrobial-Resistant Escherichia coli in Children Living in Semirural Communities of Quito, Ecuador.

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.

Waterborne Urinary Tract Infections: Have We Overlooked an Important Source of Exposure?

The presence of intestinal pathogenic Escherichia coli in drinking water is well recognized as a risk for diarrhea. The role of drinking water in extraintestinal infections caused by E. coli-such as urinary tract infections (UTIs)-remains poorly understood. Urinary tract infections are a leading cause of outpatient infections globally, with a lifetime incidence of 50-60% in adult women. We reviewed the scientific literature on the occurrence of uropathogenic E. coli (UPEC) in water supplies to determine whether the waterborne route may be an important, overlooked, source of UPEC. A limited number of studies have assessed whether UPEC isolates are present in drinking water supplies, but no studies have measured whether their presence in water may increase UPEC colonization or the risk of UTIs in humans. Given the prevalence of drinking water supplies contaminated with E. coli across the globe, efforts should be made to characterize UTI-related risks associated with drinking water, as well as other pathways of exposure.

Caretaker knowledge, attitudes, and practices (KAP) and carriage of extended-spectrum beta-lactamase-producing E. coli (ESBL-EC) in children in Quito, Ecuador.

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.

Effects of concentrated poultry operations and cropland manure application on antibiotic resistant Escherichia coli and nutrient pollution in Chesapeake Bay watersheds.

Manure from poultry operations is typically applied to nearby cropland and may affect nutrient loading and the spread of antibiotic resistance (ABR). We analyzed the concentrations of nitrogen and phosphorus and the occurrence of ABR in Escherichia coli (E. coli) and extra-intestinal pathogenic E. coli isolates from streams draining 15 small (<19 km2) watersheds of the Chesapeake Bay with contrasting levels of concentrated poultry operations. Total nitrogen and nitrate plus nitrite concentrations increased with poultry barn density with concentrations two and three times higher, respectively, in watersheds with the highest poultry barn densities compared to those without poultry barns. Analysis of N and O isotopes in nitrate by mass spectrometry showed an increase in the proportion of 15N associated with an increase in barn density, suggesting that the nitrate associated with poultry barns originated from manure. Phosphorus concentrations were not correlated with barn density. Antibiotic susceptibility testing of putative E. coli isolates was conducted using the disk diffusion method for twelve clinically important antibiotics. Of the isolates tested, most were completely susceptible (67%); 33% were resistant to at least one antibiotic, 24% were resistant to ampicillin, 13% were resistant to cefazolin, and 8% were multi-drug resistant. Resistance to three cephalosporin drugs was positively associated with an index of manure exposure estimated from poultry barn density and proportion of cropland in a watershed. The proportion of E. coli isolates resistant to cefoxitin, cefazolin, and ceftriaxone, broad-spectrum antibiotics important in human medicine, increased by 18.9%, 16.9%, and 6.2%, respectively, at the highest estimated level of manure exposure compared to watersheds without manure exposure. Our results suggest that comparisons of small watersheds could be used to identify geographic areas where remedial actions may be needed to reduce nutrient pollution and the public health risks of ABR bacteria.

Assessing the impact of sanitation on indicators of fecal exposure along principal transmission pathways: A systematic review.

OBJECTIVE: Fecal-oral transmission of enteric and other pathogens due to poor sanitation is a major cause of morbidity and mortality, especially in low- or middle-income settings. Few studies have investigated the impact of sanitation on indicators of transmission, a prerequisite to achieving health gains. This review attempts to summarize the literature to date. METHODS: We searched leading databases to identify studies that address the effect of sanitation on various transmission pathways including fecal pathogens or indicator bacteria in drinking water, hand contamination, sentinel toys, food, household and latrine surfaces and soil, as well as flies and observations of human feces. This also included studies that assessed the impact of fecal contamination of water supplies based on distance from sanitation facilities. We identified 29 studies that met the review's eligibility criteria. RESULTS AND CONCLUSION: Overall, the studies found little to no effect from sanitation interventions on these transmission pathways. There was no evidence of effects on water quality (source or household), hand or sentinel toy contamination, food contamination, or contamination of surfaces or soil. There is some evidence that sanitation was associated with reductions in flies and a small effect on observations of feces (Risk Difference -0.03, 95%CI -0.06 to 0.01). Studies show an inverse relationship between the distance of a water supply from a latrine and level of fecal contamination of such water supply. Future evaluations of sanitation interventions should include assessments of effects along transmission pathways in order to better understand the circumstances under which interventions may be effective at preventing disease.