European-wide antimicrobial resistance monitoring in commensal Escherichia coli isolated from healthy food animals between 2004 and 2018

Antimicrobial Susceptibility Profiles of Escherichia coli Isolates from Clinical Cases of Chickens in Hungary Between 2022 and 2023

Background: The global spread of antimicrobial resistance (AMR) necessitates collaborative approaches between animals, their environment, and public health sectors, fostering the One Health concept. Escherichia coli (E. coli) is a zoonotic, facultative pathogenic bacterium. Its public health significance underlines the need for the regular monitoring of different strains causing clinical disease, especially in poultry, more specifically in chickens, which have become a critical source of animal protein. Methods: The antimicrobial susceptibility of 133 E. coli strains isolated from clinical cases in large-scale Hungarian poultry between 2022 and 2023 was assessed via the gold-standard minimum inhibitory concentration (MIC) determination, which provides internationally comparable results. Results: Our findings revealed high resistance levels to widely used antibiotics, including amoxicillin (57.9%), neomycin (78.9%), doxycycline (46.6%), and potentiated sulfonamides (43.6%). Resistance to these critically important antibiotics is particularly concerning due to their public health significance. Comparison with regional human resistance data revealed similar patterns for β-lactam antibiotics; however, aminoglycosides, fluoroquinolones, and potentiated sulfonamides exhibited significantly higher resistance levels in veterinary isolates. Conclusions: Our results highlight the importance of routine surveillance, which has both veterinary and public health implications. Future efforts to correlate antibiotic usage with resistance patterns and to elucidate the genetic background of multidrug-resistant strains will further strengthen the One Health approach.

Antimicrobial Susceptibility Profiles of Commensal Escherichia coli Isolates from Chickens in Hungarian Poultry Farms Between 2022 and 2023

Background: Widespread use of antibiotics has led to a global increase in resistance. The Escherichia coli bacterium is a facultative pathogen that often develops antibiotic resistance and is easily transmitted, not only in animal health but also in public health. Within the poultry sector, domestic fowl is widespread and one of the most dynamically growing sectors, which is why regular, extensive monitoring is crucial. Among economically important livestock, poultry as a major source of animal protein for humans is a frequent carrier of Escherichia coli, also with sporadically detected clinical disease. Methods: Our research evaluates the susceptibility of commensal Escherichia coli strains, isolated from large domestic fowl flocks in Hungary, to antibiotics of animal and public health importance, by determining the minimum inhibitory concentration value. Results: A total of 410 isolates were tested, with the highest level of resistance being found for florfenicol (62.7%). Particularly alarming are the resistance rates to enrofloxacin (52.9%), colistin (30.7%), and ceftriaxone (23.9%). We also found a resistance of 56.1% to amoxicillin and 22.2% to amoxicillin-clavulanic acid, which suggests that the majority of strains are β-lactamase-producing. When compared with the national human resistance data, we found with similar values for amoxicillin and amoxicillin-clavulanic acid, but the resistance rates of aminoglycosides, fluoroquinolones, and potency sulfonamide were worse in animal health. Conclusions: In conclusion, our results suggest that periodic surveys should be carried out and that long-term trends can be established that allow the monitoring of resistance patterns over time. For multidrug-resistant strains, new generation sequencing can be used to investigate the genetic background of resistance.

Surveillance of antimicrobial resistance in Escherichia coli, Salmonella, and Campylobacter recovered from laying hens, their environment and products in Canada indicated a stable level of resistance to critically important antimicrobials, in varying time periods between 2007 and 2021

The study objective was to determine the occurrence and antimicrobial resistance (AMR) attributes of select foodborne bacteria recovered from egg-producing (layer) chickens between 2007 and 2021 using different sample matrices (Study 1: liquid whole eggs, Study 2: spent hen cecal samples, Study 3: environmental sponge swabs and fecal samples from layer chicken barns, and Study 4: fecal samples from layer chicken barns). Samples from each study were submitted for the culture of Escherichia coli and Salmonella. In addition, samples from layer chicken barns were submitted for the culture of Campylobacter. Isolates were tested by microbroth dilution and interpreted using both clinical breakpoints and epidemiological cut-offs (ECOFFs). The ECOFFs were applied to detect non-wild type (NWT) strains. The proportion of resistant, NWT, and distribution of minimum inhibitory concentrations (MIC) were assessed. Ceftriaxone resistance was detected at a low-level in E. coli (< 2 %, all studies) and Salmonella (4.3 %, Study 2). Very low-level ciprofloxacin resistance was detected in E. coli (<1 %, Study 1) but a slightly elevated ciprofloxacin NWT E. coli (1 % to 6 %) observed. Only the farm fecal samples in Studies 2 and 3 were tested for Campylobacter as part of its study design, and moderate level ciprofloxacin resistance (<15 %) was observed. The MIC distribution patterns were similar across the organisms tested/studies and no substantial shifts in the distributions were detected. This analysis demonstrated that resistance to very important antimicrobials in bacteria from layers in Canada remains low, however, the detection of ciprofloxacin-resistant Campylobacter and the implications of this observation to the safety of egg products, and the role of laying flocks (i.e., as reservoir for resistant organisms) needs to be investigated.

Longitudinal analysis of differences and similarities in antimicrobial resistance among commensal Escherichia coli isolated from market swine and sows at slaughter in the United States of America, 2013-2019

The emergence of antimicrobial resistance in swine enteric bacteria poses a significant public health challenge. Our study evaluated publicly available data collected by the National Antimicrobial Resistance Monitoring System for Enteric Bacteria (NARMS) between 2013 and 2019 at slaughter plants across the United States of America, focusing on commensal E. coli isolated from swine cecal contents originating from two distinct swine production systems: market hogs (n = 2090) and sows (n = 1147). In both production types, the highest pairwise correlations were detected among β-lactam antimicrobials, including resistance to amoxicillin-clavulanic acid, ceftriaxone, and cefoxitin, suggesting a co-selection for resistance. Compared to 2013, an increase in the rate of E. coli isolates that were resistant to β-lactam antimicrobials was higher in 2017, 2018, and 2019, and this increase was more pronounced in isolates obtained from market hogs. Differences in antimicrobial resistance between these two distinct swine production systems warrant production-type focused mitigation efforts.

Antimicrobial Resistance in Commensal Escherichia coli of the Porcine Gastrointestinal Tract

Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.

Identification, Typing, and Drug Resistance Analysis of Escherichia coli in Two Different Types of Broiler Farms in Hebei Province

Hebei Province is an important area for breeding broiler chickens in China, but the antimicrobial resistance and prevalence of Escherichia coli (E. coli) are still unclear. A total of 180 cloacal samples from broiler farms in Hebei Province were collected and used for the isolation and identification of E. coli. The isolates were subjected to resistance phenotyping, resistance profiling, and genotyping, and some multiresistant strains were subjected to multilocus sequence typing (MLST). The results showed that 175 strains were isolated. Among both types of broiler farms, the ampicillin resistance rate was the highest, and the meropenem resistance rate was the lowest. Serious multiresistance was present in both types of broiler farms. Thirty strains of multidrug-resistant E. coli were typed by MLST to obtain a total of 18 ST types, with ST10 being the most prevalent. This study was to simply analyze the antimicrobial resistance and prevalence of E. coli in broiler chickens in Hebei Province after the implementation of the pilot work program of action to reduce the use of veterinary antimicrobials in standard farms (SFs) and nonstandard farms (NSFs). This study will provide a research basis and data support for the prevention and control of E. coli in Hebei.

An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species

Understanding the microbial genomic contributors to antimicrobial resistance (AMR) is essential for early detection of emerging AMR infections, a pressing global health threat in human and veterinary medicine. Here we used whole genome sequencing and antibiotic susceptibility test data from 980 disease causing Escherichia coli isolated from companion and farm animals to model AMR genotypes and phenotypes for 24 antibiotics. We determined the strength of genotype-to-phenotype relationships for 197 AMR genes with elastic net logistic regression. Model predictors were designed to evaluate different potential modes of AMR genotype translation into resistance phenotypes. Our results show a model that considers the presence of individual AMR genes and total number of AMR genes present from a set of genes known to confer resistance was able to accurately predict isolate resistance on average (mean F1 score = 98.0%, SD = 2.3%, mean accuracy = 98.2%, SD = 2.7%). However, fitted models sometimes varied for antibiotics in the same class and for the same antibiotic across animal hosts, suggesting heterogeneity in the genetic determinants of AMR resistance. We conclude that an interpretable AMR prediction model can be used to accurately predict resistance phenotypes across multiple host species and reveal testable hypotheses about how the mechanism of resistance may vary across antibiotics within the same class and across animal hosts for the same antibiotic.

Evaluating Antimicrobial Resistance Trends in Commensal Escherichia coli Isolated from Cecal Samples of Swine at Slaughter in the United States, 2013-2019

The emergence of antimicrobial resistance (AMR) in commensal and pathogenic enteric bacteria of swine is a public health threat. This study evaluated publicly available AMR surveillance data collected by the National Antimicrobial Resistance Monitoring System (NARMS) by assessing AMR patterns and temporal trends in commensal E. coli isolated from cecal samples of swine at slaughter across the United States. We applied the Mann-Kendall test (MKT) and a linear regression trend line to detect significant trends in the proportion of resistant isolates to individual antimicrobials over the study period. A Poisson regression model assessed differences among years in the number of antimicrobials to which an E. coli isolate was resistant. Among the 3237 E. coli isolates, a very high prevalence of resistance for tetracycline (67.62%), and high resistance for streptomycin (24.13%), and ampicillin (21.10%) were identified. The MKT and the linear trend line showed a significantly increasing temporal trend for amoxicillin-clavulanic acid, ampicillin, azithromycin, cefoxitin, ceftriaxone, and trimethoprim-sulfamethoxazole. Compared to 2013 the number of antimicrobials to which an E. coli isolate was resistant was significantly higher in the years 2017, 2018, and 2019. The increasing temporal trend of resistance to important antimicrobials for human medicine (e.g., third-generation cephalosporins) and the increase in multidrug resistance in the later years of the study are concerning and should be followed up by studies to identify sources and risk factors for the selection of AMR.

Antimicrobial Resistant Coagulase-Negative Staphylococci Carried by House Flies (Musca domestica) Captured in Swine and Poultry Farms

House flies (Musca domestica) are very diffuse insects attracted by biological materials. They are abundantly present in farm environments and can frequently come in contact with animals, feed, manure, waste, surfaces, and fomites; consequently, these insects could be contaminated, carry, and disperse several microorganisms. The aim of this work was to evaluate the presence of antimicrobial-resistant staphylococci in house flies collected in poultry and swine farms. Thirty-five traps were placed in twenty-two farms; from each trap, 3 different kinds of samples were tested: attractant material present in the traps, the body surface of house flies and the body content of house flies. Staphylococci were detected in 72.72% of farms, 65.71% of traps and 43.81% of samples. Only coagulase-negative staphylococci (CoNS) were isolated, and 49 isolates were subjected to an antimicrobial susceptibility test. Most of the isolates were resistant to amikacin (65.31%), ampicillin (46.94%), rifampicin (44.90%), tetracycline (40.82%) and cefoxitin (40.82%). Minimum Inhibitory concentration assay allowed to confirm 11/49 (22.45%) staphylococci as methicillin-resistant; 4 of them (36.36%) carried the mecA gene. Furthermore, 53.06% of the isolates were classified as multidrug-resistant (MDR). Higher levels of resistance and multidrug resistance were detected in CoNS isolated from flies collected in poultry farms than in swine farms. Therefore, house flies could carry MDR and methicillin-resistant staphylococci, representing a possible source of infection for animals and humans.

One Health: a holistic approach for food safety in livestock

The food safety of livestock is a critical issue between animals and humans due to their complex interactions. Pathogens have the potential to spread at every stage of the animal food handling process, including breeding, processing, packaging, storage, transportation, marketing and consumption. In addition, application of the antibiotic usage in domestic animals is a controversial issue because, while they can combat food-borne zoonotic pathogens and promote animal growth and productivity, they can also lead to the transmission of antibiotic-resistant microorganisms and antibiotic-resistant genes across species and habitats. Coevolution of microbiomes may occur in humans and animals as well which may alter the structure of the human microbiome through animal food consumption. One Health is a holistic approach to systematically understand the complex relationships among humans, animals and environments which may provide effective countermeasures to solve food safety problems aforementioned. This paper depicts the main pathogen spectrum of livestock and animal products, summarizes the flow of antibiotic-resistant bacteria and genes between humans and livestock along the food-chain production, and the correlation of their microbiome is reviewed as well to advocate for deeper interdisciplinary communication and collaboration among researchers in medicine, epidemiology, veterinary medicine and ecology to promote One Health approaches to address the global food safety challenges.