Extended-spectrum β-lactamase/AmpC- and carbapenemase-producing Enterobacteriaceae in animals: a threat for humans?

Shelter dogs as reservoirs of international clones of Escherichia coli carrying mcr-1.1 and blaCTX-M resistance genes in Lima, Peru

Antimicrobial resistance (AMR) poses a critical public health threat worldwide, particularly at the human-animal interface where cross-transmission of critical priority Enterobacterales, such as Escherichia coli, have become increasingly reported. Worryingly, E. coli encoding extended-spectrum β-lactamases (ESBLs) has been documented in companion animals worldwide. Conversely, the presence of mcr genes, which confer resistance to polymyxins, in bacteria from pets remains more infrequent. In this study, we sequenced and reported on the first genomic data of E. coli strains carrying mcr-1 and/or blaCTX-M genes isolated from rectal swabs of stray dogs in a shelter in the city of Lima, Peru. Antimicrobial susceptibility revealed that E. coli strains exhibited a multidrug resistance profile. In addition to mcr-1 and blaCTX-M genes, other clinically relevant resistance determinants were identified, with notably presence of blaTEM-176 and the novel blaSCO-2 variant. The association of mcr-1.1 and IncI2 plasmid was confirmed. Several virulence genes were detected, classifying strains as putative extraintestinal pathogenic E. coli. Multilocus sequence typing prediction recognized diverse sequence types (ST), including ST155, ST189, ST657, ST746, ST1140, ST3014, and ST7188. This study represents the first report of mcr-positive E. coli in dogs from Peru, emphasizing the need for continuous surveillance and genomic characterization to better understand the transmission dynamics of these critical resistance genes at the human-animal interface. Furthermore, our results provide evidence that stray, and shelter dogs could be a reservoir for the spread of WHO priority pathogens, and/or polymyxin and β-lactam resistance genes, which is a public health and One Health concern that requires appropriate management strategies.

Drivers of the emergence and dissemination of high-risk resistance genes in cattle farm

Extended spectrum β-lactamase (ESBL)- and carbapenemase-producing Enterobacterales (CPE) are recognized by WHO as critical concerns. The high cephalosporin resistance rate in a cattle farm in 2018 prompted us to conduct long-term (2019-2023) and extensive monitoring to explore risk factors for the import and transmission of ESBLs and CPE in this farm. Among 1288 samples from cattle, the environment, milk, and biological vectors, 48.8 % carried blaCTX-M-positive Enterobacterales with blaCTX-M-55 being dominant (76.4 %), and blaNDM-5-positive strains emerged in 2022 with a 1.9 % detection rate. blaCTX-M-55 and blaNDM-5 were likely introduced through various routes, especially wild birds, and have persisted due to overuse of cephalosporins in the farm. The spread of these genes was driven by the horizontal transmission of IncHI2 and IncX3 plasmids and clonal dissemination of certain clones. Cross-regional and cross-border transmission of blaCTX-M-55- and/or blaNDM-5-bearing bacteria and plasmids possibly occurred via wild birds, animal trade, and other means. Our findings suggest that the import, persistence, and dissemination of these genes within and beyond this farm, were fueled by suboptimal biosecurity practices and inadequate antibiotic stewardship, highlighting the urgency for integrated public and ecosystem health policies to prevent the spread of resistance genes as part of a holistic One Health strategy. ENVIRONMENTAL IMPLICATION: The high prevalence and long-term persistence of extended-spectrum β-lactamases and the emergence of carbapenemases in cattle and the environment signify a critical risk of transmitting high-risk resistance genes, posing a significant threat to human health. Consequently, bacteria carrying these genes in animal farms should be regarded as "hazardous materials". Import, persistence, and dissemination of these genes within and beyond this farm were exacerbated by suboptimal biosecurity practices and inadequate antibiotic stewardship, highlighting the urgency for integrated public and ecosystem health policies to mitigate the environmental risks associated with gene transmission as part of a comprehensive One Health strategy.

Fecal carriage of extended-spectrum β-lactamase-, AmpC β-lactamase- and carbapenemase-producing Escherichia coli in stray cats in Italy

The spread of carbapenem-resistant bacteria is a global threat to public health and the role of pets in the rise in antimicrobial resistance is gaining attention worldwide. This study aimed to determine the fecal carriage of extended-spectrum β-lactamase (ESBL)-, AmpC- and carbapenemase (CP)-producing E. coli and associated risk factors in healthy and unhealthy stray cats admitted to the Veterinary Teaching Hospital of Lodi, University of Milan, Italy. Fecal samples collected in, 2020-2022 were microbiologically and molecularly analyzed. Overall, ESBL-/AmpC-/CP-producing E. coli were detected in 18/94 (19.1 %) stray cats. Twelve (12.8 %), 4 (4.3 %) and 7 (7.4 %) stray cats carried ESBL-, AmpC- and CP-producing E. coli phenotypes respectively, supported by the detection of blaCTX-M in all ESBL-producing E. coli, blaCMY-2 in all AmpC-producing E. coli and blaNDM (4/7; 57.1 %) or blaOXA-48 (3/7; 42.9 %) genes in CP-producing E. coli. Multiple combination of resistance genes and phenotypes were detected. MIC results showed that all E. coli were multidrug resistant isolates. Risk factors associated with ESBL-, AmpC- and/or CP-producing E. coli fecal carriage were hospitalization (P < 0.0001), antibiotic treatment during hospitalization (P < 0.0001) and unhealthy status (P < 0.0001). Fecal carriage of CP-producing E. coli is of concern and highlights the need of specific surveillance programs for CP-producing Enterobacteriaceae and antimicrobial stewardship in stray cats to reduce the emergence and spread of resistant bacteria. Limitations of this study suggest a One Health approach to characterize the whole genome of the isolates and the epidemiology of AMR bacteria among stray cats, including additional bacterial species and the environment.

Molecular epidemiology of extended-spectrum beta-lactamases and carbapenemases-producing Shigella in Africa: a systematic review and meta-analysis

BACKGROUND

The treatment of Shigella infections has become a major challenge due to the emergence of multidrug-resistant Shigella. There is however insufficient knowledge regarding the molecular epidemiology of Shigella strains producing beta-lactamases in Africa. This systematic review investigated the scientific literature on the molecular epidemiology of extended-spectrum beta-lactamase (ESBL) and carbapenemases producing Shigella in Africa.

METHODS

Papers published in English and French from African countries on the molecular epidemiology of ESBL and carbapenemase producing Shigella from January 1999 to July 5, 2024 were reviewed. An extensive literature search was conducted through electronic databases including PubMed, Scopus, Web of Sciences, African Journals Online (AJOL) and Google scholar using specific keywords. The meta-analysis and forest plots of Shigella species, ESBL and carbapenemases genes were done using the comprehensive Meta-Analysis software. All data were analyzed using a binary random-effects model by the DerSimonian-Laird method at a 95% confidence interval.

RESULTS

Out of the 583 research articles, only 18 (3.1%) articles representing eleven countries were included in the meta-analysis. The overall pooled prevalence of ESBL and Carbapenem Resistant (CR)-producing Shigella was estimated as 41.2% (95% CI: 22.8-62.4; I2 = 93.7%, p < 0.05). The leading ESBL and CR-producing Shigella species reported in this review was Shigella flexneri, 34.5% (95% CI: 16.6-58.2; I2 = 94.9%, p < 0.05). ESBL and CR-producing Shigella sonnei was the least reported with estimated prevalence of 6.7% (95% CI: 3.4-13.2; I2 = 80.7%, p < 0.05). In this review, blaTEM, blaOXA-1, and blaCTX-M were the most prevalent genes in Africa with prevalence of 25.9% (95% CI: 13.9-43.2; I2 = 90.9%, p < 0.05), 25.7% (95% CI: 14.9-43.0; I2 = 93.7%, p < 0.05), and 10.8% (95% CI: 4.5-23.4; I2 = 85.6%, p < 0.05) respectively. The prevalence of Carbapenemases genes on the other hand was low, reported as 0.8% (95% CI: 0.2-10.3; I2 = 51.4%; p < 0.05) for blaNDM, 1.1% for blaKPC, and 0.5% for blaIMP.

CONCLUSION

This study highlighted Shigella flexneri as the most prevalent ESBL and CR-producing Shigella species found in various African countries. The findings from this review indicate blaTEM, blaOXA-1 and blaCTX-M as the most prevalent genes in Africa while carbapenemases are least prevalent. The findings from the study suggest that ESBL and CR-producing Shigella pose a significant public health threat in Africa. Effective antimicrobial resistance (AMR) surveillance strategies are needed to improve the management and treatment of Shigella infections in Africa.

Neglected class A carbapenemases: Systematic review of IMI/NmcA and FRI from a One Health perspective

Carbapenemase-producing Enterobacterales are pathogens classified as a critical priority by the World Health Organization and a burden on human health worldwide. IMI, NmcA, and FRI are under-detected class A carbapenemases that have been reported in the human, animal and environmental compartments, particularly these last 5 years. Bacteria producing these carbapenemases have been mostly identified in digestive carriage screenings, but they are also involved in severe infections, such as bacteremia. Their increasing detection in wild fauna and natural environments confirms their ubiquitous nature. Indeed, they have been especially found in aquatic ecosystems and in many animals living in close association with them. Therefore, the hydric compartment is suspected to be the main reservoir of IMI carbapenemases. Although they are almost confined to Enterobacter cloacae complex species, some variants are plasmid-encoded and may diffuse to other bacterial species that are more virulent or more adapted to humans. Furthermore, their association with other resistance mechanisms, such as Extended Spectrum Beta-Lactamases, leaves only few therapeutic options and raises concerns about the environmental spread of Multi-Drug-Resistant bacteria. These carbapenemase might be responsible of "mixed" outbreaks of CPE with a community origin and a possible secondary nosocomial spread. Therefore, more studies from a One Health perspective are needed to identify as many primary environmental (aquatic) reservoirs as possible, as well as secondary distribution routes (directly from the environment, via the food chain or animals…) which may also become secondary reservoirs for these carbapenemases, in order to implement measures to combat this potential emerging threat to humans. This review summarizes the main characteristics of the IMI, NmcA, and FRI carbapenemases, covering their detection, epidemiology, genetic environment, and associated resistance genes using a One Health approach.

Genotyping of extended-spectrum beta-lactamase-producing Escherichia coli isolated from wastewater of dairy farms in East Java, Indonesia

Background and Aim

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in dairy farm wastewater represents a significant threat to environmental and public health due to the dissemination of antibiotic-resistance genes. This study investigates the molecular profiles of ESBL-producing E. coli isolates harboring bla CTX-M, bla TEM, and bla SHV genes from dairy farm wastewater in East Java, Indonesia.

Materials and Methods

Wastewater samples (n = 342) were collected from six major dairy regions in East Java: Pasuruan, Malang, Tulungagung, Blitar, Batu, and Kediri. The samples underwent bacterial isolation, identification, and ESBL phenotypic screening using the double-disk synergy test (DDST). Molecular genotyping of bla CTX-M, bla TEM, and bla SHV was conducted using a polymerase chain reaction.

Results

Of the samples, 69.30% (237/342) tested positive for E. coli, with 32.91% (78/237) identified as ESBL producers through DDST. Molecular genotyping confirmed ESBL genes in 28.20% (22/78) of the isolates. The genotypic distribution was 77.2% (17/22) bla TEM, 4.5% (1/22) bla CTX-M, 9.0% (2/22) bla TEM + bla SHV, and 9.0% (2/22) bla TEM + bla CTX-M. These findings highlight the dominance of bla TEM and the presence of multi-gene combinations in East Java's dairy farm wastewater.

Conclusion

The identified molecular profiles underscore dairy farm wastewater as a critical reservoir for antibiotic resistance genes, particularly bla TEM. Addressing this issue necessitates stringent antimicrobial use policies, improved wastewater management, and enhanced biosecurity measures. These findings support a One Health approach to mitigate environmental and public health risks associated with AMR.

Public health concern of antimicrobial resistance and virulence determinants in E. coli isolates from oysters in Egypt

The emergence of critical-priority E. coli, carrying a wide array of resistance and virulence factors through food sources, poses a significant challenge to public health. This study aimed to investigate the potential role of oysters sold in Egypt as a source for E. coli, identify their resistance and virulence-associated gene profiles, and assess associated zoonotic risks. A total of 33 pooled fresh oyster samples were obtained from various retail fish markets in Egypt and examined bacteriologically for the presence of E. coli. Antimicrobial resistance was performed by the disk-diffusion method, and the multiple antibiotic resistance index (MAR) was calculated. All isolates were screened for extended-spectrum beta-lactamase (ESBL) (blaTEM, blaSHV, blaCTX-M, and blaOXA-1), plasmid-mediated AmpC blaCMY-2, and carbapenemases (blaKPC, blaNDM, blaVIM, and blaOXA-48) genes by Polymerase chain reaction. Moreover, the presence of virulence-encoding genes was investigated. The virulent MDR strains were clustered using R with the pheatmap package. The prevalence of E. coli was 72.7% (24 out of 33), with 66.7% of the isolates classified as multi-drug resistant, and 75% exhibited MAR values exceeding the 0.2 threshold. Different antimicrobial sensitivity phenotypes and genotype profiles were identified in E. coli isolates. The most prevalent gene detected among all isolates was blaTEM (22/24, 91.7%). Notably, all non-ESBL producers were positive for blaCMY2. Carbapenem-resistant and carbapenem-intermediate strains were carbapenemase producers, with the predominance of the blaKPC gene (11/24, 45.8%). Remarkably, twelve out of sixteen virulence genes were identified, with papC (21/24, 87.5%) and sfa (16/24, 66.7%) genes being the most prevalent. Most isolates carry virulence genes primarily associated with extra-intestinal pathogenic E. coli (ExPEC) (87.5%) and enteropathogenic (EPEC) (70.8%) pathotypes. Four E. coli isolates exhibit cluster patterns. This study provides the first insight into the emergence of virulent MDR E. coli among oysters in Egypt. It underscores the potential role of oysters as a source for disseminating these strains within aquatic ecosystems, presenting a possible threat to public health.

Wastewater and environmental sampling holds potential for antimicrobial resistance surveillance in food-producing animals - a pilot study in South African abattoirs

Antimicrobial resistance (AMR) poses a significant global One Health challenge that causes increased mortality and a high financial burden. Animal production contributes to AMR, as more than half of antimicrobials are used in food-producing animals globally. There is a growing body of literature on AMR in food-producing animals in African countries, but the surveillance practices across countries vary considerably. This pilot study aims to explore the potential of wastewater and environmental surveillance (WES) of AMR and its extension to the veterinary field. Floor drainage swab (n = 18, 3/abattoir) and wastewater (n = 16, 2-3/abattoir) samples were collected from six South African abattoirs that handle various animal species, including cattle, sheep, pig, and poultry. The samples were tested for Extended-Spectrum Beta-Lactamase (ESBL) and Carbapenemase-producing Enterobacterales, Methicillin-Resistant Staphylococcus aureus (MRSA), Vancomycin-resistant Enterococci (VRE), and Candida auris by using selective culturing and MALDI-TOF MS identification. The phenotype of all presumptive ESBL-producing Escherichia coli (n = 60) and Klebsiella pneumoniae (n = 24) isolates was confirmed with a disk diffusion test, and a subset (15 and 6 isolates, respectively), were further characterized by whole-genome sequencing. In total, 314 isolates (0-12 isolates/sample) withstood MALDI-TOF MS, from which 37 species were identified, E. coli and K. pneumoniae among the most abundant. Most E. coli (n = 48/60; 80%) and all K. pneumoniae isolates were recovered from the floor drainage samples, while 21 presumptive carbapenem-resistant Acinetobacter spp. isolates were isolated equally from floor drainage and wastewater samples. MRSA, VRE, or C. auris were not found. All characterized E. coli and K. pneumoniae isolates represented ESBL-phenotype. Genomic analyses revealed multiple sequence types (ST) of E. coli (n = 10) and K. pneumoniae (n = 5), including STs associated with food-producing animals globally, such as E. coli ST48 and ST10 and K. pneumoniae ST101. Common beta-lactamases linked to food-producing animals, such as bla CTX-M-55 and bla CTX-M-15, were detected. The presence of food-production-animal-associated ESBL-gene-carrying E. coli and K. pneumoniae in an abattoir environment and wastewater indicates the potential of WES in the surveillance of AMR in food-producing animals. Furthermore, the results of this pilot study encourage studying the topic further with refined methodologies.

Association analysis of antibiotic and disinfectant resistome in human and foodborne E. coli in Beijing, China

The widespread use of chemical disinfectants and antibiotics poses a major threat to food safety and human health. However, the mechanisms of co-transmission of antimicrobial resistance genes (ARGs) and biocides and metal resistance genes (BMRGs) of foodborne pathogens in the food chain is still unclear. This study isolated 343 E. coli strains from animal-derived foods in Beijing and incorporated online data of human-derived E. coli strains from NCBI. Our results demonstrated a relatively uniform distribution of strains from various regions in Beijing, indicating a lack of region-specific clustering. Additionally, predominant sequence types varied between food- and human-derived strains, suggesting a preference for different hosts and environments. Phenotypic association analysis showed that the chlorine disinfectants peroxides had a significant positive correlation with tetracyclines. Many more ARGs and BMRGs were enriched in human-associated E. coli compared with those in chicken- and pork-origin. The quaternary ammonium compounds (QACs) resistance gene qacEΔ1 had a strong correlation with aminoglycoside resistance gene aadA5, folate pathway antagonist resistance gene dfrA17, sul1 and macrolide resistance gene mph(A). The correlation results indicated a significant association between the copper resistance gene cluster pco and the silver resistance gene cluster sil. Coexistence of many resistance genes was observed within the qacEΔ1 gene structure, with qacEΔ1-sul1 being the most common combination. Our findings demonstrated that the epidemiological spread of resistance is affected by a combination of heavy metals, disinfectants and antibiotic use, suggesting that the prevention and control strategies of antimicrobial resistance need to be multifaceted and comprehensive.

Conventional and unsupervised artificial intelligence analyses identified risk factors for antimicrobial resistance on dairy farms in the province of Québec, Canada

Antimicrobial resistance (AMR) is one of the greatest threats to global health worldwide and is threatening not only humans, but also animal production systems, including dairy farms. The objective of this paper was to describe risks factors associated with AMR on dairy farms in Québec, Canada. This observational cross-sectional study included 101 commercial dairy farms and took place between the springs of 2017 and 2018 for a one-year period. We explored risk factors such as farm practices and producer's knowledge (measured using a questionnaire), antimicrobial use (quantified using veterinary invoices), and the presence of Salmonella Dublin (tested by serology). We evaluated AMR with fecal Escherichia coli retrieved from pre-weaned calves and lactating cows using the following outcomes: the presence of extended-spectrum-β-lactamase/AmpC resistance and the number of resistances to antimicrobial classes. We used logistic regression models to evaluate the association between each risk factor and the 2 outcomes for the 2 types of samples (pre-weaned calves and lactating cows). Furthermore, we explored the relationships between these risk factors utilizing data dimensionality reduction and hierarchical clustering. Outputs of these analyses were used as regressors for AMR in regression models. While the results for univariate analyses were ambiguous, the unsupervised analysis naturally categorized the sample of farms according to their health/treatment status (dimension 1, explaining 12.9% of the variance) and herd size (dimension 2, explaining 7.8%). Three clusters of farms were identified (cluster 1: mainly healthy herds and low ceftiofur users, cluster 2: relatively high ceftiofur users, cluster 3: farms with a higher incidence of diseases and higher antimicrobial treatment rates). Dimension 1 and cluster membership were statistically associated with the presence of extended-spectrum-β-lactamase/AmpC resistance in lactating cows and in pre-weaned calves. Dimension 1 was also statistically associated with the number of resistances in lactating cows and in pre-weaned calves. This study highlights the complexity of analyzing risk factors associated with AMR. Our results suggest that the herd health status and the AMU-related practices used are associated with AMR in dairy farms. However, prospective studies are needed to confirm a causal relation.

Environment, animals, and food as reservoirs of antibiotic-resistant bacteria for humans: One health or more?

Antimicrobial resistance (AMR) is a major public health challenge. For several years, AMR has been addressed through a One Health approach that links human health, animal health, and environmental quality. In this review, we discuss AMR in different reservoirs with a focus on the environment. Anthropogenic activities produce effluents (sewage, manure, and industrial wastes) that contaminate soils and aquatic environments with antibiotic-resistant bacteria (ARB), antibiotic-resistant genes (ARGs), and selective agents such as antibiotics, biocides, and heavy metals. Livestock treated with antibiotics can also contaminate food with ARB. In high-income countries (HICs), effective sanitation infrastructure and limited pharmaceutical industries result in more controlled discharges associated with human activities. Hence, studies using genome-based typing methods have revealed that, although rare inter-reservoir transmission events have been reported, human acquisition in HICs occurs primarily through person-to-person transmission. The situation is different in low- and middle-income countries (LMICs) where high population density, poorer sanitation and animal farming practices are more conducive to inter-reservoir transmissions. In addition, environmental bacteria can be a source of ARGs that, when transferred to pathogenic species under antibiotic selection pressure in environmental hotspots, produce new antibiotic-resistant strains that can potentially spread in the human community through human-to-human transmission. The keys to reducing AMR in the environment are (i) better treatment of human waste by improving wastewater treatment plants (WWTPs) in HICs and improving sanitation infrastructure in LMICs, (ii) reducing the use of antibiotics by humans and animals, (iii) prioritizing the use of less environmentally harmful antibiotics, and (iv) better control of pharmaceutical industry waste.

Antibiotic susceptibility and genomic analysis of ciprofloxacin-resistant and ESBLs-producing Escherichia coli in vegetables and their irrigation water and growing soil

The rise of antibiotic resistance in Escherichia coli has become a major global public health concern. While there is extensive research on antibiotic-resistant E. coli from human and animal sources, studies on vegetables and their environments are limited. This study investigated the prevalence and characteristics of ciprofloxacin-resistant (CIPR) E. coli in 13 types of edible raw vegetables, along with their irrigation water and soil in Shaanxi, China. Of 349 samples collected (157 vegetables, 59 water, and 133 soil), a total of 48 positive samples were detected, with one CIPRE. coli strain isolated from each sample being selected for further analyses. A striking observation was its high prevalence in irrigation water at 44.1 %, markedly exceeding that in vegetables (12.0 %) and soil (4.5 %). The susceptibility of Forty-eight CIPRE. coli isolates was evaluated using the disc diffusion method for 18 different antibiotics, all these isolates were not only resistant to the tested fluoroquinolones antibiotics (levofloxacin, nalidixic acid), but also displayed a multi-drug resistance (MDR) pattern. Twenty-eight (58.3 %) of 48 CIPRE. coli isolates exhibited extended spectrum β-lactamases (ESBLs) (CIPR-ESBLs) producing phenotype. Subsequently, whole-genome sequencing was performed on these 28 isolates. We identified 12 serotypes and STs each, with O101: H9 (35.7 %, 10/28) and ST10 (21.4 %, 6/28) being the most common. Further classification placed these isolates into five phylogenetic groups: A (57.1 %, 16/28), B1 (32.1 %, 9/28), D (3.6 %, 1/28), B2 (3.6 %,1/28), and F (3.6 %,1/28). Notelly, Identical ST types, serotypes and phylogroups were found in certain CIPR-ESBLs-producing E. coli from both vegetables and adjacent irrigation water. Genomic analysis of the 28 CIPR-ESBLs-producing E. coli isolates unveiled 73 resistance genes, associated with 13 amino acid mutations in resistance-determining regions (QRDRs) and resistance to 12 types of antibiotics. Each isolate was confirmed to carry both ESBLs and fluoroquinolone resistance genes, with the Ser83Ala mutation in GyrA (96.4 %, 27/28) being the most prevalent. A detailed analysis of Mobile Genetic Elements (MGEs) revealed that IncFIB and IncFII plasmid subtypes were most prevalent in 60.7 % and 67.9 % of isolates, respectively, with 75 % containing over 10 insertion sequences (IS) each. Furthermore, we observed that certain ESBL and PMQR genes were located on plasmids or in proximity to insertion sequences. In conclusion, our research highlights the widespread presence of CIPRE. coli in irrigation water and thoroughly examines the genetic characteristics of CIPR-ESBLs-producing E. coli strains, underlining the need for ongoing monitoring and management to reduce multidrug-resistant bacteria in vegetables and their environment.

Beta-lactamase genes in bacteria from food animals, retail meat, and human surveillance programs in the United States from 2002 to 2021

The spread of beta-lactamase-producing bacteria is a global public-health concern. This study aimed to explore the distribution of beta-lactamases reported in three sampling sources (cecal, retail meat, and human) collected as part of integrated surveillance in the United States. We retrieved and analyzed data from the United States National Antimicrobial Resistance Monitoring Systems (NARMS) from 2002 to 2021. A total of 115 beta-lactamase genes were detected in E. coli, Salmonella enterica, Campylobacter, Shigella and Vibrio: including 35 genes from cecal isolates, 32 genes from the retail meat isolates, and 104 genes from the human isolates. Three genes in E. coli (blaCMY-2,blaTEM-1A, and blaTEM-1B), 6 genes in Salmonella enterica (blaCARB-2, blaCMY-2, blaCTXM-65, blaTEM-1A, blaTEM-1B, and blaHERA-3), and 2 genes in Campylobacter spp. (blaOXA-61 and blaOXA-449) have been detected across food animals (cattle, chicken, swine, and turkey) and humans over the study period. blaCTXM-55 has been detected in E. coli isolates from the four food animal sources while blaCTXM-15 and blaCTXM-27 were found only in cattle and swine. In Salmonella enterica, blaCTXM-2, blaCTXM-9, blaCTXM-14, blaCTXM-15, blaCTXM-27, blaCTXM-55, and blaNDM-1 were only detected among human isolates. blaOXAs and blaCARB were bacteria-specific and the only beta-lactamase genes detected in Campylobacter spp. and Vibrio spp respectively. The proportions of beta-lactamase genes detected varies from bacteria to bacteria. This study provided insights on the beta-lactamase genes detected in bacteria in food animals and humans in the United States. This is necessary for better understanding the molecular epidemiology of clinically important beta-lactamases in one health interface.

Genetic epidemiology and plasmid-mediated transmission of mcr-1 by Escherichia coli ST155 from wastewater of long-term care facilities

Long-term care facilities (LTCFs) for older people play an important and unique role in multidrug-resistant organism transmission. Herein, we investigated the genetic characteristics of mobile colistin resistance gene (mcr-1)-carrying Escherichia coli strains isolated from wastewater of LTCFs in Shanghai. Antimicrobial susceptibility test was carried out by agar dilution methods. Whole-genome sequencing and plasmid sequencing were conducted, and resistance genes and sequence types of colistin in E. coli isolates were analyzed. Core genome multilocus sequence typing (cgMLST) analysis was performed by the Ridom SeqSphere+ software. Phylogenetic tree through the maximum likelihood method was constructed by MEGA X. Out of 306 isolates, only 1 E. coli named ECSJ33 was found, and the plasmid pECSJ33 from ECSJ33 harbored the mcr-1 gene that was located with 59,080 bp belonging to IncI2 type. The plasmid pECSJ33 was capable of conjugation with an efficiency of 2.9 × 10-2. Bioinformatic analysis indicated pECSJ33 shared backbone with the previously reported mcr-1-harboring pHNGDF93 isolated from fish source. Moreover, the cgMLST analysis revealed that ECSJ33 belongs to different lineages from those reported from previous E. coli strains but shared high similarity to NCTC11129 in cluster 11. The phylogenetic tree revealed MCR-1 of ECSJ33 in this study was mostly of animal food origin and that they were closely related. Our study firstly reports detection of genome sequence of a multidrug-resistant mcr-1-harboring E. coli ST155 from wastewater of LTCF source in China. The data may prove that the plasmid pECSJ33 belongs to food origin and help to understand the antimicrobial resistance mechanisms and genomic features of colistin resistance under One Health approach.IMPORTANCEOne Escherichia coli named ECSJ33 was found from wastewater of a long-term care facility (LTCF) and the plasmid pECSJ33 from ECSJ33 harbored the mobile colistin resistance gene (mcr-1) that was located with 59,080 bp belonging to IncI2 type, which was capable of conjugation with an efficiency of 2.9 × 10-2. This paper firstly reports an mcr-1-carrying E. coli strain ST155 isolated from LTCF in China. Comparative genomics analysis indicated pECSJ33 shared backbone with the previously reported mcr-1-harboring pHNGDF93 isolated from fish source. The phylogenetic tree revealed MCR-1 protein of ECSJ33 in this study was mostly of animal food origin and that they were closely related. Therefore, the pECSJ33 could be considered as food-origin transmission mcr-1-harboring plasmid.

The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021-2022

This report by the European Food Safety Authority and the European Centre for Disease prevention and Control, provides an overview of the main findings of the 2021-2022 harmonised Antimicrobial Resistance (AMR) monitoring in Salmonella spp., Campylobacter jejuni and C. coli from humans and food-producing animals (broilers, laying hens and fattening turkeys, fattening pigs and cattle under one year of age) and relevant meat thereof. For animals and meat thereof, AMR data on indicator commensal Escherichia coli, presumptive extended-spectrum beta-lactamases (ESBL)-/AmpC beta-lactamases (AmpC)-/carbapenemase (CP)-producing E. coli, and the occurrence of methicillin-resistant Staphylococcus aureus (MRSA) are also analysed. Generally, resistance levels differed greatly between reporting countries and antimicrobials. Resistance to commonly used antimicrobials was frequently found in Salmonella and Campylobacter isolates from humans and animals. In humans, increasing trends in resistance to one of two critically antimicrobials (CIA) for treatment was observed in poultry-associated Salmonella serovars and Campylobacter, in at least half of the reporting countries. Combined resistance to CIA was however observed at low levels except in some Salmonella serovars and in C. coli from humans and animals in some countries. While CP-producing Salmonella isolates were not detected in animals in 2021-2022, nor in 2021 for human cases, in 2022 five human cases of CP-producing Salmonella were reported (four harbouring bla OXA-48 or bla OXA-48-like genes). The reporting of a number of CP-producing E. coli isolates (harbouring bla OXA-48, bla OXA-181, bla NDM-5 and bla VIM-1 genes) in fattening pigs, cattle under 1 year of age, poultry and meat thereof by a limited number of MSs (5) in 2021 and 2022, requires a thorough follow-up. The temporal trend analyses in both key outcome indicators (rate of complete susceptibility and prevalence of ESBL-/AmpC-producers in E. coli) showed an encouraging progress in reducing AMR in food-producing animals in several EU MSs over the last 7 years.

Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh

IMPORTANCE

Through the use of DNA sequencing, our study shows that there is no significant difference in the antibiotic resistance genes found in stool samples taken from individuals with high exposure to poultry routinely fed antibiotics and those without such exposure. This finding is significant as it suggests limited transmission of antibiotic resistance genes between poultry and humans in these circumstances. However, our research also demonstrates that commercially reared poultry are more likely to possess resistance genes to antibiotics commonly administered on medium-sized farms. Additionally, our study highlights the under-explored potential of wastewater as a source of various antibiotic resistance genes, some of which are clinically relevant.

Comparative analyses of the faecal resistome against β-lactam and quinolone antibiotics in humans and livestock using metagenomic sequencing

To assess the prevalence and abundance of antibiotic resistance genes in human and livestock gut microbiomes, 87 humans (healthy individuals and patients with Clostridioides difficile infection (CDI)) and 108 livestock (swine, cattle, and chickens) were enrolled. Gut microbiomes and fluoroquinolone-resistant Escherichia coli isolates were sequenced, and mobile genetic elements adjacent to the β-lactamase (bla) and transferable quinolone resistance (qnr) genes were compared using metagenomic contigs. Each group of humans and livestock exhibited distinctive microbiota and resistome compositions in the gut. Concerning the resistome of bla and qnr, the prevalence rates between chickens and patients with CDI were the most similar (R2 = 0.46); blaTEM, blaOXA, blaCTX-M, and qnrS were highly prevalent in both groups. According to genomic and phylogenetic analyses, blaCTX-M and blaOXA expressed lineage specificity to either humans or livestock, while qnrS and blaTEM displayed a shared lineage between humans and livestock. A qnrS1 mobilome comprising five genes, including two recombinases, a transposase, and a plasmid gene, is commonly found in human and chicken gut microbiomes. Humans and chickens showed the most similar gut resistomes to β-lactams and quinolones. QnrS and blaTEM displayed especially strong co-occurrence between the guts of humans and livestock.

Situation Report on mcr-Carrying Colistin-Resistant Clones of Enterobacterales: A Global Update Through Human-Animal-Environment Interfaces

In the twenty-first century, antibiotic resistance (ABR) is one of the acute medical emergencies around the globe, overwhelming human-animal-environmental interfaces. Hit-or-mis use of antibiotics exacerbates the crisis of ABR, dispersing transferable resistance traits and challenging treatment regimens based on life-saving drugs such as colistin. Colistin is the highest priority critically important antimicrobials for human medicine, but its long use as a growth promoter in animal husbandry reduces clinical efficacy. Since 2015, the emergence and spread of mobile colistin resistance (mcr)-carrying colistin-resistant clones of Enterobacterales have been markedly sustained in both humans and animals, especially in developing countries. Hospital and community transmissions of mcr clones pose a high risk for infection prevention and outbreaks at the national and international levels. Several public health and limited one health studies have highlighted the genomic insights of mcr clones, clarifying the chromosomal sequence types (STs) and plasmid incompatibility (Inc) types. But this information is segregated into humans and animals, and rarely are environmental sectors complicating the understanding of possibly intercontinental and sectoral transmission of these clones. India is the hotspot for superbugs, including mcr-carrying colistin-resistant isolates that threaten cross-border transmission. The current review provided an up-to-date worldwide scenario of mcr-carrying STs and plasmid Inc types among the Gram-negative bacilli of Enterobacterales across human-animal-environmental interfaces and correlated with the available information from India.

Evaluating the incidence of ampC-β-lactamase genes, biofilm formation, and antibiotic resistance among hypervirulent and classical Klebsiella pneumoniae strains

AIM

Both immunocompetent and healthy individuals can become life-threateningly ill when exposed to the hypervirulent (hvKp) strains of Klebsiella pneumoniae (Kp). The main objectives of this study were to evaluate the presence of ampC-lactamase genes, biofilm formation, and antibiotic resistance in clinical strains of hvKp and cKp (classical K. pneumoniae).

MATERIALS AND METHODS

Kp strains were collected from patients referred to Shahidzadeh Hospital in Behbahan City, Khuzestan Province, Iran. Several techniques were used to identify hvKp. The hypermucoviscosity phenotype was determined using the string test. Isolates that developed dark colonies on tellurite agar were assumed to be hvKp strains. If any of the iucA, iutA, or peg-344 genes were detected, the isolates were classified as hvKp. Phenotypic and genotypic detection of AmpC β-lactamases of hvKp strains was performed by the combined disk method and polymerase chain reaction, respectively. In addition, crystal violet staining was used to determine the biofilm formation of these isolates.

RESULTS

For this study, 76 non-duplicative isolates of Kp were collected. Overall, 22 (28.94%) strains had positive string test results, and 31 (40.78%) isolates were grown in tellurite-containing medium. The genes iucA and iutA or peg-344 were found in 23.68% of all Kp strains and in 50% of tellurite-resistant isolates, respectively. The most effective antibiotics against hvKp isolates were tetracycline (85.52%) and chloramphenicol (63.15%). Using the cefoxitin disc diffusion method, we observed that 56.57% (43/76) of the strains were AmpC producer. A total of 30.26% (n = 23/76) of the isolates tested positive for at least one ampC gene, including blaDHA (52.63%, n = 40), blaCIT (40.78%, n = 31), blaACC (19.76%, n = 15), blaMOX (25%, n = 19), and blaFOX (43.42%, n = 33). Biofilm formation analysis revealed that most hvKp isolates were weak (n = 6, 40%) and moderate (n = 5, 33.33%) biofilm producers.

CONCLUSION

Healthcare practitioners should consider the possibility of the existence and acquisition of hvKp everywhere. The exact mechanisms of bacterial acquisition are also unknown, and it is unclear whether the occurrence of infections is related to healthcare or not. Thus, there are still many questions about hvKp that need to be investigated.

Extended-Spectrum β-Lactamases (ESBL): Challenges and Opportunities

The rise of antimicrobial resistance, particularly from extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E), poses a significant global health challenge as it frequently causes the failure of empirical antibiotic therapy, leading to morbidity and mortality. The E. coli- and K. pneumoniae-derived CTX-M genotype is one of the major types of ESBL. Mobile genetic elements (MGEs) are involved in spreading ESBL genes among the bacterial population. Due to the rapidly evolving nature of ESBL-E, there is a lack of specific standard examination methods. Carbapenem has been considered the drug of first choice against ESBL-E. However, carbapenem-sparing strategies and alternative treatment options are needed due to the emergence of carbapenem resistance. In South Asian countries, the irrational use of antibiotics might have played a significant role in aggravating the problem of ESBL-induced AMR. Superbugs showing resistance to last-resort antibiotics carbapenem and colistin have been reported in South Asian regions, indicating a future bleak picture if no urgent action is taken. To counteract the crisis, we need rapid diagnostic tools along with efficient treatment options. Detailed studies on ESBL and the implementation of the One Health approach including systematic surveillance across the public and animal health sectors are strongly recommended. This review provides an overview of the background, associated risk factors, transmission, and therapy of ESBL with a focus on the current situation and future threat in the developing countries of the South Asian region and beyond.

Genome analysis of third-generation cephalosporin-resistant Escherichia coli and Salmonella species recovered from healthy and diseased food-producing animals in Europe

The animal reservoir of Enterobacterales producing Extended-Spectrum-β-Lactamases (ESBL) and plasmid-borne cephalosporinases (pAmpC) is a global concern. Using genome data, we analyzed a population of Escherichia coli and Salmonella species resistant to third-generation cephalosporins (3GC-R) recovered from healthy food animals (HA) and diseased food animals (DA) across Europe. Among the isolates collected from HA (n = 4,498) and DA (n = 833) in up to twelve European countries, 62 (1.4%) and 45 (5.4%) were 3GC-R, respectively. The genomes of these 3GC-R 107 isolates were sequenced to identify blaESBL and blaAmpC, sequence types (STs), virulence-associated genes, and Salmonella serovars. We also assessed their population structure using core genome multilocus sequence typing. The 78 3GC-R Escherichia coli originated from poultry (n = 27), swine (n = 26), and cattle (n = 25). Almost all (n = 77; 98.7%) harbored at least one blaESBL or blaAmpC, with blaCTX-M-1 predominating. We identified 51 STs, with ST10 and ST101 being the most frequent. The population of 3GC-R E. coli was polyclonal. The 29 3GC-R Salmonella spp. were mostly retrieved from healthy broiler (96.5%). blaCMY-2 dominated in this population. We found two clusters of CMY-2-producing Salmonella spp. in Germany: one with 15 isolates of S. Heidelberg isolates and another with six S. Minnesota, all of them with blaCMY-2. Our results confirm the low prevalence of 3GC-R E. coli and Salmonella spp. in HA and DA. blaCTX-M-1 was dominating in a highly diverse population of E. coli. 3GC-R E.coli isolated from HA and DA were genetically unrelated, with high clonal diversity suggesting multiple origins of contamination. This contrasted with the clonal population of 3GC-R Salmonella spp. in which blaCMY-2 dominated through two dominant serovars in this collection.

Emergence of ST1193 Clone in Maternal and Neonatal ESBL-Producing E. coli Isolates

Objective

The emerging epidemic of extended-spectrum β-lactamase-producing E. coli (ESBL-EC) is a global public health crisis. ESBL-EC infections are increasing worldwide and contribute to morbidity and mortality among newborn infants. However, the antimicrobial resistance characteristics and clonal transmission of maternal and neonatal ESBL-EC isolates need to be further deciphered.

Materials and Methods

We performed phenotypic and genotypic characterization of 33 ESBL-EC isolates from pregnant women and newborn during 2019-2020.

Results

Minimum inhibitory concentrations of 17 antimicrobial agents showed that all isolates were multidrug-resistant (MDR) and had a resistance rate of 100% to ampicillin, and mild resistance to florfenicol, gentamicin, ceftazidime, and amoxicillin-clavulanate. Additionally, imipenem, meropenem, polymyxin, and tigecycline exhibited good activity against the tested ESBL-EC isolates with low MIC50 (0.06-1 μg/mL) and MIC90 (0.06-1 μg/mL). Whole genome sequencing indicated that ESBL-EC isolates contained diverse antimicrobial resistant genes (blaCTX-M, blaTEM, blaSHV, tetA, etc.) and toxin genes (ompA, csg, fimH, hybtA, etc.). blaCTX-M genes were the main ESBL genotype. ST1193 (18.2%) was the second most abundant ST among the ESBL-EC isolates (ST131 was the most common, with 30.3%), and this is the first report of its mother-to-infant colonization transmission in China.

Conclusion

These findings revealed the occurrence of high-risk ST1193 clone among ESBL-EC isolates from pregnant women and newborn colonization in China. Further national or regional multicenter studies are needed to assess the dissemination and evolution of ESBL-EC ST1193 clone as a nosocomial pathogen in China.

Analyses of Extended-Spectrum-β-Lactamase, Metallo-β-Lactamase, and AmpC-β-Lactamase Producing Enterobacteriaceae from the Dairy Value Chain in India

The consumption of milk contaminated with antibiotic-resistant bacteria poses a significant health threat to humans. This study aimed to investigate the prevalence of Enterobacteriaceae producing β-lactamases (ESBL, MBL, and AmpC) in cow and buffalo milk samples from two Indian states, Haryana and Assam. A total of 401 milk samples were collected from dairy farmers and vendors in the specified districts. Microbiological assays, antibiotic susceptibility testing, and PCR-based genotyping were employed to analyze 421 Gram-negative bacterial isolates. The overall prevalence of β-lactamase genes was 10% (confidence interval (CI) (7-13)), with higher rates in Haryana (13%, CI (9-19)) compared to Assam (7%, CI (4-11)). The identified β-lactamase genes in isolates were blaCMY, blaMOX, blaFOX, blaEBC, and blaDHA, associated with AmpC production. Additionally, blaCTX-M1, blaSHV, and blaTEM were detected as ESBL producers, while blaVIM, blaIMP, blaSPM, blaSIM, and blaGIM were identified as MBL producers. Notably, Shigella spp. were the dominant β-lactamase producers among identified Enterobacteriaceae. This study highlights the presence of various prevalent β-lactamase genes in milk isolates, indicating the potential risk of antimicrobial-resistant bacteria in dairy products. The presence of β-lactam resistance raises concern as this could restrict antibiotic options for treatment. The discordance between genotypic and phenotypic methods emphasizes the necessity for comprehensive approaches that integrate both techniques to accurately assess antibiotic resistance. Urgent collaborative action incorporating rational and regulated use of antibiotics across the dairy value chain is required to address the global challenge of β-lactam resistance.

Do Pathogenic Escherichia coli Isolated from Gallus gallus in South Africa Carry Co-Resistance Toward Colistin and Carbapenem Antimicrobials?

Colistin and carbapenems are critically important antimicrobials often used as a last resort to manage multidrug-resistant bacterial infections in humans. With limited alternatives, resistance to these antimicrobials is of concern as organisms could potentially spread horizontally rendering treatments ineffective. The aim of this study was to investigate co-resistance to colistin and carbapenems among Escherichia coli isolated from poultry in South Africa. Forty-six E. coli strains obtained from clinical cases of breeder and broiler chickens were used. In addition to other antibiotics, all the isolates were tested against colistin and carbapenems using broth microdilution. Multiplex polymerase chain reactions were used to investigate the presence of colistin (mcr-1 to 5) and carbapenem (blaOXA-48, blaNDM-1, and blaVIM) resistance genes. Isolates exhibiting colistin resistance (>2 μg/mL) underwent a whole-genome sequencing analysis. Resistance to colistin (10.9%) and cefepime (6.5%) was noted with all colistin-resistant strains harboring the mcr-1 gene. None of the E. coli isolates were resistant to carbapenems nor carried the other resistant genes (mcr-2 to 5, blaOXA-48, blaNDM-1, and blaVIM). The mcr-1-positive strains belonged to sequence types ST117 and ST156 and carried virulence genes ompA, aslA, fdeC, fimH, iroN, iutA, tsh, pic, ast A and set 1A/1B. In conclusion, clinical E. coli strains from chickens in this study possessed mobile resistance genes for colistin and several other clinically relevant antimicrobials but not carbapenems. Additionally, they belonged to sequence types in addition to carrying virulence factors often associated with human extraintestinal pathogenic E. coli infections. Thus, the potential risk of transmitting these strains to humans cannot be underestimated especially if sick birds are dispatched into the thriving poorly regulated Cornish hen industry. The need for routine veterinary surveillance and monitoring of antimicrobial resistance, antimicrobial use and the importance of strengthening regulations guiding the informal poultry sector remains important.

Isolation, Identification and Antimicrobial Resistance Analysis of Canine Oral and Intestinal Escherichia coli Resistant to Colistin

In recent years, the antimicrobial resistance in Escherichia coli has gradually developed into a global problem. These resistant bacteria could be transmitted to humans through animal feces in the environment or direct contact with pets, leading to a problem in bacterial treatment for humans and animals. Now, the antibiotic resistance of oral and intestinal microbiota from dog origins remains unclear in China. Therefore, this study first analyzed the current colistin resistance of oral and intestinal microbiota from dog origins in mainland China. A total of 536 samples were collected from dogs in mainland China and, respectively, cultured on the SS and MacConkey agar plate containing colistin (4 μg/mL) to obtain bacteria, and the antibiotic-resistance phenotype of Escherichia coli was investigated for nine antibiotics. Results showed that a total of 2259 colistin-resistant bacteria were isolated from samples and identified, and among them, the isolated rate of Escherichia coli (34.01%, 769/2259) was relatively higher than that of other bacteria. Subsequently, it was found that the resistance of these Escherichia coli was very severe by exploring its resistance to different antibiotics, particularly to three common antibiotics in a clinic which were ceftriaxone, ampicillin and trimethoprim/sulfamethoxazole, with the resistance rates of 60.60% (466/769), 57.22% (440/769), and 53.06% (408/769), respectively. Moreover, the simultaneous resistance of Escherichia coli to one or more antibiotics was determined, and 69.96% (538/769) strains have defined the resistance to both two or more antibiotics, and even 13 of Escherichia coli strains that were resistant to all nine antibiotics, indicating that the Escherichia coli from dog origins has severe antibiotic resistance in the clinic. In conclusion, this study guided the use of antibiotics and could draw attention to antibiotic resistance in veterinary clinical treatment for animals in the future.

The Antimicrobial Resistance (AMR) Rates of Enterobacterales in a Rural Hospital from the Eastern Region, Ghana: A Retrospective Study, 2022

Low- and middle-income countries bear a disproportionate burden of antimicrobial resistance and often lack adequate surveillance due to a paucity of microbiological studies. In this 2022 study, our goal was to contribute to a more precise antimicrobial treatment by understanding the prevalence of resistance in a rural environment, promoting antibiotic stewardship, and raising awareness about antimicrobial resistance. We assessed the prevalence of Multidrug-Resistant (MDR) and Extensively Drug-Resistant (XDR) Enterobacterales in clinical samples from 2905 patients being treated at Saint Dominic's Hospital, Akwatia, in the countryside of the Eastern Region, Ghana, in the year 2022. To this purpose, the samples were cultured on agar plates prepared in the laboratory using purified Oxoid™ Thermo Scientific™ agar (Thermo Fisher Scientific; Waltham, MA, USA). Cystine Lactose Electrolyte-Deficient (CLED) agar was used for urine samples, while blood agar, chocolate agar, and MacConkey agar were used for the rest of the specimens tested (HVS, blood, BFA, sputum). Antimicrobial susceptibility was determined on site using the disc diffusion method (Kirby-Bauer test). MDR bacteria accounted for more than half (53.7%) of all microorganisms tested for three or more antibiotics and 37.3% of these were XDR. Multivariate regression analysis was performed to identify risk factors associated with acquiring MDR/XDR bacteria. The results showed an increased likelihood of MDR acquisition linked to being male (OR 2.39, p < 0.001 for MDR and OR 1.95, p = 0.027 for XDR), higher age (OR 1.01, p = 0.049 for MDR), non-sputum samples (OR 0.32, p = 0.009 for MDR), and urine samples (OR 7.46, p < 0.001 for XDR). These findings emphasize the urgency for surveillance and control of antimicrobial resistance; to this end, making accurate diagnostics, studying the microorganism in question, and conducting susceptibility testing is of the utmost importance.

Evaluation and validation of laboratory procedures for the surveillance of ESBL-, AmpC-, and carbapenemase-producing Escherichia coli from fresh meat and caecal samples

Introduction

Extended-spectrum β-lactamase- (ESBL) and AmpC- β-lactamase-producing Enterobacterales are widely distributed and emerging in both human and animal reservoirs worldwide. A growing concern has emerged in Europe following the appearance of carbapenemase-producing Escherichia coli (E. coli) in the primary production of food animals. In 2013, the European Commission (EC) issued the Implementing Decision on the monitoring and reporting of antimicrobial resistance in zoonotic and commensal bacteria. The European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR) was tasked with providing two laboratory protocols for samples derived from meat and caecal content, respectively, for the isolation of ESBL- and AmpC-producing E. coli (part 1) and carbapenemase-producing (CP) E. coli (part 2). In this study, we describe the current protocols, including the preparatory work for the development.

Methods

Up to nine laboratory procedures were tested using minced meat as the matrix from beef, pork, and chicken as well as six procedures for the caecal content of cattle, pigs, and chicken. Variables included sample volume, pre-enrichment volume, pre-enrichment broth with and without antimicrobial supplementation, and incubation time/temperature. The procedures were evaluated against up to nine E. coli strains harboring different AMR genes and belonging to the three β-lactamase groups.

Results and discussion

The laboratory procedures tested revealed that the most sensitive and specific methodologies were based on a Buffered Peptone Water pre-enrichment of 225 ml to 25 g or 9 ml to 1 g for minced meat and caecal content, respectively, incubated at 37°C overnight, followed by inoculation onto MacConkey agar supplemented with 1 mg/L cefotaxime for detecting ESBL- and AmpC-producing E. coli and Chrom ID SMART (Chrom ID CARBA and OXA) for CP E. coli, incubated overnight at 37 and 44°C, respectively. We provided two isolation protocols for the EU-specific monitoring of ESBL- and AmpC- producing E. coli (part 1) and CP E. coli (part 2) from fresh meat (protocol 1) and caecal (protocol 2) samples, which have been successfully implemented by all EU Member States for the monitoring period 2014-2027 (EU 2020/1729).

Risk Factors for Community Colonization With Extended-Spectrum Cephalosporin-Resistant Enterobacterales (ESCrE) in Botswana: An Antibiotic Resistance in Communities and Hospitals (ARCH) Study

BACKGROUND

The epidemiology of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) in low- and middle-income countries (LMICs) is poorly described. Identifying risk factors for ESCrE colonization is critical to inform antibiotic resistance reduction strategies because colonization is typically a precursor to infection.

METHODS

From 15 January 2020 to 4 September 2020, we surveyed a random sample of clinic patients at 6 sites in Botswana. We also invited each enrolled participant to refer up to 3 adults and children. All participants had rectal swabs collected that were inoculated onto chromogenic media followed by confirmatory testing. Data were collected on demographics, comorbidities, antibiotic use, healthcare exposures, travel, and farm and animal contact. Participants with ESCrE colonization (cases) were compared with noncolonized participants (controls) to identify risk factors for ESCrE colonization using bivariable, stratified, and multivariable analyses.

RESULTS

A total of 2000 participants were enrolled. There were 959 (48.0%) clinic participants, 477 (23.9%) adult community participants, and 564 (28.2%) child community participants. The median (interquartile range) age was 30 (12-41) and 1463 (73%) were women. There were 555 cases and 1445 controls (ie, 27.8% of participants were ESCrE colonized). Independent risk factors (adjusted odds ratio [95% confidence interval]) for ESCrE included healthcare exposure (1.37 [1.08-1.73]), foreign travel [1.98 (1.04-3.77]), tending livestock (1.34 [1.03-1.73]), and presence of an ESCrE-colonized household member (1.57 [1.08-2.27]).

CONCLUSIONS

Our results suggest healthcare exposure may be important in driving ESCrE. The strong links to livestock exposure and household member ESCrE colonization highlight the potential role of common exposure or household transmission. These findings are critical to inform strategies to curb further emergence of ESCrE in LMICs.

Characterization of an Escherichia coli Isolate Coharboring the Virulence Gene astA and Tigecycline Resistance Gene tet(X4) from a Dead Piglet

tet(X4) is the critical resistance gene for tigecycline degradation that has been continually reported in recent years. In particular, pathogenic bacteria carrying tet(X4) are a severe threat to human health. However, information describing Escherichia coli coharboring tet(X4) with virulence genes is limited. Here, we isolated an E. coli strain coharboring tet(X4) and the heat-stable toxin gene astA from a dead piglet. The strain named 812A1-131 belongs to ST10. The genome was sequenced using the Nanopore and Illumina platforms. The virulence genes astA and tet(X4) are located on the chromosome and in the IncHI1-type plasmid p812A1-tetX4-193K, respectively. The plasmid could be conjugatively transferred to recipient E. coli J53 with high frequency. In vivo experiments showed that strain 812A1-131 is pathogenic to Galleria mellonella and could colonize the intestines of mice. In summary, pathogenic E. coli could receive a plasmid harboring the tet(X4) gene, which can increase the difficulty of treatment. The prevalence and transmission mechanisms of pathogenic bacteria coharboring the tet(X4) gene need more attention.

Phylogenetic Analysis of Escherichia coli Isolated from Australian Feedlot Cattle in Comparison to Pig Faecal and Poultry/Human Extraintestinal Isolates

The similarity of commensal Escherichia coli isolated from healthy cattle to antimicrobial-resistant bacteria causing extraintestinal infections in humans is not fully understood. In this study, we used a bioinformatics approach based on whole genome sequencing data to determine the genetic characteristics and phylogenetic relationships among faecal Escherichia coli isolates from beef cattle (n = 37) from a single feedlot in comparison to previously analysed pig faecal (n = 45), poultry extraintestinal (n = 19), and human extraintestinal E. coli isolates (n = 40) from three previous Australian studies. Most beef cattle and pig isolates belonged to E. coli phylogroups A and B1, whereas most avian and human isolates belonged to B2 and D, although a single human extraintestinal isolate belonged to phylogenetic group A and sequence type (ST) 10. The most common E. coli sequence types (STs) included ST10 for beef cattle, ST361 for pig, ST117 for poultry, and ST73 for human isolates. Extended-spectrum and AmpC β-lactamase genes were identified in seven out of thirty-seven (18.9%) beef cattle isolates. The most common plasmid replicons identified were IncFIB (AP001918), followed by IncFII, Col156, and IncX1. The results confirm that feedlot cattle isolates examined in this study represent a reduced risk to human and environmental health with regard to being a source of antimicrobial-resistant E. coli of clinical importance.

β-Lactamase Genes (blaCTX-M, blaSHV, blaTEM, blaOXA1 and blaOXA2) and Phylogenetic Groups in ESBL Producing Commensal Escherichia coli Isolated from Faecal Samples from Dairy Farm in the Municipality of Debar

β-lactamases are a diverse class of enzymes produced by bacteria that present a major cause for resistance to β-lactams. In this study we analysed 159 fecal samples from dairy cows, for the presence of presumptive ESBL, AmpC, and carbapenemase-producing E. coli. Phylotyping was done using Clermont phylo-typing method, targeting arpA, ChuA, and YjaA genes, along with the DNA fragment TspE4.C2. Convetional PCR method was used to confirm the presence of bla genes among 39 phenotypically confirmed ESBL producing E. coli. The results showed presence of CTX-M, SHV, TEM and OXA1 bla genes in 28 (71.79%), 1 (2.56%), 29 (74.35%), 2 (5.12%) of isolates, respectively Twenty (51.28%) isolates showed presence of both blaCTX-M and TEM genes. The strain that carried the blaSHV gene was found to carry blaTEM gene as well, while one of the strains that carried blaOXA1 gene was also carrying blaCTX-M and TEM gene. The ration between isolates and phylo-groups was as follows: 9 (23.07%) strains were assigned to phyllo-group D; 14 (35.89%) to phyllo-group B; 16 (41.02%) to phyllo-group A. Out of the 39 strains where bla genes were identified, 29 (74.35%) were categorized as multi drug resistant.

Portable Differential Detection of CTX-M ESBL Gene Variants, blaCTX-M-1 and blaCTX-M-15, from Escherichia coli Isolates and Animal Fecal Samples Using Loop-Primer Endonuclease Cleavage Loop-Mediated Isothermal Amplification

Cefotaximase-Munich (CTX-M) extended-spectrum beta-lactamase (ESBL) enzymes produced by Enterobacteriaceae confer resistance to clinically relevant third-generation cephalosporins. CTX-M group 1 variants, CTX-M-1 and CTX-M-15, are the leading ESBL-producing Enterobacteriaceae associated with animal and human infection, respectively, and are an increasing antimicrobial resistance (AMR) global health concern. The blaCTX-M-1 and blaCTX-M-15 genes encoding these variants have an approximate nucleotide sequence similarity of 98.7%, making effective differential diagnostic monitoring difficult. Loop-primer endonuclease cleavage loop-mediated isothermal amplification (LEC-LAMP) enables rapid real-time multiplex pathogen detection with single-base specificity and portable on-site testing. We have developed an internally controlled multiplex CTX-M-1/15 LEC-LAMP assay for the differential detection of blaCTX-M-1 and blaCTX-M-15. Assay analytical specificity was established using a panel of human, animal, and environmental Escherichia coli isolates positive for blaCTX-M-1 (n = 18), blaCTX-M-15 (n = 35), and other closely related blaCTX-Ms (n = 38) from Ireland, Germany, and Portugal, with analytical sensitivity determined using probit regression analysis. Animal fecal sample testing using the CTX-M-1/15 LEC-LAMP assay in combination with a rapid DNA extraction protocol was carried out on porcine fecal samples previously confirmed to be PCR-positive for E. coli blaCTX-M. Portable instrumentation was used to further analyze each fecal sample and demonstrate the on-site testing capabilities of the LEC-LAMP assay with the rapid DNA extraction protocol. The CTX-M-1/15 LEC-LAMP assay demonstrated complete analytical specificity for the differential detection of both variants with sensitive low-level detection of 8.5 and 9.8 copies per reaction for blaCTX-M-1 and blaCTX-M-15, respectively, and E. coli blaCTX-M-1 was identified in all blaCTX-M positive porcine fecal samples tested. IMPORTANCE CTX-M ESBL-producing E. coli is an increasing AMR public health issue with the transmission between animals and humans via zoonotic pathogens now a major area of interest. Accurate and timely identification of ESBL-expressing E. coli CTX-M variants is essential for disease monitoring, targeted antibiotic treatment and infection control. This study details the first report of portable diagnostics technology for the rapid differential detection of CTX-M AMR markers blaCTX-M-1 and blaCTX-M-15, facilitating improved identification and surveillance of these closely related variants. Further application of this portable internally controlled multiplex CTX-M-1/15 LEC-LAMP assay will provide new information on the transmission and prevalence of these CTX-M ESBL alleles. Furthermore, this transferable diagnostic technology can be applied to other new and emerging relevant AMR markers of interest providing more efficient and specific portable pathogen detection for improved epidemiological surveillance.

Prevalence of Antimicrobial Resistance and Clonal Relationship in ESBL/AmpC-Producing Proteus mirabilis Isolated from Meat Products and Community-Acquired Urinary Tract Infection (UTI-CA) in Southern Brazil

The present study aimed to evaluate the prevalence of antimicrobial resistance and clonal relationships in Proteus mirabilis isolated from chicken meat, beef, pork, and community-acquired urinary tract infections (UTI-CA). Chicken meat isolates showed the highest multidrug resistance (MDR), followed by those from pork and UTI-CA, whereas beef had relatively few MDR strains. All sources had strains that carried blaCTX-M-65, whereas blaCTX-M-2 and blaCMY-2 were only detected in chicken meat and UTI-CA isolates. This indicates that chicken meat should be considered an important risk factor for the spread of P. mirabilis carrying ESBL and AmpC. Furthermore, ESBL/AmpC producing strains were resistant to a greater number of antimicrobials and possessed more resistance genes than non-producing strains. In addition, the antimicrobial resistance genes qnrD, aac(6')-Ib-cr, sul1, sul2, fosA3, cmlA, and floR were also found. Molecular typing showed a genetic similarity between chicken meat and UTI-CA isolates, including some strains with 100% similarity, indicating that chicken can be a source of P. mirabilis causing UTI-CA. It was concluded that meat, especially chicken meat, can be an important source of dissemination of multidrug-resistant P. mirabilis in the community.

The crisis of carbapenemase-mediated carbapenem resistance across the human-animal-environmental interface in India

Carbapenems are the decision-making antimicrobials used to combat severe Gram-negative bacterial infections in humans. Carbapenem resistance poses a potential public health emergency, especially in developing countries such as India, accounting for high morbidity, mortality, and healthcare cost. Emergence and transmission of plasmid-mediated "big five" carbapenemase genes including KPC, NDM, IMP, VIM and OXA-48-type among Gram-negative bacteria is spiralling the issue. Carbapenemase-producing carbapenem-resistant organisms (CP-CRO) cause multi- or pan-drug resistance by co-harboring several antibiotic resistance determinants. In addition of human origin, animals and even environmental sites are also the reservoir of CROs. Spillage in food-chains compromises food safety and security and increases the chance of cross-border transmission of these superbugs. Metallo-β-lactamases, mainly NDM-1 producing CROs, are commonly shared between human, animal and environmental interfaces worldwide, including in India. Antimicrobial resistance (AMR) surveillance using the One Health approach has been implemented in Europe, the United-Kingdom and the United-States to mitigate the crisis. This concept is still not implemented in most developing countries, including India, where the burden of antibiotic-resistant bacteria is high. Lack of AMR surveillance in animal and environmental sectors underestimates the cumulative burden of carbapenem resistance resulting in the silent spread of these superbugs. In-depth indiscriminate AMR surveillance focusing on carbapenem resistance is urgently required to develop and deploy effective national policies for preserving the efficacy of carbapenems as last-resort antibiotics in India. Tracking and mapping of international high-risk clones are pivotal for containing the global spread of CP-CRO.

Antimicrobial Resistance and Virulence Factors Assessment in Escherichia coli Isolated from Swine in Italy from 2017 to 2021

Prudent antibiotic use in pigs is critical to ensuring animal health and preventing the development of critical resistance. We evaluated the antimicrobial resistance (AMR) pattern in commensal and enterotoxigenic Escherichia coli (ETEC) isolates obtained in 2017−2021 from pigs suffering from enteric disorders. Overall, the selected 826 E. coli isolates showed the highest level of resistance to ampicillin (95.9%), tetracycline (89.7%), cefazolin (79.3%), and trimethoprim/sulfamethoxazole (74.8%). The resistance rates of the isolates to ampicillin increased (p < 0.05), reaching 99.2% of resistant strains in 2021. Regarding isolates harboring virulence genes, ETEC F18+ were significantly more resistant to florfenicol, gentamicin, kanamycin, and trimethoprim/sulfamethoxazole than ETEC F4+ strains. E. coli lacking virulence factor genes were more resistant to amoxicillin with clavulanic acid and cefazolin, but less resistant to gentamicin (p < 0.01) than isolates harboring virulence factors. Throughout the study period, a significant number of ETEC F18+ isolates developed resistance to florfenicol, gentamicin, and kanamycin. Finally, ETEC 18+ significantly (p < 0.05) increased resistance to all the tested antibiotics. In conclusion, AMR varied for E. coli over time and showed high levels for molecules widely administered in the swine industry, emphasizing the need for continuous surveillance. The observed differences in AMR between commensal and ETEC isolates may lead to the hypothesis that plasmids carrying virulence genes are also responsible for AMR in E. coli, suggesting more research on genetic variation between pathogenic and nonpathogenic E. coli.

Emergence of plasmid-mediated colistin resistance mcr-3.5 gene in Citrobacter amalonaticus and Citrobacter sedlakii isolated from healthy individual in Thailand

Citrobacter spp. are Gram-negative bacteria commonly found in environments and intestinal tracts of humans and animals. They are generally susceptible to third-generation cephalosporins, carbapenems and colistin. However, several antibiotic resistant genes have been increasingly reported in Citrobacter spp., which leads to the postulation that Citrobacter spp. could potentially be a reservoir for spreading of antimicrobial resistant genes. In this study, we characterized two colistin-resistant Citrobacter spp. isolated from the feces of a healthy individual in Thailand. Based on MALDI-TOF and ribosomal multilocus sequence typing, both strains were identified as Citrobacter sedlakii and Citrobacter amalonaticus. Genomic analysis and S1-nuclease pulsed field gel electrophoresis/DNA hybridization revealed that Citrobacter sedlakii and Citrobacter amalonaticus harbored mcr-3.5 gene on pSY_CS01 and pSY_CA01 plasmids, respectively. Both plasmids belonged to IncFII(pCoo) replicon type, contained the same genetic context (Tn3-IS1-ΔTnAs2-mcr-3.5-dgkA-IS91) and exhibited high transferring frequencies ranging from 1.03×10-4 - 4.6×10-4 CFU/recipient cell Escherichia coli J53. Colistin-MICs of transconjugants increased ≥ 16-fold suggesting that mcr-3.5 on these plasmids can be expressed in other species. However, beside mcr, other major antimicrobial resistant determinants in multidrug resistant Enterobacterales were not found in these two isolates. These findings indicate that mcr gene continued to evolve in the absence of antibiotics selective pressure. Our results also support the hypothesis that Citrobacter could be a reservoir for spreading of antimicrobial resistant genes. To the best of our knowledge, this is the first report that discovered human-derived Citrobacter spp. that harbored mcr but no other major antimicrobial resistant determinants. Also, this is the first report that described the presence of mcr gene in C. sedlakii and mcr-3 in C. amalonaticus.

Genomic Characterization of ESBL/AmpC-Producing Escherichia coli in Stray Dogs Sheltered in Yangzhou, China

Purpose

Limited data are available on the prevalence and antimicrobial resistance of extended spectrum β-lactamase- (ESBL) and AmpC β-lactamase-producing Escherichia coli in stray dogs. We aimed to investigate the genomic characteristics of ESBL/AmpC-producing E. coli isolated from stray dogs sheltered in Yangzhou, China.

Methods

We collected 156 samples including 115 fecal swabs, 35 kennel floor swabs, two breeder hand and shoe sole swabs, and four feed samples. The isolates were tested for resistance by antimicrobial susceptibility testing and further analyzed for cefotaxime-resistant E. coli isolates by whole genome sequencing.

Results

We identified 80 cefotaxime-resistant E. coli isolates (51.3%), 59 isolates (73.8%) from feces and 21 (26.2%) from the environment. Whole-genome sequencing analysis showed that bla _CTX-M-15 (n=30) and bla _CTX-M-55 (n=29) were the most prevalent genotypes. Two isolates only carried the AmpC β-lactamase gene bla _CMY-2; one isolate had a combination of AmpC β-lactamase gene bla _DHA-1 and ESBL β-lactamase gene bla _CTX-M-14. Other important resistance genes such as bla _OXA-10, bla _TEM-1B, bla _TEM-135, bla _TEM-106, tet(A), qnrS1, qnrB4, and oqxAB were also detected. The serotype combination was highly abundant, with O10:H25 predominating (n=12). Most cefotaxime-resistant E. coli isolates belonged to phylogroup A (62.5%, n=50), followed by phylogroup B1 (26.3%, n=21). Thirty different sequence types (STs) and 27 distinct plasmid replicons were identified, among which ST2325 (n=12) and IncFII (n=38) was the most frequent ST and plasmid, respectively. ESBL/AmpC-producing isolates were divided into four major clades; clade IV was the primary lineage containing 37 isolates from feces and 13 from the environment. Three high-risk E. coli clone ST23 strains and one ST10 strain belonged to clades III and IV, respectively.

Conclusion

Our study provides a comprehensive overview of resistance profiles and genomic characteristics in ESBL/AmpC-producing E. coli and highlights the possible role of stray dogs as an antibiotic resistance gene reservoir.

Rapid On-Site Detection of Extensively Drug-Resistant Genes in Enterobacteriaceae via Enhanced Recombinase Polymerase Amplification and Lateral Flow Biosensor

The widespread emergence of transferable extensively drug-resistant (XDR) genes, including blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance, in Enterobacteriaceae poses a major threat to public health. Thus, rapid on-site detection of these XDR genes is urgently needed. We developed a cascade system with a unitary polyethylene glycol (PEG) 200-enhanced recombinase polymerase amplification (RPA) as the core, combined with a modified Chelex-100 lysis method and a horseradish peroxidase (HRP)-catalyzed lateral flow immunoassay (LFIA) biosensor, to accurately detect these genes in Enterobacteriaceae. The conventional Chelex-100 lysis method was modified to allow in situ extraction of bacterial DNA in 20 min without requiring bulky high-speed centrifuges. Using PEG 200 increased the amplification efficiency of the RPA by 13%, and the HRP-catalyzed LFIA biosensor intensified the colorimetric signal of the test line. Following optimization, the sensitivity of the cascade system was <10 copies/μL with satisfactory specificity, allowing for highly sensitive detection of these XDR genes in Enterobacteriaceae. The complete detection procedure can be completed in less than 1 h without using large-scale instruments. This assay is conducive to rapid on-site visual detection of these XDR genes in Enterobacteriaceae in practical applications, thus providing better technical support for clinical surveillance of these genes and better treatment of XDR pathogens. IMPORTANCE Carbapenem, colistin, and tigecycline are considered the last resorts for treating severe bacterial infections caused by extensively drug-resistant (XDR) pathogens. A major threat to public health is the emergence and prevalence of transferable XDR genes in Enterobacteriaceae, such as blaNDM and blaKPC for carbapenem resistance, mcr-1 for colistin resistance, and tet(X4) and tet(X6) for tigecycline resistance. Therefore, it is imperative to develop rapid on-site methods to detect these XDR genes. In this study, we constructed a cascade system for detecting these genes based on PEG 200-enhanced recombinase polymerase amplification combined with a modified Chelex-100 lysis method and HRP-catalyzed lateral flow immunoassay. The current method is capable of detecting the above-mentioned XDR genes in situ with satisfactory specificity and sensitivity, which could provide technical support for the surveillance of these genes and provide medication recommendations for the treatment of relevant clinical infections.

Integrated surveillance of extended-spectrum beta-lactamase (ESBL)-producing Salmonella and Escherichia coli from humans and animal species raised for human consumption in Canada from 2012 to 2017

Resistance to beta-lactam antimicrobials caused by extended-spectrum beta-lactamase (ESBL)-producing organisms is a global health concern. The objectives of this study were to (1) summarise the prevalence of potential ESBL-producing Escherichia coli (ESBL-EC) and Salmonella spp. (ESBL-SA) isolates from agrifood and human sources in Canada from 2012 to 2017, and (2) describe the distribution of ESBL genotypes among these isolates. All data were obtained from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). CIPARS analysed samples for the presence of ESBLs through phenotypic classification and identified beta-lactamase genes (bla_TEM, bla_SHV, bla_CTX, bla_OXA, bla_CMY-2) using polymerase chain reaction (PCR) and whole genome sequencing (WGS). The prevalence of PCR-confirmed ESBL-EC in agrifood samples ranged from 0.5% to 3% across the surveillance years, and was detected most frequently in samples from broiler chicken farms. The overall prevalence of PCR-confirmed ESBL-SA varied between 1% and 4% between 2012 and 2017, and was most frequently detected in clinical isolates from domestic cattle. The TEM-CMY2 gene combination was the most frequently detected genotype for both ESBL-EC and ESBL-SA. The data suggest that the prevalence of ESBL-EC and ESBL-SA in Canada was low (i.e. <5%), but ongoing surveillance is needed to detect emerging or changing trends.

Occurrence and potential transmission of extended-spectrum beta-lactamase-producing extraintestinal pathogenic and enteropathogenic Escherichia coli in domestic dog faeces from Minnesota

Interactions between humans and pets are increasingly valued in western countries, leading to more extensive contact between humans and their pets within households. Although the magnitude of the risk of transfer of Escherichia coli between humans and their companion animals is undefined, that such transmission occurs has been established and warrants attention. This study examined 186 fresh faecal samples from companion dogs visiting 22 municipal dog parks in the Minneapolis/Saint Paul metropolitan area, Minnesota, USA. Samples were processed to isolate 3rd-generation cephalosporin-resistant E. coli, which were further characterized using PCR-based virulence genotyping, antimicrobial susceptibility profiling and whole-genome sequencing. Of the 186 faecal samples, 29% yielded cephalosporin-resistant E. coli, and 2.2% yielded extended-spectrum beta-lactamase producers. Co-resistance to sulfonamides was typical (77.3% of isolates), and multidrug resistance (i.e. to ≥3 antimicrobial classes), including to combinations of tetracyclines, phenicols, quinolones and aminoglycosides, was substantial (18.9% of isolates). Identified beta-lactamase genes included bla_CMY-2 , bla_TEM-1B , bla_TEM-1 , bla_CTX-M-24 , bla_CTX-M-15 and bla_OXA-1 . Genome sequencing of 14 isolates identified genes typical of extraintestinal pathogenic E. coli or enteropathogenic E. coli. In three instances, closely related isolates were recovered from different dogs, within either the same park-suggesting transfer of E. coli between dogs within the park-or different parks-suggesting that dogs may be pre-disposed to carry certain E. coli types, such as those from serogroups O4, O71 and O157. This study adds to the existing evidence that companion dogs can harbour and share antimicrobial-resistant E. coli with presumed intestinal or extraintestinal pathogenic potential.

The Antibacterial Activity of Egyptian Wasp Chitosan-Based Nanoparticles against Important Antibiotic-Resistant Pathogens

The current work discusses the production and characterization of new biodegradable nanoparticles for biomedical applications based on insect chitosan. Chitosan has numerous features due to the presence of primary amine groups in repeating units, such as antibacterial and anticancer activities. When polyanion tripolyphosphate is added to chitosan, it creates nanoparticles with higher antibacterial activity than the original chitosan. In this study, the ionic gelation technique was used to make wasp chitosan nanoparticles (WCSNPs) in which TEM and FTIR were used to investigate the physicochemical properties of the nanoparticles. In addition, the antibacterial activities of chitosan nanoparticles against extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa were evaluated. The extracted wasp chitosan exhibited high solubility in acetic acid and met all standard criteria of all characterization testes for nanoparticles; the zeta potential indicated stable WCSNPs capable of binding to cellular membrane and increasing the cellular uptake. The produced WCSNPs showed growth inhibition activity against all tested strains, and the bacterial count was lower than the initial count. The inhibition percent of WCSNPs showed that the lowest concentration of WCSNPs was found to be effective against tested strains. WCSNPs’ antibacterial activity implies that they could be used as novel, highly effective antibacterial agents in a variety of biological applications requiring antibacterial characteristics.

Detection of an IMI-2 carbapenemase-producing Enterobacter asburiae at a Swedish feed mill

Occurrence of multidrug resistant Enterobacteriaceae in livestock is of concern as they can spread to humans. A potential introduction route for these bacteria to livestock could be animal feed. We therefore wanted to identify if Escherichia spp., Enterobacter spp., Klebsiella spp., or Raoutella spp. with transferable resistance to extended spectrum cephalosporins, carbapenems or colistin could be detected in the environment at feed mills in Sweden. A second aim was to compare detected isolates to previous described isolates from humans and animals in Sweden to establish relatedness which could indicate a potential transmission between sectors and feed mills as a source for antibiotic resistant bacteria. However, no isolates with transferable resistance to extended-cephalosporins or colistin could be identified, but one isolate belonging to the Enterobacter cloacae complex was shown to be carbapenem-resistant and showing carbapenemase-activity. Based on sequencing by both short-read Illumina and long-read Oxford Nanopore MinIon technologies it was shown that this isolate was an E. asburiae carrying a bla_IMI-2 gene on a 216 Kbp plasmid, designated pSB89A/IMI-2, and contained the plasmid replicons IncFII, IncFIB, and a third replicon showing highest similarity to the IncFII(Yp). In addition, the plasmid contained genes for various functions such as plasmid segregation and stability, plasmid transfer and arsenical transport, but no additional antibiotic resistance genes. This isolate and the pSB89A/IMI-2 was compared to three human clinical isolates positive for bla_IMI-2 available from the Swedish antibiotic monitoring program Swedres. It was shown that one of the human isolates carried a plasmid similar with regards to gene content to the pSB89A/IMI-2 except for the plasmid transfer system, but that the order of genes was different. The pSB89A/IMI-2 did however share the same transfer system as the bla_IMI-2 carrying plasmids from the other two human isolates. The pSB89A/IMI-2 was also compared to previously published plasmids carrying bla_IMI-2, but no identical plasmids could be identified. However, most shared part of the plasmid transfer system and DNA replication genes, and the bla_IMI-2 gene was located next the transcription regulator imiR. The IS3-family insertion element downstream of imiR in the pSB89A was also related to the IS elements in other bla_IMI-carrying plasmids.

Surveillance for multidrug resistant Escherichia coli carriage in cattle, dogs and humans reveals predominance of CMY-2, CTX-M-15 and CTX-M-9 groups of β-lactamases

Global spread of antimicrobial multidrug resistance (MDR) in human and veterinary medicine relies upon diagnostics, surveillance and stewardship to guide mitigation. Utilizing surveillance of fecal samples from our service area for detecting MDR Escherichia coli carriage in humans (2143), dogs (627), and cattle (130), we found isolates resistant to third/fourth generation cephems present in 3.7 %, 13.1 %, and 51.5 %, respectively. CMY-2, CTX-M-15-like and CTX-M9 group genes in descending order were predominant in all hosts and accounted for 83.3 % of non-wild-type gene targets. MDR carriage mirrored cephem non-susceptibility rates as published in annual antibiograms for humans and dogs; notably, no carbapenem-resistant carriage isolates were detected. Given the scale of MDR E. coli carriage in cattle (14X) and dogs (3.5X) compared to humans, bench-marking of the resistance gene pool by host species utilizing regional One Health surveillance may aid in assessing occupational and geographic risks for acquiring resistance and for monitoring of mitigation strategies.

Potential of ESBL-producing Escherichia coli selection in bovine feces after intramammary administration of first generation cephalosporins using in vitro experiments

Selection and spread of Extended Spectrum Beta-Lactamase (ESBL) -producing Enterobacteriaceae within animal production systems and potential spillover to humans is a major concern. Intramammary treatment of dairy cows with first-generation cephalosporins is a common practice and potentially selects for ESBL-producing Enterobacteriaceae, although it is unknown whether this really occurs in the bovine fecal environment. We aimed to study the potential effects of intramammary application of cephapirin (CP) and cefalonium (CL) to select for ESBL-producing Escherichia coli in the intestinal content of treated dairy cows and in manure slurry, using in vitro competition experiments with ESBL and non-ESBL E. coli isolates. No selection of ESBL-producing E. coli was observed at or below concentrations of 0.8 µg/ml and 4.0 µg/ml in bovine feces for CP and CL, respectively, and at or below 8.0 µg/ml and 4.0 µg/ml, respectively, in manure slurry. We calculated that the maximum concentration of CP and CL after intramammary treatment with commercial products will not exceed 0.29 µg/ml in feces and 0.03 µg/ml in manure slurry. Therefore, the results of this study did not find evidence supporting the selection of ESBL-producing E. coli in bovine feces or in manure slurry after intramammary use of commercial CP or CL-containing products.

Phenotypic and Genotypic Analysis of Antimicrobial Resistance in Escherichia coli Recovered from Feedlot Beef Cattle in Australia

This study investigated the antimicrobial resistance (AMR) profile of fecal Escherichia coli isolates from beef cattle (n = 150) at entry and exit from an Australian feedlot. Sample plating on MacConkey agar and Brilliance ESBL agar differentiated generic from extended-spectrum β-lactamase (ESBL)-producing E. coli, respectively. Resistance profiles were determined by minimum inhibitory concentration (MIC) testing and further analyzed by whole-genome sequencing (WGS). At entry, the prevalence of antimicrobial resistance to amoxicillin/clavulanic acid, ampicillin, streptomycin, and trimethoprim/sulfamethoxazole was very low (0.7%, each). At the exit, the resistance prevalence was moderate to tetracycline (17.8%) and low to ampicillin (5.4%), streptomycin (4.7%), and sulfisoxazole (3.9%). The most common AMR genes observed in phenotypically resistant isolates were tet(B) (43.2%), aph(3″)-Ib and aph(6)-Id (32.4%), blaTEM-1B, and sul2 (24.3%, each), which are responsible for resistance to tetracyclines, aminoglycosides, β-lactams, and sulfonamides, respectively. The ESBL-producing E. coli were recovered from one sample (0.7%) obtained at entry and six samples (4.0%) at the exit. The ESBL-producing E. coli harbored blaTEM (29.7%), blaCTX m(13.5%), and blaCMY (5.4%). The resistance phenotypes were highly correlated with resistance genotypes (r ≥ 0.85: p < 0.05). This study demonstrated that E. coli isolated from feedlot beef cattle can harbour AMR genes, but the low incidence of medically important resistance reflected the prudent antimicrobial use in the Australian industry.

Antimicrobial (ESBL) resistance genes in faecal E. coli of calves fed waste milk with antimicrobial residues

This research paper aimed to evaluate the association between feeding waste milk to calves and the occurrence of antimicrobial multi-resistance by extended spectrum β-lactamase (ESBL) enzymes through determining their production by E. coli isolates from 32 dairy farms. Among β-lactamase enzymes, ESBL provide resistance to a wide variety of β-lactam antimicrobials including penicillin and 2nd, 3rd and 4th generation cephalosporins. Feeding waste milk to calves has been observed to lead to increased antimicrobial resistance in faecal isolates of calves. In each farm included in this study, faecal samples were collected from the rectum of five healthy calves in the first month of life and pooled into a single container. Five isolates from each pool were selected and confirmed to be E. coli by amplification of the 16S rRNA gene. ESBL production was confirmed phenotypically on 148 isolates from 31 farms by use of the double-disk synergy test. Genotypic confirmation of ESBL production was performed by PCR for the genes blaCTX-M-1, -2, -8, -9 and blaCMY-2. A questionnaire was also performed and a mixed logistic regression model was used to identify risk factors for the occurrence of antimicrobial resistance. A negative binomial regression model was also used, in order to assess whether there was any association between certain farm management practices and the number of ESBL-producing E. coli isolates from each farm. Phenotypic confirmation of ESBL production was obtained on 40 E. coli isolates from 15 farms (48.4%), whereas genotypic confirmation was obtained on 55 isolates from 20 farms (64.5%). The use of three or more different intramammary antimicrobials to treat mastitis within the previous year significantly impacted the number of ESBL-producing E. coli isolates; on farms that did so, there were more isolates in which ESBL-producing E. coli was present, when compared to farms that had used less formulations within the same time span.

Antimicrobial, Multi-Drug and Colistin Resistance in Enterobacteriaceae in Healthy Pigs in the Greater Accra Region of Ghana, 2022: A Cross-Sectional Study

There is little published information on antimicrobial resistance (AMR) in animals in Ghana. We determined the prevalence and factors associated with AMR, multi-drug resistance (MDR-resistance to ≥3 antimicrobial classes) and colistin resistance in Enterobacteriaceae in healthy pigs in Accra, Ghana. Rectal swabs obtained from the pigs on 20 farms from January to March 2022, were examined for Escherichia coli, Enterobacter spp. and Klebsiella pneumoniae. AMR was determined using standard microbiological techniques and the mcr-1 gene detected through molecular analysis. Enterobacteriaceae were isolated from 197 of 200 pigs: these comprised 195 E. coli isolates, 38 Enterobacter spp. and 3 K. pneumoniae, either singly or combined. Over 60% of E. coli were resistant to tetracycline, with 27% and 34% being resistant to amoxicillin/clavulanic acid and ampicillin, respectively; 23% of E. coli and 5% of Enterobacter spp. exhibited MDR phenotypes. Phenotypic colistin resistance was found in 8% of E. coli and Enterobacter spp., with the mcr-1 gene detected in half. Our study findings should be incorporated into on-going AMR, MDR and colistin resistance surveillance programs in Ghana. We further advocate for tailored-specific education for pig farmers on animal antimicrobial use and for strengthened regulatory policy on antimicrobial usage and monitoring in the animal production industry.

Lineages, Virulence Gene Associated and Integrons among Extended Spectrum β-Lactamase (ESBL) and CMY-2 Producing Enterobacteriaceae from Bovine Mastitis, in Tunisia

Extended Spectrum Beta-Lactamase (ESBL) Enterobacteriaceae are becoming widespread enzymes in food-producing animals worldwide. Escherichia coli and Klebseilla pneumoniae are two of the most significant pathogens causing mastitis. Our study focused on the characterization of the genetic support of ESBL/pAmpC and antibiotic resistance mechanisms in cefotaxime-resistant (CTXR) and susceptible (CTXS) Enterobacteriaceae isolates, recovered from bovine mastitis in Tunisia, as well as the analyses of their clonal lineage and virulence-associated genes. The study was carried out on 17 ESBL/pAmpC E. coli and K. pneumoniae and 50 CTXS E. coli. Detection of resistance genes and clonal diversity was performed by PCR amplification and sequencing. The following β-lactamase genes were detected: blaCTX-M-15 (n = 6), blaCTX-M-15 + blaOXA-1 (2), bla CTX-M-15 + blaOXA-1 + blaTEM-1b (2), blaCTX-M-15 + blaTEM-1b (4), blaCMY-2 (3). The MLST showed the following STs: ST405 (n = 4 strains); ST58 (n = 3); ST155 (n = 3); ST471 (n = 2); and ST101 (n = 2). ST399 (n = 1) and ST617 (n = 1) were identified in p(AmpC) E. coli producer strains. The phylogroups A and B1 were the most detected ones, followed by the pathogenic phylogroup B2 that harbored the shigatoxin genes stx1/stx2, associated with the cnf, fimA, and aer virulence factors. The qnrA/qnrB, aac(6′)-Ib-cr genes and integrons class 1 with different gene cassettes were detected amongst these CTXR/S isolated strains. The presence of different genetic lineages, associated with resistance and virulence genes in pathogenic bacteria in dairy farms, may complicate antibiotic therapies and pose a potential risk to public health.

Study of the Antimicrobial Activity of the Chinese Dong Ethnic Minority Medicine, Madeng’ai

The overuse of antibiotics has contributed to the emergence of multidrug-resistant bacteria, which poses a challenging task for clinical therapy. Thus, new agents with antibiotic efficacy against multidrug-resistant infections are needed. The traditional Dong ethnic minority medicines have emerged as a new source for prodrug selection. Among them, Madeng'ai (PotentillafreynianaBornm) is widely used by the folk for anti-infection and wound healing, although the mechanisms remain unclear. In this study, the antimicrobial activities of Dong medicine Madeng'ai were evaluated both in vitro and in vivo. S. aureus, E. coli, E. faecalis, P. aeruginosa, K. pneumoniae, and A. baumannii were cultured in LB media, different concentrations of Madeng'ai powder solution were added to the LB agar plates to evaluate minimal inhibitory concentration. An animal study was performed on a mouse excisional wound model combined with bacterial solution injection in the wound area. After Madeng'ai or PBS treatment, hematoxylin and eosin analysis were used for pathological analysis of skin tissues from the infected area. Madeng'ai powder solution over 2 mg/mL concentration completely inhibited E. coli growth. At 4.0 mg/mL, Madeng'ai significantly inhibited the growth of E. faecalis, Pseudomonas aeruginosa (PAE), Klebsiella pneumoniae, and Acinetobacter baumannii. The mouse model revealed that Madeng'ai could suppress the growth of MRSA and PAE and accelerate healing of cutaneous wounds. Madeng'ai, a newly discovered Dong ethnic minority medicine possesses considerable antimicrobial activity against both human normal pathogenic bacteria and multiresistance bacteria such as Pseudomonas aeruginosa, S. aureus, and Acinetobacter baumannii. Therefore, Madeng'ai has great potential for further study and clinical application.