Antimicrobial resistance of Escherichia coli and therapeutic implications

Diarrhoeagenic Escherichia coli associated with childhood diarrhoea in Osun state, Nigeria

INTRODUCTION

Diarrhoea is a major public health concern in developing countries, usually exacerbated by poor water, sanitation and hygiene but its aetiology is under-studied, particularly away from capital cities. We identified diarrhoeagenic Escherichia coli (DEC) from stools collected in Ile-Ife and Ilesa, Osun state, Nigeria and determined their antibiotic resistance profiles.

METHODS

Stool samples from 167 children with diarrhoea and 334 controls under the age of 5 years were cultured for Escherichia coli and Salmonella. Bacterial isolates were identified biochemically and DEC were identified by PCR. Antimicrobial susceptibility testing was by modified Kirby-Bauer disc diffusion method in accordance with the CLSI guidelines. Data were analyzed using Chi-square and Fisher's exact tests.

RESULT

Diarrhoea infection is significantly high among children under 12 months (p = 0.002), caregivers without at least primary school education (p = 0.006), breastfeeding for under 6 months (p˂0.001), and caregivers who were siblings (p = 0.004). DEC was detected in 69(41.3%) cases but only 86(25.7%) controls (p < 0.001) and more commonly recovered during the wet season (p < 0.001). Enterotoxigenic E. coli (p = 0.031), enteropathogenic E. coli (p = 0.031) and Shiga-toxin-producing E. coli (p = 0.044) were recovered more commonly from cases than controls. DEC from patients with diarrhoea were commonly resistant to sulphonamides (91.3%), trimethoprim (82.6%), and ampicillin (78.3%) but were largely susceptible to quinolones and carbapenems (97.1%).

CONCLUSION

Enteropathogenic, enterotoxigenic and Shiga toxin-producing E. coli are associated with diarrhoea in our setting, and show considerable resistance to first-line antimicrobials. Risk factors for DEC diarrhoea include infancy, inadequate breastfeeding and caregivers with education below primary school.

Photodynamic and Antibacterial Assessment of Gold Nanoparticles Mediated by Gold (III) Chloride Trihydrate and Sodium Citrate under Alkaline Conditions

Sodium citrate (SC) is sensitive to violet light illumination (VLI) and acts as a weak reductant. Conversely, gold (III) chloride trihydrate (GC) often acts as an oxidant in a redox reaction. In this study, the influences of colored light on the production of gold nanoparticles (AuNPs) in a mixture of gold (III) ions and citrate via VLI and the antibacterial photodynamic inactivation (aPDI) of Escherichia coli (E. coli) are determined under alkaline conditions. The diameter of AuNPs is within the range of 3-15 nm, i.e., their mean diameter is 9 nm; when citrate is mixed with gold (III) ions under VLI, AuNPs are formed via an electron transfer process. Additionally, GC mixed with SC (GCSC) inhibits E. coli more effectively under VLI than it does under blue, green, or red light. GCSC and SC are shown to inhibit E. coli populations by 4.67 and 1.12 logs, respectively, via VLI at 10 W/m2 for 60 min under alkaline conditions. GCSC-treated E. coli has a more significant photolytic effect on anionic superoxide radical (O2•-) formation under VLI, as more O2•- is formed within E. coli if the GCSC-treated samples are subjected to VLI. The O2•- exhibits a greater effect in a solution of GCSC than that shown by SC alone under VLI treatment. Gold (III) ions in a GCSC system appear to act as an oxidant by facilitating the electron transfer from citrate under VLI and the formation of AuNPs and O2•- via GCSC photolysis under alkaline conditions. As such, the photolysis of GCSC under VLI is a useful process that can be applied to aPDI.

Prevalence of Antibiotic Resistance and Virulence Genes in Escherichia coli Carried by Migratory Birds on the Inner Mongolia Plateau of Northern China from 2018 to 2023

(1) Background: Antibiotic resistance in bacteria is an urgent global threat to public health. Migratory birds can acquire antibiotic-resistant and pathogenic bacteria from the environment or through contact with each other and spread them over long distances. The objectives of this study were to explore the relationship between migratory birds and the transmission of drug-resistant pathogenic Escherichia coli. (2) Methods: Faeces and swab samples from migratory birds were collected for isolating E. coli on the Inner Mongolia Plateau of northern China from 2018 to 2023. The resistant phenotypes and spectra of isolates were determined using a BD Phoenix 100 System. Conjugation assays were performed on extended-spectrum β-lactamase (ESBL)-producing strains, and the genomes of multidrug-resistant (MDR) and ESBL-producing isolates were sequenced and analysed. (3) Results: Overall, 179 isolates were antibiotic-resistant, with 49.7% MDR and 14.0% ESBL. Plasmids were successfully transferred from 32% of ESBL-producing strains. Genome sequencing analysis of 91 MDR E. coli strains identified 57 acquired resistance genes of 13 classes, and extraintestinal pathogenic E. coli and avian pathogenic E. coli accounted for 26.4% and 9.9%, respectively. There were 52 serotypes and 54 sequence types (STs), including ST48 (4.4%), ST69 (4.4%), ST131 (2.2%) and ST10 (2.2%). The international high-risk clonal strains ST131 and ST10 primarily carried blaCTX-M-27 and blaTEM-176. (4) Conclusions: There is a high prevalence of multidrug-resistant virulent E. coli in migratory birds on the Inner Mongolian Plateau. This indicates a risk of intercontinental transmission from migratory birds to livestock and humans.

Bacteriophage LHE83 targeting OmpA as a receptor exhibited synergism with spectinomycin against Escherichia coli

Understanding the characteristics of bacteriophages is crucial for the optimization of phage therapy. In this study, the biological and genomic characteristics of coliphage LHE83 were determined and its synergistic effects with different types of antibiotics against E. coli E82 were investigated. Phage LHE83 displayed a contractile tail morphology and had a titer of 3.02 × 109 pfu/mL at an optimal MOI of 0.01. Meanwhile, phage LHE83 exhibited good physical and chemical factors tolerance. The 1-step growth analysis revealed a latent period of approx. 10 min with a burst size of 87 pfu/infected cell. Phage LHE83 belongs to the genus Dhakavirus. Its genome consists of 170,464 bp with a 40% GC content, and a total of 268 Open Reading Frames (ORF) were predicted with no detected virulent or resistant genes. ORF 213 was predicted to encode the receptor binding protein (RBP) and confirmed by the antibody-blocking assay. Furthermore, a phage-resistant strain E. coli E82R was generated by co-culturing phage LHE83 with E. coli E82. Genomic analysis revealed that OmpA served as the receptor for phage LHE83, which was further confirmed by phage adsorption assay using E. coli BL21ΔOmpA, E. coli BL21ΔOmpA: OmpA and E. coli BL21:OmpA strains. Additionally, a synergistic effect was observed between phage LHE83 and spectinomycin against the drug-resistant strain E. coli E82. These results provide a theoretical basis for understanding the interactions between phages, antibiotics, and host bacteria, which can assist in the clinical application of phages and antibiotics against drug-resistant bacteria.

UV-Triggered Drug Release from Mesoporous Titanium Nanoparticles Loaded with Berberine Hydrochloride: Enhanced Antibacterial Activity

Mesoporous titanium nanoparticles (MTN) have always been a concern and are considered to have great potential for overcoming antibiotic-resistant bacteria. In our study, MTN modified with functionalized UV-responsive ethylene imine polymer (PEI) was synthesized. The characterization of all products was performed by different analyses, including SEM, TEM, FT-IR, TGA, XRD, XPS, and N2 adsorption-desorption isotherms. The typical antibacterial drug berberine hydrochloride (BH) was encapsulated in MTN-PEI. The process exhibited a high drug loading capacity (22.71 ± 1.12%) and encapsulation rate (46.56 ± 0.52%) due to its high specific surface area of 238.43 m2/g. Moreover, UV-controlled drug release was achieved by utilizing the photocatalytic performance of MTN. The antibacterial effect of BH@MTN-PEI was investigated, which showed that it could be controlled to release BH and achieve a corresponding antibacterial effect by UV illumination for different lengths of time, with bacterial lethality reaching 37.76% after only 8 min of irradiation. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of the nanoparticles have also been studied. The MIC of BH@MTN-PEI was confirmed as 1 mg/mL against Escherichia coli (E. coli), at which the growth of bacteria was completely inhibited during 24 h and the concentration of 5 mg/mL for BH@MTN-PEI was regarded as MBC against E. coli. Although this proof-of-concept study is far from a real-life application, it provides a possible route to the discovery and application of antimicrobial drugs.

Bacterial Efflux Pump Inhibitors Reduce Antibiotic Resistance

Bacterial resistance is a growing problem worldwide, and the number of deaths due to drug resistance is increasing every year. We must pay great attention to bacterial resistance. Otherwise, we may go back to the pre-antibiotic era and have no drugs on which to rely. Bacterial resistance is the result of several causes, with efflux mechanisms widely recognised as a significant factor in the development of resistance to a variety of chemotherapeutic and antimicrobial medications. Efflux pump inhibitors, small molecules capable of restoring the effectiveness of existing antibiotics, are considered potential solutions to antibiotic resistance and have been an active area of research in recent years. This article provides a review of the efflux mechanisms of common clinical pathogenic bacteria and their efflux pump inhibitors and describes the effects of efflux pump inhibitors on biofilm formation, bacterial virulence, the formation of bacterial persister cells, the transfer of drug resistance among bacteria, and mismatch repair. Numerous efforts have been made in the past 20 years to find novel efflux pump inhibitors which are known to increase the effectiveness of medicines against multidrug-resistant strains. Therefore, the application of efflux pump inhibitors has excellent potential to address and reduce bacterial resistance.

Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China

Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.

Application of coliphage as biocontrol agent in combination with gamma irradiation to eliminate multi-drug-resistant E. coli in minimally processed vegetables

Biofilm formation is a rising concern in the food industry. Escherichia coli (E. coli) is one of the most important food-borne pathogens that can survive in food and food-related environments and eventually produce biofilms. This study suggested that both coliphages used were successful in preventing the creation of new biofilms as well as removing existing ones. Confocal laser scanning microscopy verified these findings. According to the findings, neither coliphage survived at 37 °C, but both remained stable at 4 °C and - 20 °C for extended periods of time. The study revealed that both coliphages demonstrated a greater degree of gamma irradiation resistance when compared to E. coli. The study's results indicate that the implementation of a dual method, which incorporates gamma irradiation (1.5 kGy) and coliphage treatment, on various kinds of vegetables that were infected with E. coli, resulted in a significant reduction in bacterial count (surpassing 99.99%) following a 24-h incubation period. Combining gamma irradiation and the coliphage approach was significantly effective at lowering polysaccharide concentrations and proteins in the biofilm matrix. The results revealed that the pairing of gamma irradiation and coliphages acted in conjunction to cause disruptions in the matrix of biofilm, thereby promoting cell removal compared with either of the individual treatments. Ca+ ions strengthen the weak virion interaction with the relevant bacterial host cell receptors during the adsorption process. In conclusion, use of coliphage in combination with gamma irradiation treatment can be applied to improve fresh produce's microbial safety and enhance its storability in supermarkets.

Comparative Evaluation of Existing and Rationally Designed Novel Antimicrobial Peptides for Treatment of Skin and Soft Tissue Infections

Skin and soft tissue infections (SSTIs) and acne are among the most common skin conditions in primary care. SSTIs caused by ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) can range in severity, and treating them is becoming increasingly challenging due to the growing number of antibiotic-resistant pathogens. There is also a rise in antibiotic-resistant strains of Cutibacterium acne, which plays a role in the development of acne. Antimicrobial peptides (AMPs) are considered to be a promising solution to the challenges posed by antibiotic resistance. In this study, six new AMPs were rationally designed and compared to five existing peptides. The MIC values against E. coli, P. aeruginosa, K. pneumoniae, E. faecium, S. aureus, and C. acnes were determined, and the peptides were evaluated for cytotoxicity using Balb/c 3T3 cells and dermal fibroblasts, as well as for hemolytic activity. The interaction with bacterial membranes and the effect on TNF-α and IL-10 secretion were also evaluated for selected peptides. Of the tested peptides, RP556 showed high broad-spectrum antibacterial activity without inducing cytotoxicity or hemolysis, and it stimulated the production of IL-10 in LPS-stimulated peripheral blood mononuclear cells. Four of the novel AMPs showed pronounced specificity against C. acnes, with MIC values (0.3–0.5 μg/mL) below the concentrations that were cytotoxic or hemolytic.

Isolation, Identification and Genetic Characterization of Antibiotic Resistant Escherichia coli from Frozen Chicken Meat Obtained from Supermarkets at Dhaka City in Bangladesh

Antimicrobials have been used to improve animal welfare, food security, and food safety that promote the emergence, selection, and dissemination of antimicrobial-resistant (AMR) bacteria. In this study, 50 E. coli were isolated from frozen chicken meat samples in Dhaka city. Antibiotic sensitivity patterns were assessed through the disk diffusion method and finally screened for the presence of antimicrobial resistance genes (ARG) using the polymerase chain reaction (PCR). Among the 160 samples, the prevalence of E. coli was observed in fifty samples (31.25%). All of these isolates were found resistant to at least one antimicrobial agent, and 52.0% of the isolates were resistant against 4-7 different antimicrobials. High resistance was shown to tetracycline (66.0%), followed by resistance to erythromycin (42.0%), ampicillin and streptomycin (38.0%), and sulfonamide (28.0%). In addition, the most prevalent ARGs were tet(A) (66.0%), ereA (64.0%), tet(B) (60.0%), aadA1 and sulI (56.0%), blaCITM (48.0%) and blaSHV (40.0%). About 90.0% of isolates were multidrug resistant. This study reveals for the first time the current situation of E. coli AMR in broilers, which is helpful for the clinical control of disease as well as for the development of policies and guidelines to reduce AMR in broilers production in Bangladesh.

Plant Lectins: A Review on their Biotechnological Potential Toward Human Pathogens

The indiscriminate use of antibiotics is associated with the appearance of bacterial resistance. In light of this, plant-based products treating infections are considered potential alternatives. Lectins are a group of proteins widely distributed in nature, capable of reversibly binding carbohydrates. Lectins can bind to the surface of pathogens and cause damage to their structure, thus preventing host infection. The antimicrobial activity of plant lectins results from their interaction with carbohydrates present in the bacterial cell wall and fungal membrane. The data about lectins as modulating agents of antibiotic activity, potentiates the effect of antibiotics without triggering microbial resistance. In addition, lectins play an essential role in the defense against fungi, reducing their infectivity and pathogenicity. Little is known about the antiviral activity of plant lectins. However, their effectiveness against retroviruses and parainfluenza is reported in the literature. Some authors still consider mannose/ glucose/N-Acetylglucosamine binding lectins as potent antiviral agents against coronavirus, suggesting that these lectins may have inhibitory activity against SARS-CoV-2. Thus, it was found that plant lectins are an alternative for producing new antimicrobial drugs, but further studies still need to decipher some mechanisms of action.

Escherichia coli Isolated from Vegans, Vegetarians and Omnivores: Antibiotic Resistance, Virulence Factors, Pathogenicity Islands and Phylogenetic Classification

Pathogenic strains of Escherichia coli have acquired virulence factors, which confer an increased ability to cause a broad spectrum of enteric diseases and extraintestinal infections. The aim of this study was to analyze the antimicrobial resistance profile of and the presence of virulence-associated genes (VAGs) in E. coli fecal isolates from omnivores, vegetarians and vegans. A control group of 60 isolates from omnivores, as well as a study group with 41 isolates from vegetarians and 17 from vegans, were analyzed. Isolates from both groups showed a high rate of resistance to ampicillin, amoxicillin-clavulanic acid and nalidixic acid, and some of them were positive for the ESBL test (12% of isolates from vegetarians/vegans and 5% of isolates from omnivores). The most predominant VAGs detected in isolates from omnivores were fimH (70%), iutA (32%), fyuA (32%) and traT (32%), while among isolates from vegetarians or vegans, the most predominant were traT (62%), kpsMT k1 (28%) and iutA (22%). Most isolates from omnivores (55%) were positive for PAI I536, while most of those from vegetarians/vegans (59%) were positive for PAI IV536. Phylogenetic group A, composed of commensal non-pathogenic isolates that survive in the intestinal tract, was the most prevalent in both control and study groups. Some VAGs were found in only one of the groups, such as the pathogenicity island PAI III536, found in 12% of the isolates from omnivores, while the kpsMT III gene (15%) was detected only among isolates from vegetarians/vegans. Interestingly, this gene codes for a polysaccharide capsule found mainly in E. coli isolates causing intestinal infections, including EPEC, ETEC and EHEC. Finally, our results show that there were no advantages in vegetarian or vegan diets compared to the omnivorous diet, as in both groups we detected isolates harboring VAGs and displaying resistance to antibiotics, especially those most commonly used to treat urinary tract infections.

Prevalence and Antimicrobial Resistance of Escherichia coli in Chicken Meat and Edible Poultry Organs Collected from Retail Shops and Supermarkets of North Western Province in Sri Lanka

Escherichia coli is a commensal bacterium that lives in human and animal intestines. Shiga toxin-producing strains of E. coli STECs are responsible for most food-related E. coli infections. Pathogenic E. coli transmits to human bodies due to the consumption of contaminated, raw, or undercooked food. This study was conducted to identify the prevalence of E. coli contamination in edible poultry meat and meat organs in the North Western Province of Sri Lanka. A total of 250 samples consisting of chicken meat (n = 144) and edible organs (n = 106) were collected from retail shops (n = 181) and supermarkets (n = 69), in both Kurunegala and Puttlam districts. The prevalence of E. coli from 250 chicken meat samples was 66.80% (167/250); E. coli prevalence at retail shops (66.85%) was higher than that at supermarkets (66.67%) and was not statistically significant. E. coli prevalence in chicken meat and edible organs was 65.73% and 69.16%, respectively. Molecular confirmation for the positive samples was done through polymerase chain reaction (PCR) using previously designed primers. An antibiotic susceptibility test was performed according to CLSI using nine antibiotics: ampicillin, amoxicillin, chloramphenicol, ceftazidime, ciprofloxacin, cephalexin, erythromycin, gentamicin, and tetracycline. Most isolates were resistant to erythromycin (80.84%) and amoxicillin (76.05%), while the least resistance was observed for gentamicin (4.79%). This study indicates the potential public health risk associated with chicken sold at retail and supermarket levels in the North Western Province of Sri Lanka.

A study of the effect of reactive oxygen species induced by violet and blue light from oxytetracycline on the deactivation of Escherichia coli

Oxytetracycline (OTC), a tetracycline antibiotic, is a broad-spectrum antibacterial agent. In this investigation, liquid chromatography-mass spectrometry (LC-MS) is utilized to determine the effects of blue light (λ = 448 nm) illumination (BLIA) and violet light (λ = 403 nm) illumination (VLIA) on conformational changes in OTC at pH 7.8. The photochemical effect of OTC that is exposed to BLIA and VLIA on the deactivation of Escherichia coli (E. coli) is studied. The deactivation of E. coli has an insignificant effect on treatment with OTC alone. OTC is relatively unstable under BLIA and VLIA illumination in an alkaline solution, and OTC has been shown to inactivate E. coli by generating reactive oxygen species (ROS). Less anionic superoxide radicals (O₂^•-) are generated from OTC that is treated with BLIA than that from VLIA treatment, so OTC is more efficient in inactivating E. coli under VLIA. Inactivation of reduction rates of 0.51 and 3.65 logs in E. coli are achieved using 0.1 mM OTC under BLIA for 120 min and VLIA for 30 min, respectively, under the same illumination intensity (20 W/m²). Two photolytic products of OTC (PPOs) are produced when OTC is exposed to BLIA and VLIA, with molecular ions at m/z 447 and 431, molecular formulae C₂₁H₂₂N₂O₉ and C₂₁H₂₂N₂O₈, and masses of 446.44 and 430.44 g/mol, respectively. The results show that when exposed to VLIA, OTC exhibits enhanced inactivation of E. coli, suggesting that the photochemical treatment of OTC is a potential supplement in a hygienic process.

High Carriage of Extended-Spectrum, Beta Lactamase-Producing, and Colistin-Resistant Enterobacteriaceae in Tibetan Outpatients with Diarrhea

Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) have been detected in human-impacted habitats, especially in densely populated cities. The Qinghai–Tibet Plateau is located far from the heavily populated regions of China, and Tibetan residents have distinct dietary habits and gut microbes. Antibiotic-resistance monitoring in the Tibetan population is rare. Here, we collected stool samples from Tibetan outpatients with diarrhea. From 59 samples, 48 antibiotic-resistant Enterobacteriaceae isolates were obtained, including 19 extended-spectrum beta lactamase (ESBL)-producing isolates from 16 patients and 29 polymyxin-resistant isolates from 22 patients. Either ESBL or mcr genes were found in 17 Escherichia coli isolates, approximately 58.8% of which were multidrug-resistant, and ten incompatible plasmid types were found. The gene bla_CTX-M was a common genotype in the ESBL-producing E. coli isolates. Four E. coli isolates contained mcr-1. The same mcr-1-carrying plasmid was found in distinct E. coli isolates obtained from the same sample, thus confirming horizontal transmission of mcr-1 between bacteria. Genomic clustering of E. coli isolates obtained from Lhasa, with strains from other regions providing evidence of clone spreading. Our results reveal a strong presence of ARB and ARGs in Tibetan outpatients with diarrhea, implying that ARB and ARGs should be monitored in the Tibetan population.

Multidrug-Resistant Bacteria and Enterobacteriaceae Count in Abattoir Wastes and Its Receiving Waters in Limbe Municipality, Cameroon: Public Health Implications

The release of untreated wastes from abattoirs into the environment and nearby water bodies poses a significant threat to public health. Such litters may contain pathogens, including antibiotic-resistant bacteria. This study investigated 80 samples collected from butchering tables, slaughter slabs, meat rinsing points, and abattoir wastes receiving water from two abattoirs (A and B). Total Enterobacteriaceae count (TEC) for each sample was determined, and Escherichia coli (E. coli), Salmonella spp., Shigella spp., and Staphylococcus aureus (S. aureus) were isolated and identified. Antimicrobial susceptibility testing was done on all bacterial isolates against nine locally used antibiotics. Overall, 118 bacterial isolates, comprising E. coli (42.5%), Salmonella spp. (27.5%), Shigella spp. (37.5%), and S. aureus (40.0%), were recovered. Of the 118 bacterial isolates, 104 (88.1%) were multidrug-resistant, including 58 (55.8%) from abattoir A and 46 (44.2%) from abattoir B; however, this difference was not statistically significant (p = 0.6837). Of the 32 S. aureus isolates, 29 (90.6%) were multidrug-resistant. All S. aureus were 100% sensitive to vancomycin, kanamycin, and amikacin. Similarly, 31 (91.2%) of the 34 E. coli isolates recovered in this study were multidrug-resistant. Salmonella spp. and Shigella spp. also showed high levels of multidrug resistance corresponding to 81.8% and 86.7%, respectively. All isolates of E. coli, Salmonella, and Shigella were 100% resistant to ampicillin and 100% sensitive to ciprofloxacin. Minimum and maximum mean values for TEC were 3.62-5.83 log CFU/mL for abattoir A and 4.08-5.56 log CFU/mL for abattoir B. The highest and lowest TEC counts were from slaughter slab and upstream water, respectively, in each abattoir. Our results indicate a predominance of multidrug-resistant bacteria in abattoir wastes and their receiving waters in the study sites. Hence, we recommend the treatment of abattoir wastes before disposal and improved hygiene and sanitation practices to enhance public health.

Gut Commensal Escherichia coli, a High-Risk Reservoir of Transferable Plasmid-Mediated Antimicrobial Resistance Traits

Background

Escherichia coli (E. coli), the main human gut microorganism, is one of the evolved superbugs because of acquiring antimicrobial resistance (AMR) determinants via horizontal gene transfer (HGT).

Purpose

This study aimed to screen isolates of gut commensal E. coli from healthy adult individuals for antimicrobial susceptibility and plasmid-mediated AMR encoding genes.

Methods

Gut commensal E. coli bacteria were isolated from fecal samples that were taken from healthy adult individuals and investigated phenotypically for their antimicrobial susceptibility against diverse classes of antimicrobials using the Kirby Bauer disc method. PCR-based molecular assays were carried out to detect diverse plasmid-carried AMR encoding genes and virulence genes of different E. coli pathotypes (eaeA, stx, ipaH, est, elt, aggR and pCVD432). The examined AMR genes were β-lactam resistance encoding genes (bla_CTX-M1, bla_TEM, bla_CMY-2), tetracycline resistance encoding genes (tetA, tetB), sulfonamides resistance encoding genes (sul1, sulII), aminoglycoside resistance encoding genes (aac(3)-II, aac(6′)-Ib-cr) and quinolones resistance encoding genes (qnrA, qnrB, qnrS).

Results

PCR results revealed the absence of pathotypes genes in 56 isolates that were considered gut commensal isolates. E. coli isolates showed high resistance rates against tested antimicrobial agents belonging to both β-lactams and sulfonamides (42/56, 75%) followed by quinolones (35/56, 62.5%), tetracyclines (31/56, 55.4%), while the lowest resistance rate was to aminoglycosides (24/56, 42.9%). Antimicrobial susceptibility profiles revealed that 64.3% of isolates were multidrug-resistant (MDR). High prevalence frequencies of plasmid-carried AMR genes were detected including bla_TEM (64%) sulI (60.7%), qnrA (51.8%), aac(3)-II (37.5%), and tetA (46.4%). All isolates harbored more than one gene with the most frequent genetic profile among isolates was bla_TEM-bla_CTX-M1-like-qnrA-qnrB-tetA-sulI.

Conclusion

Results are significant in the evaluation of plasmid-carried AMR genes in the human gut commensal E. coli, suggesting a potential human health risk and the necessity of strict regulation of the use of antibiotics in Egypt. Commensal E. coli bacteria may constitute a potential reservoir of AMR genes that can be transferred to other bacterial species.

Innovative next-generation therapies in combating multi-drug-resistant and multi-virulent Escherichia coli isolates: insights from in vitro, in vivo, and molecular docking studies

Despite notable advances in vaccine and antimicrobial therapies, treatment failure has been increasingly reported worldwide. Of note, multi-drug-resistant (MDR) Escherichia coli (E. coli) strains have a considerable share in the evolution of this crisis. So, current practice guidelines are directed towards complementary and alternative therapies. Therefore, we evaluated the antibacterial and antivirulence activities of curcumin, thymol, and eugenol essential oils (EOs) as well as EOs-EOs and EOs-antibiotics interactions on MDR and multi-virulent E. coli isolates. Unfortunately, MDR E. coli could be isolated with a prevalence rate of 95.6% (86/90). Additionally, the majority of our isolates harbored both fimH (95.6%) and ompA (91.1%) genes, and half of them (45/90) were multi-virulent. Interestingly, all the tested EOs, especially curcumin, exhibited inhibitory activities against all MDR and multi-virulent E. coli isolates. The addition of thymol enhanced the antibacterial activities of curcumin and eugenol. Moreover, the activities of piperacillin/tazobactam and imipenem were increased by adding any one of the tested EOs. Regarding the antivirulence activities of the tested EOs, the cell surfaces of treated E. coli isolates under transmission electron microscope (TEM) were uneven. The cells appeared damaged and lost their appendages. Furthermore, EOs strongly reduced the transcription of ompA and fimH genes. The antibacterial and antivirulence activities of the used EOs were confirmed by in silico and mice protection assays. Hereby, we introduced the promising uses of curcumin, thymol, and eugenol oils as complementary and alternative therapies for combating MDR and multi-virulent E. coli isolates. KEY POINTS: • Our promising results confirmed that we were right for renewed interest of EOs. • The EOs, especially curcumin, can be used to prevent treatment failure. • We supposed a new pharmaceutical formulation of antibiotic powders dissolved in EOs.

Frequency of hlyA, hlyB, hlyC and hlyD genes in uropathogenic Escherichia coli isolated from UTI patients in Shiraz

Background and objectives: One of the most important causes of urinary tract infections (UTI) is Escherichia coli. The infection is mainly due to the uropathogenic strain (UPEC), which has key virulence factors, including hemolysis. In this study, we evaluated the frequency of hlyA, hlyB, hlyC and hlyD genes in UPEC strains isolated from clinical samples from Shiraz city, Iran.

Materials and methods: 130 urine samples with suspected UTI were collected from Shiraz medical centers and cultured on blood agar and EMB media. Colonies were then characterized by biochemical methods. The genomes were extracted and the presence of hemolysis genes was detected by polymerase chain reaction (PCR) using hly gene specific primers and 16S rRNA. Drug resistance was assessed by using 10 antibiotic disks in the disk diffusion method, according to CLSI criteria.

Results: Out of the 130 collected UTI samples, 100 were identified as UPECs. Within isolates, the hlyD gene had the highest frequency – 95% – and hlyC had the lowest, with 23%. The frequencies of hlyA and hlyB genes were calculated as 50% and 43%, respectively. The rates of antibiotic resistance to Azithromycin, Ampicillin, Cefotaxime, Nalidixic Acid, Tetracycline, Trimethoprim-Sulfamethoxazole, Cefepime, Aztreonam, Gentamicin, and Nitrofurantoin were 95%, 86%, 68%, 66%, 65%, 64%, 51%, 46%, 44%, 14%, respectively. 98% of these isolates belonged to the MDR group.

Conclusion: This study shows diversity of hemolysis virulence factor in UPECs and unique UPEC drug resistance that would indicate a high antibiotic use in the general population.

Antimicrobial resistance patterns among different Escherichia coli isolates in the Kingdom of Saudi Arabia

Antimicrobial resistance patterns among different Escherichia coli isolates in the Kingdom of Saudi Arabia. This study aimed to investigate the patterns of antimicrobial resistance in E. coli isolated from different samples, and to identify potential pathogenic isolates in Riyadh, Kingdom of Saudi Arabia (KSA). In total, 51 bacterial isolates were recovered from 113 samples of human urine, food (raw meat, raw chicken, raw egg surface, and fresh vegetables), water, and air. Twenty-four E. coli isolates were tested for susceptibility to 26 antibiotics. The air sample isolates were most resistant to amoxicillin, ampicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, piperacillin/tazobactam, cefalotin, cefuroxime, cefoxitin, cefixime, nitrofurantoin, and trimethoprim/sulfamethoxazol. The isolates from vegetable samples were resistant to amoxicillin, ampicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, cefalotin, cefuroxime, cefoxitin, and cefixime. By contrast, the isolates from the water samples were resistant only to amoxicillin and ampicillin. The isolates from the human urine samples were most frequently resistant to norfloxacin (80%) followed by amoxicillin and ampicillin (70%), trimethoprim/sulfamethoxazole (55%), ciprofloxacin and ofloxacin (50%), cefalotin (30%), cefuroxime, cefixime and cefotaxime (25%), ceftazidime, ceftriaxone, cefepime and aztreonam (20%), amoxicillin/clavulanic acid, piperacillin/tazobactam and gentamicin (10%), and amoxicillin/sulbactam and cefoxitin (5%). Almost all (23/25, 95.8%) (n = 23) of the isolates were multi-drug resistant (MDR) (i.e., resistant to 3 or more classes of antibiotics), and 16.7% (n = 4) of those were positive for extended spectrum β-lactamase (ESBL). Of the 4 ESBL-producers, 3 were positive for blaCTX-M-15 and blaCTX-M1group, 2 were positive for blaCMY-2, and 1 each was positive for blaCTX-M-2 group, blaSHV, and blaOXA-47. The quinolone resistance gene qnrS was detected in 25% (n = 6) of the E. coli strains isolated from urine (N = 5) and air (N = 1) samples. The considerable number of antimicrobial resistance genes detected among E. coli isolates tested here is alarming and should raise public health concern.

Bilateral orbital cellulitis in an infant: An unusual case

Bilateral orbital cellulitis is an uncommon presentation in infants, and its association with rhinosinusitis has been scantily reported in the literature. An infant underwent bilateral uncinectomy and right ethmoidal decompression for bilateral orbital cellulitis with right ethmoidal sinusitis, after a period of non-recovery with conservative treatment. Mixed infection with Escherichia coli and methicillin-sensitive Staphylococcus aureus was observed. The right eyelid swelling began to resolve; however, the left lower eyelid showed an increase in the fluctuant swelling. Transconjunctival incision and drainage of pus was done in the left eye subsequently. The patient showed marked clinical recovery and is doing well. A multidisciplinary management approach can avert potentially life-threatening sequelae of this condition.

Epidemiology of antimicrobial resistance (AMR) on California dairies: descriptive and cluster analyses of AMR phenotype of fecal commensal bacteria isolated from adult cows

Background

This study describes the occurrence of antimicrobial resistance (AMR) in commensal Escherichia coli and Enterococcus/Streptococcus spp. (ES) isolated from fecal samples of dairy cows and assesses the variation of AMR profiles across regions and seasons following the implementation of the Food and Agricultural Code (FAC) Sections 14400–14408 (formerly known as Senate Bill, SB 27) in California (CA).

Methods

The study was conducted on ten dairies distributed across CA’s three milk sheds: Northern California (NCA), Northern San Joaquin Valley (NSJV), and the Greater Southern California (GSCA). On each study dairy, individual fecal samples were collected from two cohorts of lactating dairy cows during the fall/winter 2018 and spring/summer 2019 seasons. Each cohort comprised of 12 cows per dairy. The fecal samples were collected at enrollment before calving (close-up stage) and then monthly thereafter for four consecutive time points up to 120 days in milk. A total of 2,171 E. coli and 2,158 ES isolates were tested for antimicrobial susceptibility using the broth microdilution method against a select panel of antimicrobials.

Results

The E. coli isolates showed high resistance to florfenicol (83.31% ± 0.80) and sulphadimethoxine (32.45%), while resistance to ampicillin (1.10% ± 0.21), ceftiofur (1.93% ± 0.29), danofloxacin (4.01% ± 0.42), enrofloxacin (3.31% ± 0.38), gentamicin (0.32% ± 0.12) and neomycin (1.61% ± 0.27) had low resistance proportions. The ES isolates were highly resistant to tildipirosin (50.18% ± 1.10), tilmicosin (48% ± 1.10), tiamulin (42%) and florfenicol (46% ± 1.10), but were minimally resistant to ampicillin (0.23%) and penicillin (0.20%). Multidrug resistance (MDR) (resistance to at least 1 drug in ≥3 antimicrobial classes) was observed in 14.14% of E. coli isolates and 39% of ES isolates. Escherichia coli isolates recovered during winter showed higher MDR prevalence compared to summer isolates (20.33% vs. 8.04%). A higher prevalence of MDR was observed in NSJV (17.29%) and GSCA (15.34%) compared with NCA (10.10%).

Conclusions

Our findings showed high rates of AMR to several drugs that are not labeled for use in lactating dairy cattle 20 months of age or older. Conversely, very low resistance was observed for drugs labeled for use in adult dairy cows, such as cephalosporins and penicillin. Overall, our findings identified important differences in AMR by antimicrobial class, region and season.

Mechanisms of Antibiotic Resistance in Important Gram-Positive and Gram-Negative Pathogens and Novel Antibiotic Solutions

Multidrug-resistant bacteria have on overwhelming impact on human health, as they cause over 670,000 infections and 33,000 deaths annually in the European Union alone. Of these, the vast majority of infections and deaths are caused by only a handful of species-multi-drug resistant Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Enterococcus spp., Acinetobacter spp. and Klebsiella pneumoniae. These pathogens employ a multitude of antibiotic resistance mechanisms, such as the production of antibiotic deactivating enzymes, changes in antibiotic targets, or a reduction of intracellular antibiotic concentration, which render them insusceptible to multiple antibiotics. The purpose of this review is to summarize in a clinical manner the resistance mechanisms of each of these 6 pathogens, as well as the mechanisms of recently developed antibiotics designed to overcome them. Through a basic understanding of the mechanisms of antibiotic resistance, the clinician can better comprehend and predict resistance patterns even to antibiotics not reported on the antibiogram and can subsequently select the most appropriate antibiotic for the pathogen in question.

Bioactive Bromotyrosine Derivatives from the Pacific Marine Sponge Suberea clavata (Pulitzer-Finali, 1982)

Chemical investigation of the South-Pacific marine sponge Suberea clavata led to the isolation of eight new bromotyrosine metabolites named subereins 1-8 (2-9) along with twelve known co-isolated congeners. The detailed configuration determination of the first representative major compound of this family 11-epi-fistularin-3 (11R,17S) (1) is described. Their chemical characterization was achieved by HRMS and integrated 1D and 2D NMR (nuclear magnetic resonance) spectroscopic studies and extensive comparison with literature data. For the first time, a complete assignment of the absolute configurations for stereogenic centers C-11/17 of the known members (11R,17S) 11-epi-fistularin-3 (1) and 17-deoxyfistularin-3 (10) was determined by a combination of chemical modifications, Mosher's technology, and ECD spectroscopy. Consequently, the absolute configurations of all our new isolated compounds 2-9 were determined by the combination of NMR, Mosher's method, ECD comparison, and chemical modifications. Interestingly, compounds 2-7 were obtained by chemical transformation of the major compound 11-epi-fistularin-3 (1). Evaluation for acetylcholinesterase inhibition (AChE), DNA methyltransferase 1 (DNMT1) modulating activity and antifouling activities using marine bacterial strains are also presented.

Electrochemical Genosensing of E. coli Based on Padlock Probes and Rolling Circle Amplification

Isothermal amplification techniques are emerging nowadays for the rapid and accurate detection of pathogenic bacteria in low resource settings, where many infectious diseases are endemic, and the lack of reliable power supply, trained personnel and specialized facilities pose critical barriers for timely diagnosis. This work addresses the detection of E. coli based on DNA isothermal amplification performed on magnetic particles (MPs) followed by electrochemical genosensing on disposable electrodes by square-wave voltammetry. In this approach, the bacterial DNA is preconcentrated using a target-specific magnetic probe and then amplified on the MPs by rolling circle amplification (RCA). Two different electrochemical readout methods for the RCA amplicons are tested. The first one relied on the labelling of the magnetic RCA product with a digoxigenin probe followed by the incubation with antiDIG-HRP antibody as electrochemical reporter. In the second case, the direct detection with an HRP-probe was performed. This latter strategy showed an improved analytical performance, while simultaneously avoiding the use of thermocyclers or bulky bench top equipment.

Monitoring the Bacterial Response to Antibiotic and Time Growth Using Near-infrared Spectroscopy Combined with Machine Learning

Assessing and monitoring the growth and response of bacteria to antibiotics is of crucial importance in research laboratories, as well as in food, environment, medical, and pharmaceutical industrial applications. In this study, Escherichia coli was chosen as the model microorganism to evaluate its response (e.g., growth) to a commercial antibiotic-tetracycline. Thus, the objective of this work was to explore the ability of NIR data combined with machine learning tools (e.g., partial least squares discriminant analysis) to monitor the response and growth of Escherichia coli cultured with different concentrations of tetracycline (ranging from 0 to 50 μg/mL). This study demonstrated a novel method capable of analyzing samples of a complex matrix, while still contained in a 96-well plate. This work will pave the way as a new machine learning method to detect resistance changes in microorganisms without the laborious and, in some cases, time-consuming protocols currently in use in research and by the industry.

Into the sea: Antimicrobial resistance determinants in the microbiota of little penguins (Eudyptula minor)

Terrestrial and aquatic birds have been proposed as sentinels for the spread of antimicrobial resistant bacteria, but few species have been investigated specifically in the context of AMR in the marine ecosystem. This study contrasts the occurrence of class 1 integrons and associated antimicrobial resistance genes in wild and captive little penguins (Eudyptula minor), an Australian seabird with local population declines. PCR screening of faecal samples (n = 448) revealed a significant difference in the prevalence of class 1 integrons in wild and captive groups, 3.2% and 44.7% respectively, with genes that confer resistance to streptomycin, spectinomycin, trimethoprim and multidrug efflux pumps detected. Class 1 integrons were not detected in two clinically relevant bacterial species, Klebsiella pneumoniae or Escherichia coli, isolated from penguin faeces. The presence of class 1 integrons in the little penguin supports the use of marine birds as sentinels of AMR in marine environments.

Integron mediated antimicrobial resistance in diarrheagenic Escherichia coli in children: in vitro and in silico analysis

The exchange of genes between bacterial chromosome and plasmid(s) and their integration into integrons are mainly responsible for acquisition and dissemination of antibiotic resistance. We investigated the role of integrons and their underlying molecular mechanisms leading to development of adaptability in E. coli and eventual resistance to antimicrobials. Escherichia coli isolates (n = 120); including 40 diarrheagenic isolates, an even number of isolates from cases other than diarrhea, and equal number of isolates from healthy children recovered from fresh stool samples were used for identification of integron genes and gene cassettes. The association of integrons with antibiotic resistance was assayed before phylogenetic analysis. DNA sequence analysis revealed class 1 and 2 integrons in 55.83% and 21.66% isolates, respectively. The integron presence was found significantly associated with the probability of antibiotic resistance in E. coli; the association being highest with class 1 integron. Modelling and molecular docking along with molecular dynamics simulation analyses found ceftriaxone and amoxicillin as potential inhibitors of dihydrofolate reductase (DHFR). The class 1 integrons of these pathogenic isolates can serve as prospective therapeutic targets using specific silencing strategies and combinational antimicrobial therapy. The findings may be useful for the development of a potent and versatile drug for DHFR inhibition.

Occurrence of Potentially Pathogenic Bacteria in Epilithic Biofilm Forming Bacteria isolated from Porter Brook River-stones, Sheffield, UK

Biofilms in aquatic ecosystems develop on wet benthic surfaces and are primarily comprised of various allochthonous microorganisms, including bacteria embedded within a self-produced matrix of extracellular polymeric substances (EPS). In such environment, where there is a continuous flow of water, attachment of microbes to surfaces prevents cells being washed out of a suitable habitat with the added benefits of the water flow and the surface itself providing nutrients for growth of attached cells. When watercourses are contaminated with pathogenic bacteria, these can become incorporated into biofilms. This study aimed to isolate and identify the bacterial species within biofilms retrieved from river-stones found in the Porter Brook, Sheffield based on morphological, biochemical characteristics and molecular characteristics, such as 16S rDNA sequence phylogeny analysis. Twenty-two bacterial species were identified. Among these were 10 gram-negative pathogenic bacteria, establishing that potential human pathogens were present within the biofilms. Klebsiella pneumoniae MBB9 isolate showed the greatest ability to form a biofilm using a microtiter plate-based crystal violet assay. Biofilm by K. pneumoniae MBB9 formed rapidly (within 6 h) under static conditions at 37 °C and then increased up to 24 h of incubation before decreasing with further incubation (48 h), whereas the applied shear forces (horizontal orbital shaker; diameter of 25 mm at 150 rpm) had no effect on K. pneumoniae MBB9 biofilm formation.

The Frequency and Antimicrobial Resistance of blaTEM and blaCTX-M Genes in Escherichia coli Isolated From Patients With a Urinary Tract Infection

Introduction: The production of β-lactamase in bacteria, especially in Escherichia coli as a prevalent opportunistic bacterium, has caused many problems in patient treatment. β-lactamases are encoded by extended-spectrum β-lactamase (ESBL) genes such as blaTEM and blaCTX-M. We aimed to assess the prevalence and antibiotic sensitivity of β-lactamases encoded by blaCTX-M and blaTEM in E. coli isolated from patients suffering from urinary tract infections (UTIs). Methods: Escherichia coli strains were isolated from the patients’ urine culture presented to medical diagnostic laboratories in Zabol, Iran. The agar disc-diffusion test was performed on Müller-Hinton agar to investigate the antibiotic resistance of these isolates using eight antimicrobial paper discs including gentamicin, tetracycline, co-trimoxazole, norfloxacin, cefuroxime, ampicillin, neomycin, and amoxicillin. A conventional polymerase chain reaction (PCR) was used to detect blaCTX-M and blaTEM. Results: The frequencies of resistance to cefuroxime, norfloxacin, co-trimoxazole, neomycin, amoxicillin, tetracycline, gentamicin, and ampicillin were found to be 45 (90%), 15 (30%), 33 (66%), 33 (66%), 44 (88%), 34 (68%), 4 (8%), and 50 (100%), respectively. Moreover, the prevalence of blaCTX-M was 25 (50%) while that of blaTEM was 16 (32%). Conclusion: Based on the results, gentamicin and norfloxacin can be recommended as effective antibacterials for treating UTI caused by E. coli in the study population. Moreover, the frequency of resistant genes including blaCTX-M and blaTEM was high in the isolated E. coli. Effective control systems including appropriate treatments for ESBL-producing strains are therefore required for humans and food animals.

Prevalence and antibiotic susceptibility pattern of Escherichia coli O157:H7 isolated from harvested fish at Lake Hayq and Tekeze dam, Northern Ethiopia

Fisheries play a significant role in food security, livelihood, and source of income in developing countries. Although fish are a healthy source of protein, they can also spread diseases caused by pathogenic micro-organisms they may harbor. Epidemiology of foodborne pathogens is not well studied in Ethiopia. To address this issue to some extent, a cross-sectional study with a simple random sampling approach was conducted from October 2017 to May 2018 with the objectives of to isolate and estimate the prevalence of Escherichia coli O157: H7 in fish, and to evaluate the antimicrobial susceptibility pattern of the isolates in selected Lakes of Northern Ethiopia. All the microbial identification and isolation procedures were conducted based on ISO 6887-3:2017 recommendations. Antimicrobial susceptibility test was also performed following the standard procedure of Kirby-Bauer disk diffusion protocol. From the total 410 fish samples examined, six (1.46%) of them were found contaminated with Shiga toxin-producing Escherichia coli O157: H7 strain. The organism was isolated from landing sites (5/293) and local retail markets (1/75). Besides, Escherichia coli O157: H7 was isolated from filleted fish (5/214) and whole fish (1/125); however, it was not isolated from samples of ready to eat fish and working environments of restaurants. The antibiotic susceptibility test revealed that the isolates were resistant to Ampicillin and Streptomycin disks. However, Ciprofloxacin, Gentamicin and Nalidixic acid were found effective in inhibiting the growth of all of the isolates. Since pathogenic Escherichia coli strain was detected from fish, raw and undercooked fish consumption in Ethiopia may result in contracting infections. The occurrence of such pathogenic organisms in fish indicates the need for intervention by stakeholders. Supports like freezers, generators, the establishment of fish processing plants and on job training about proper fish handling practices may play a tremendous role in decreasing the level of contamination of fish in Ethiopia.

Genomic Analysis of Multidrug-Resistant Escherichia coli from Surface Water in Northeast Georgia, United States: Presence of an ST131 Epidemic Strain Containing blaCTX-M-15 on a Phage-Like Plasmid

Surface water is suspected of playing a role in the development and spread of antimicrobial-resistant (AR) bacteria, including human pathogens. In our previous study, 496 Escherichia coli isolates were recovered from water samples collected over a 2-year period from the Upper Oconee watershed, Athens, GA, United States, of which 34 (6.9%) were AR isolates. Of these, six isolates were selected based on their multidrug resistance (MDR) phenotypes, the presence of mobile genetic elements, and their pathogenic potential and were subjected to whole-genome sequence (WGS) analysis to enhance our understanding of environmental MDR E. coli isolates. This study is the first report on genomic characterization of MDR E. coli from environmental water in the United States through a WGS approach. The sequences of the six MDR E. coli isolates were analyzed and the locations of their AR genes were identified. One of the E. coli isolates was an ST131 epidemic strain, which also produced an extended-spectrum β-lactamase encoded by the bla_CTX-M-15 gene, carried on a plasmid that is a member of a very rarely reported family of phage-like plasmids. This is the first time an in-depth sequence analysis has been done on a bla_CTX-M-15- containing phage-like plasmid, the presence of which suggests a new emerging mechanism of AR gene transmission.

Genetic Characterization of Antimicrobial-Resistant Escherichia coli Isolated from a Mixed-Use Watershed in Northeast Georgia, USA

In order to determine the role of surface water in the development and spread of antibiotic-resistant (AR) bacteria, water samples were collected quarterly from 2015 to 2016 from a mixed-use watershed in Georgia. In our previous study, 496 Escherichia coli were isolated from surface water, out of which, 34 isolates were resistant to antimicrobials. For the current study, these 34 AR E. coli were characterized using pulsed-field gel electrophoresis, AR gene detection, plasmid replicon typing, class I integron detection, and multi-locus sequence typing. Genes were identified as conferring resistance to azithromycin (mph(A)); β-lactams (bla_CMY, bla_CTX, bla_TEM); chloramphenicol (floR); streptomycin (strA, strB); sulfisoxazole (sul1, sul2); tetracycline (tetA, tetB, tetC); and trimethoprim/sulfamethoxazole (dhfr5, dhfr12). Five ciprofloxacin- and/or nalidixic-resistant isolates contained point mutations in gyrA and/or parC. Most of the isolates (n = 28) carried plasmids and three were positive for class I integrons. Twenty-nine sequence types (ST) were detected, including three epidemic urinary-tract-infection-associated ST131 isolates. One of the ST131 E. coli isolates exhibited an extended-spectrum β-lactamase (ESBL) phenotype and carried bla_CTX-M-15 and bla_TEM-1. To our knowledge, this is the first study on the emergence of an ESBL-producing E. coli ST131 from environmental water in the USA, which poses a potential risk to human health through the recreational, agricultural, or municipal use of this natural resource. This study identified E. coli with AR mechanisms to commonly used antimicrobials and carrying mobile genetic elements, which could transfer AR genes to other bacteria in the aquatic environment.

Changing paradigm of antibiotic resistance amongst Escherichia coli isolates in Indian pediatric population

Antimicrobial resistance happens when microorganisms mutates in manners that render the drugs like antibacterial, antiviral, antiparasitic and antifungal, ineffective. The normal mutation process is encouraged by the improper use of antibiotics. Mutations leading to quinolone resistance occur in a highly conserved region of the quinolone resistance-determining region (QRDR) of DNA gyrAse and topoisomerase IV gene. We analyzed antibiotic resistant genes and single nucleotide polymorphism (SNP) in gyrA and parC genes in QRDR in 120 E. coli isolates (both diarrheagenic and non-pathogenic) recovered from fresh stool samples collected from children aged less than 5 years from Delhi, India. Antibiotic susceptibility testing was performed according to standard clinical and laboratory standards institute (CLSI) guidelines. Phylogenetic analysis showed the clonal diversity and phylogenetic relationships among the E. coli isolates. The SNP analysis depicted mutations in gyrA and parC genes in QRDR. The sul1 gene, responsible for sulfonamide resistance, was present in almost half (47.5%) of the isolates across the diseased and healthy samples. The presence of antibiotic resistance genes in E. coli isolates from healthy children indicate the development, dissemination and carriage of antibiotic resistance in their gut. Our observations suggest the implementation of active surveillance and stewardship programs to promote appropriate antibiotic use and minimizing further danger.

Identification and antimicrobial susceptibility profile of Escherichia coli isolated from backyard chicken in and around ambo, Central Ethiopia

Background

Escherichia coli is bacteria that exist as commensal in the intestine of animals and humans, but pathogenic strains cause disease in chickens. The development of antimicrobial resistance in E. coli is one of major concern worldwide. A cross-sectional study was conducted from November, 2015 to April, 2016 in and around Ambo town on backyard chicken with the objectives of isolating E. coli from selected visceral organs, assessment of potential risk factor and determination of antimicrobial resistance pattern of the isolates.

Results

The overall isolation rate of E. coli was 11.5% (80/694) [95% CI: 9.64–14.61] and 32.5% (62/191) [95% CI: 25.39–39.09] at organ and chicken level, respectively. E. coli isolation rate was 15.2% (29/191), 13.6% (27/191), 6.3% (12/191) and 10.7% (13/121) from spleen, liver, kidney and ovary samples, respectively. The multivariable logistic regression analysis revealed higher probability of E. coli isolation from adult (adjusted Odds ratio [aOR] =2.5, P = 0.013) than younger chickens, from clinically sick chickens (aOR = 3.0, P = 0.003) than apparently healthy. E. coli isolates were 100% susceptible to ciprofloxacin, norfloxacin and sulfamethoxazole-trimethoprim followed by 89–63.4% susceptibility to gentamicin, streptomycin, ceftazidime, nalidxic acid, nitrofurantoin, kanamycin, amikacin and chloramphenicol. Whereas, 100% resistance was observed against cloxacilin, cefotaxime and amoxicillin, whereas 92.7 and 46.3% were resistant to cefuroxime, and tetracycline, respectively. Multidrug resistant (MDR) was observed in 78.1% (64/82) of the isolates which exhibited 5 different MDR patterns to 7 antimicrobial classes.

Conclusions

Higher isolation rate of E. coli was observed from visceral organs of chickens. Age and health status were predictors of E. coli isolation. Remarkable numbers of the isolates are resistant to different antimicrobials and multidrug resistant E coli isolates are widespread in the area.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-1830-z) contains supplementary material, which is available to authorized users.

Changes in Cellular Elasticities and Conformational Properties of Bacterial Surface Biopolymers of Multidrug-Resistant Escherichia coli (MDR-E. coli) Strains in Response to Ampicillin

The roles of the thicknesses and grafting densities of the surface biopolymers of four multi-drug resistant (MDR) Escherichia coli bacterial strains that varied in their biofilm formation in controlling cellular elasticities after exposure to ampicillin were investigated using atomic force microscopy. Exposure to ampicillin was carried out at minimum inhibitory concentrations for different duration times. Our results indicated that the four strains resisted ampicillin through variable mechanisms. Strain A5 did not change its cellular properties upon exposure to ampicillin and as such resisted ampicillin through dormancy. Strain H5 increased its biopolymer brush thickness, adhesion and biofilm formation and kept its roughness, surface area and cell elasticity unchanged upon exposure to ampicillin. As such, this strain likely limits the diffusion of ampicillin by forming strong biofilms. At three hours’ exposure to ampicillin, strains D4 and A9 increased their roughness, surface areas, biofilm formation, and brush thicknesses and decreased their elasticities. Therefore, at short exposure times to ampicillin, these strains resisted ampicillin through forming strong biofilms that impede ampicillin diffusion. At eight hours’ exposure to ampicillin, strains D4 and A9 collapsed their biopolymers, increased their apparent grafting densities and increased their cellular elasticities. Therefore, at long exposure times to ampicillin, cells utilized their higher rigidity to reduce the diffusion of ampicillin into the cells. The findings of this study clearly point to the potential of using the nanoscale characterization of MDR bacterial properties as a means to monitor cell modifications that enhance “phenotypic antibiotic resistance”.

Effects of 462 nm Light-Emitting Diode on the Inactivation of Escherichia coli and a Multidrug-Resistant by Tetracycline Photoreaction

The adaptability of bacterial resistance to antibiotics contributes to its high efficiency during evolution. Tetracycline (TC) is a broad-spectrum antimicrobial agent. Chromatographic analyses and mass spectrometry were used to study the effects of the light illumination of a 462 nm light-emitting diode (LED) on the conformational changes of TC in a phosphate buffer solution (PBS, pH 7.8). Especially, the inactivation of superoxide anion radicals (O₂•⁻) and Escherichia coli (E. coli), including that of a multidrug-resistant E. coli (MDR E. coli), were investigated during the photolysis of TC. A photolysis product of TC (PPT) was generated in an alkaline solution after the illumination of a blue light. The mass spectra of PPT had characteristic ion signals in m/z 459, 445, and 249.1 Da. The PPT has the molecular formula of C₂₂H₂₂N₂O₉, and the exact mass is 458.44 g/mol. The inactivation of MDR E. coli is not significant with TC treatment. The drug-resistant ability of MDR E. coli has a less significant effect on PPT, and the changed conformation of TC retained the inactivation ability of MDR E. coli upon blue light photoreaction. With TC, illuminated by a blue light in a pH 7.8 PBS, O₂•⁻ was generated from TC photolysis, which enhanced the inactivation of E. coli and MDR E. coli. A 96.6% inactivation rate of MDR E. coli was reached with TC under 2.0 mW/cm² blue light illumination at 25 ± 3 °C for 120 min, and the effects of the TC-treated photoreaction on MDR E. coli viability repressed the growth of MDR E. coli by 4 to 5 logs. The present study of the blue light photoreaction of TC offers a new approach to the inactivation of MDR E. coli.

Translating Pharmacokinetic and Pharmacodynamic Data into Practice

Pharmacokinetic (PK) and pharmacodynamic (PD) publications provide scientific evidence for incorporation in evidence-based veterinary medicine, aiding the clinician in selecting doses and dosing intervals. PK and PD studies have reported wide variations within exotic species, due to physiologic differences in absorption, distribution, metabolism, and excretion. PK studies offer species-specific data to help tailor doses and dosing routes to individual patients, minimize toxicity, and provide a cornerstone for PD studies to determine drug efficacy. This article reviews the application of PK parameters and the challenges in determining the PD activity of drugs, with a particular emphasis on exotic species.

Molecular diagnosis of antimicrobial resistance in Escherichia coli

INTRODUCTION

Antimicrobial resistance is a growing global public health threat. The complexities of antimicrobial resistance in gram-negative bacteria such as Escherichia coli pose significant diagnostic and therapeutic challenges. Molecular diagnostics are emerging in this field. Areas covered: The authors review the clinical importance of pathogenic E. coli and discuss the mechanisms of resistance to common antibiotics used to treat these infections. We review the literature on antimicrobial susceptibility testing and discuss the current state of phenotypic as well as molecular methodologies. Clinical vignettes are presented to highlight how molecular diagnostics may be used for patient care. Expert commentary: The future use of molecular diagnostics for detection of antimicrobial resistance will be tailored to the context, whether hospital epidemiology, infection control, antibiotic stewardship, or clinical care. Further clinical research is needed to understand how to best apply molecular diagnostics to these settings.

Prevalence and Molecular Characterization of Antimicrobial Resistance in Escherichia coli Isolated from Raw Milk and Raw Milk Cheese in Egypt

The goal of this study was to examine antimicrobial resistance and characterize the implicated genes in 222 isolates of Escherichia coli from 187 samples of raw milk and the two most popular cheeses in Egypt. E. coli isolates were tested for susceptibility to 12 antimicrobials by a disk diffusion method. Among the 222 E. coli isolates, 66 (29.7%) were resistant to one or more antimicrobials, and half of these resistant isolates showed a multidrug resistance phenotype (resistance to at least three different drug classes). The resistance traits were observed to tetracycline (27.5%), ampicillin (18.9%), streptomycin (18.5%), sulfamethoxazole-trimethoprim (11.3%), cefotaxime (4.5%), kanamycin (4.1%), ceftazidime (3.6%), chloramphenicol (2.3%), nalidixic acid (1.8%), and ciprofloxacin (1.4%). No resistance to fosfomycin and imipenem was observed. Tetracycline resistance genes tetA, tetB, and tetD were detected in 53 isolates, 9 isolates, and 1 isolate, respectively, but tetC was not detected. Aminoglycoside resistance genes strA, strB, aadA, and aphA1 were detected in 41, 41, 11, and 9 isolates, respectively. Sulfonamide resistance genes sul1, sul2, and sul3 were detected in 7, 25, and 3 isolates, respectively. Of 42 ampicillin-resistant isolates, bla_TEM, bla_CTX-M, and bla_SHV were detected in 40, 9, and 3 isolates, respectively, and 10 (23.8%) ampicillin-resistant isolates were found to produce extended-spectrum β-lactamase. Each bla gene of extended-spectrum β-lactamase-producing E. coli was further subtyped to be bla_CTX-M-15, bla_CTX-M-104, bla_TEM-1, and bla_SHV-12. The class 1 integron was also detected in 28 resistant isolates, and three different patterns were obtained by PCR-restriction fragment length polymorphism. Sequencing analysis of the variable region revealed that four isolates had dfrA12/orfF/aadA2, two had aadA22, and one had dfrA1/aadA1. These data suggest that antimicrobial-resistant E. coli are widely distributed in the milk production and processing environment in Egypt and may play a role in dissemination of antimicrobial resistance to other pathogenic and commensal bacteria.

Synergistic Antimicrobial Interaction between Honey and Phage against Escherichia coli Biofilms

Chronic wounds afford a hostile environment of damaged tissues that allow bacterial proliferation and further wound colonization. Escherichia coli is among the most common colonizers of infected wounds and it is a prolific biofilm former. Living in biofilm communities, cells are protected, become more difficult to control and eradicate, and less susceptible to antibiotic therapy. This work presents insights into the proceedings triggering E. coli biofilm control with phage, honey, and their combination, achieved through standard antimicrobial activity assays, zeta potential and flow cytometry studies and further visual insights sought by scanning electron microscopy and transmission electron microscopy. Two Portuguese honeys (PF2 and U3) with different floral origin and an E. coli-specific phage (EC3a), possessing depolymerase activity, were tested against 24- and 48-h-old biofilms. Synergic and additive effects were perceived in some phage-honey experiments. Combined therapy prompted similar phenomena in biofilm cells, visualized by electron microscopy, as the individual treatments. Honey caused minor membrane perturbations to complete collapse and consequent discharge of cytoplasmic content, and phage completely destroyed cells leaving only vesicle-like structures and debris. Our experiments show that the addition of phage to low honey concentrations is advantageous, and that even fourfold diluted honey combined with phage, presents no loss of antibacterial activity toward E. coli. Portuguese honeys possess excellent antibiofilm activity and may be potential alternative therapeutic agents in biofilm-related wound infection. Furthermore, to our knowledge this is the first study that assessed the impacts of phage-honey combinations in bacterial cells. The synergistic effect obtained was shown to be promising, since the antiviral effect of honey limits the emergence of phage resistant phenotypes.

Proteomics for Drug Resistance on the Food Chain? Multidrug-Resistant Escherichia coli Proteomes from Slaughtered Pigs

Understanding global drug resistance demands an integrated vision, focusing on both human and veterinary medicine. Omics technologies offer new vistas to decipher mechanisms of drug resistance in the food chain. For example, Escherichia coli resistance to major antibiotics is increasing whereas multidrug resistance (MDR) strains are now commonly found in humans and animals. Little is known about the structural and metabolic changes in the cell that trigger resistance to antimicrobial agents. Proteomics is an emerging field that is used to advance our knowledge in global health and drug resistance in the food chain. In the present proteomic analysis, we offer an overview of the global protein expression of different MDR E. coli strains from fecal samples of pigs slaughtered for human consumption. A full proteomic survey of the drug-resistant strains SU60, SU62, SU76, and SU23, under normal growth conditions, was made by two-dimensional electrophoresis, identifying proteins by MALDI-TOF/MS. The proteomes of these four E. coli strains with different genetic profiles were compared in detail. Identical transport, stress response, or metabolic proteins were discovered in the four strains. Several of the identified proteins are essential in bacterial pathogenesis (GAPDH, LuxS, FKBPs), development of bacterial resistance (Omp's, TolC, GroEL, ClpB, or SOD), and potential antibacterial targets (FBPA, FabB, ACC's, or Fab1). Effective therapies against resistant bacteria are crucial and, to accomplish this, a comprehensive understanding of putative resistance mechanisms is essential. Moving forward, we suggest that multi-omics research will further improve our knowledge about bacterial growth and virulence on the food chain, especially under antibiotic stress.

Antibiotic resistance patterns of bacteria isolated from indwelling Foley catheters following tube cystostomy in goats with obstructive urolithiasis

Tube cystostomy is a surgical method used for managing obstructive urolithiasis and involves placement of a Foley catheter into the urinary bladder. We identified and evaluated the antibiotic resistance patterns of bacteria isolated from indwelling Foley catheters following tube cystostomy in goats with obstructive urolithiasis. Urine samples collected over a 10-y period from catheter tips at the time of removal were submitted for bacteriologic culture and antibiotic susceptibility testing. Resistance patterns to antibiotics, trends in the resistance patterns over the study period, and the probability of a bacterial isolate being resistant as a function of the identity of the isolate and antibiotic tested were determined. A total of 103 urine samples from 103 male goats with obstructive urolithiasis managed surgically with tube cystostomy were included in the study. Aerococcus (36.9%) and Enterococcus (30.1%) were isolated most frequently. The susceptibility patterns of all bacteria isolated did not change over the study period ( p > 0.05). Proportions of isolates resistant to 1, 2, and ≥3 antibiotics were 36.9%, 18.5%, and 23.3%, respectively. Thus, 41.8% of bacterial isolates were resistant to 2 or more antibiotics tested. The probability of Aerococcus spp., Escherichia coli, and Pseudomonas aeruginosa isolates to be resistant to ampicillin, ceftiofur, erythromycin, penicillin, or tetracycline ranged from 0.59 to 0.76.

Occurrence of multidrug resistant Escherichia coli in groundwater of Brij region (Uttar Pradesh) and its public health implications

AIM

The study evaluates the microbial as well as physicochemical pollution of groundwater of Brij region of Uttar Pradesh, a major tourist destination in the country along with estimating the drug resistance evident in the isolated Escherichia coli.

MATERIALS AND METHODS

A total of 60 samples of groundwater were collected from six different sites and assessed for physicochemical (pH, color, taste, turbidity, total dissolved solids [TDS], total hardness [TH], chlorides, fluorides, nitrates, and iron) and microbiological parameters (standard plate count [SPC], most probable number test [MPN], E. coli).

RESULTS

A majority of the samples were found to be out of the range for most of the parameters except iron. Particularly, high values of TDS (up to 9000 ppm), TH (1500 mg/L), chlorides (3250 mg/L), fluorides (2.5 mg/L), and nitrates (100.2 mg/L) were observed at most of the sites in the region highlighting the fact that groundwater of the area is not potable. Samples were turbid and salty to taste. High SPC values, up to 3500 colony-forming unit/ml and coliforms beyond BIS range were found in 40% samples suggesting gross microbial contamination. Only 2 sites (G3 and G5) had low MPN values. Overall 16 (26.67%) E. coli were isolated with 3 (18.75%) producing red colonies on conge red agar, hence supposed to be pathogenic. No E. coli O157:H7 was isolated. High antimicrobial resistance was observed against amoxicillin and erythromycin, whereas E. coli isolates were sensitive toward cefotaxime-clavulanic acid and imipenem. 12 isolates (75%) were multidrug resistant (MDR) with MDR index >20%, and 2 isolates (12.5%) were found to be extended spectrum beta-lactamases positive.

CONCLUSION

Groundwater is considered to be a safe option for potable water but it is obvious from the findings of this study that considerable physicochemical and microbial contamination is there in groundwater samples of Brij region. The occurrence of MDR E. coli in these waters is a matter of great public health concern.

Trends in Antibiotic Resistance in Urologic Practice

CONTEXT

The significant global upsurge in antimicrobial resistance, particularly among Enterobacteriaceae, represents a serious threat to health care systems. The implications for urologic practice are of particular concern.

OBJECTIVE

To review trends in antibiotic resistance in urologic practice.

EVIDENCE ACQUISITION

We report current European trends of resistance in Gram-negative uropathogens.

EVIDENCE SYNTHESIS

In addition to β-lactam resistance, Gram-negative pathogens are often resistant to multiple drug classes, including aminoglycosides, fluoroquinolones, and carbapenems, commonly used to treat urologic infections. Interest is renewed in old antibiotics, and several new antibiotics are in the pipeline to meet the challenge of treating these infections. In this review, we summarise emerging trends in antimicrobial resistance and its impact on urologic practice. We also review current guidelines on the treatment and prevention of urologic infections with these organisms, and some key antibiotics in the era of resistance.

CONCLUSIONS

Increasing antimicrobial resistance represents a challenge to urologic practice for both treatment and prophylaxis. Antibiotic choice should be determined according to risk factors for multidrug resistance. Good knowledge of the local microbial prevalence and resistance profile is required to guide antimicrobial therapy.

PATIENT SUMMARY

Antimicrobial resistance represents a challenge in urology. We summarise emerging trends in antimicrobial resistance and review current guidelines on the treatment and prevention of urologic infections, as well as some key antibiotics in the era of resistance.