A review of the mechanisms that confer antibiotic resistance in pathotypes of E. coli

Genomic approach to evaluate the intrinsic antibacterial activity of novel diazabicyclooctanes (zidebactam and nacubactam) against clinical Escherichia coli isolates from diverse clonal lineages in the United Arab Emirates

BACKGROUND

The spiking rise in the prevalence of multidrug-resistant (MDR) pathogens necessitates discovering new antimicrobial agents. This study aims to investigate the intrinsic activity of two novel diazabicyclooctane (DBO) β-lactamase inhibitors, zidebactam and nacubactam, against diverse MDR Escherichia coli isolates from the United Arab Emirates. We aimed to correlate their antibacterial efficacy with the genomic characteristics of the strains.

METHODS

This study investigated 73 E. coli strains and tested them for susceptibility to different antibiotics, including DBOs. PCR screening for carbapenemase and major β-lactamase genes was done. The strains were then grouped according to phenotypic and genotypic profiles. Whole-genome sequencing was employed to characterize the genetic landscape and clonality of selected 32 strains. Additionally, time-kill studies were conducted to confirm the bactericidal activity of DBOs.

RESULTS

Zidebactam demonstrated superior efficacy compared to nacubactam, primarily due to its higher affinity for penicillin-binding protein 2 (PBP2). Notably, zidebactam alone exhibited the most potent in vitro activity, outperforming both traditional β-lactams and novel antibiotics like cefiderocol. DBOs maintained effectiveness against strains harboring various resistance determinants, including NDM-5, OXA-181, CTX-M-15, SHV-12, CMY, and DHA. Genomic analysis revealed multiple mutations in PBP1-3, with PBP2 mutations correlating with DBO susceptibility variations. Importantly, DBOs remained highly effective against isolates with PBP mutations, even those belonging to high-risk clonal lineages (ST167, ST410, ST131). Time-kill studies confirmed the bactericidal activity of DBOs, with only one strain showing reduced susceptibility (MIC: 4 µg/ml).

CONCLUSIONS

This study provides compelling evidence for the potential of DBOs, particularly zidebactam, as novel antibacterial agents. Their unique characteristics and broad-spectrum activity position them as promising candidates for future antibiotic development. While the inclusion of DBO therapies in the antibiotic arsenal could significantly impact MDR pathogen treatment, realizing their full potential requires further research, clinical evaluation, and vigilant monitoring of resistance mechanisms through integrated genomic approaches.

Antimicrobial Resistant Staphylococcus spp., Escherichia coli, and Salmonella spp. in Food Handlers: A Global Review of Persistence, Transmission, and Mitigation Challenges

Antimicrobial resistance in foodborne pathogens represents a critical global health challenge, with food handlers serving as key contributors in their transmission. This comprehensive review synthesizes evidence on the prevalence, transmission dynamics, and antimicrobial resistance patterns of three major pathogens, Staphylococcus spp., Escherichia coli, and Salmonella spp., among food handlers worldwide. Analysis of studies across diverse geographical regions reveals considerable variation in colonization rates, with Staphylococcus spp. prevalence ranging from 19.5% to 95.0%, Escherichia coli from 2.8% to 89.3%, and Salmonella spp. from 0.07% to 9.1%. Resistance profiles demonstrate alarming trends, including widespread β-lactam resistance and emerging resistance to last-resort antibiotics like carbapenems. Particularly concerning is the high occurrence of multidrug resistant (MDR) strains and extended spectrum β-lactamase (ESBL) producers in low- and middle-income countries. This review identified inadequate handwashing, poor hygiene infrastructure, and asymptomatic carriage as critical factors facilitating the transmission of antimicrobial resistant strains. These findings underscore the urgent need for enhanced surveillance systems, targeted decolonization strategies, improved hygiene protocols, and food handler education to mitigate the spread of resistant pathogens through the food chain.

Treatment of E. coli Infections with T4-Related Bacteriophages Belonging to Class Caudoviricetes: Selecting Phage on the Basis of Their Generalized Transduction Capability

The problem of the multidrug resistance of pathogenic bacteria is a serious concern, one which only becomes more pressing with every year that passes, motivating scientists to look for new therapeutic agents. In this situation, phage therapy, i.e., the use of phages to combat bacterial infections, is back in the spotlight of research interest. Bacterial viruses are highly strain-specific towards their hosts, which makes them particularly valuable for targeting pathogenic variants amidst non-pathogenic microflora, represented by such commensals of animals and humans as E. coli, S. aureus, etc. However, selecting phages for the treatment of bacterial infections is a complex task. The prospective candidates should meet a number of criteria; in particular, the selected phage must not contain potentially dangerous genes (e.g., antibiotic resistance genes, genes of toxins and virulence factors etc.)-or be capable of transferring them from their hosts. This work introduces a new approach to selecting T4-related coliphages; it allows one to identify strains which may be safer in terms of involvement in the horizontal gene transfer. The approach is based on the search for genes that reduce the frequency of genetic transduction.

Emergence of Recurrent Urinary Tract Infection: Dissecting the mechanism of Antimicrobial Resistance, Host-Pathogen Interaction, and Hormonal Imbalance

Urinary tract infection is one of the most common infections worldwide, causing numerous deaths every year. The gut-bladder axis has been recently found to be a key factor in initiating UTI pathogenesis, along with the imbalance in the gut microbiome, which is associated with advanced susceptibility to rUTI. The patients who suffer from UTIs are, more often than not, the ones who have the lowest levels of butyrate-producing gut bacteria. Antibiotics cause dysbiosis in the gut and increase the growth of uropathogenic strains. Moreover, the gut-vagina and vagina-bladder axes are involved in UTIs by transferring microbial species, modulating the immune response, and developing intracellular bacterial reservoirs in the bladder. The rising usage of antibiotics has raised antimicrobial resistance (AMR) worldwide and recently worsened the treatment of UTIs. Resistance mechanisms include enzymatic hydrolysis of antibiotics, efflux systems, biofilm formation, horizontal gene transfer, and a weakened host's immune system, allowing bacteria to escape from the treatments. Besides, in pregnant women and adolescents, the alterations in sex hormone levels increase the risk of rUTIs. Knowledge of microbiota that harbor in the gut-vagina and vagina-bladder axes might lead to the invention of nonantibiotic preventive and therapeutic techniques in the future. In conclusion, this review emphasizes the need for a study to understand the host-microbe interactions, gut health, and AMR to effectively deal with and prevent recurrent UTIs. Also, the review explores a comprehensive analysis of the epigenetic network between host UTIs and marker genes in E. coli.

Seasonal and environmental drivers of antibiotic resistance and virulence in Escherichia coli from aquaculture and their public health implications

Aquaculture is increasingly impacted by environmental stressors such as temperature and pH fluctuations, which influence the proliferation and antibiotic resistance of Escherichia coli (E. coli). This study investigates the effects of these factors on the prevalence, virulence, and antibiotic resistance of E. coli isolated from aquaculture environments in Egypt, with a focus on public health implications. A total of 328 Oreochromis niloticus (Nile tilapia) samples were collected from Egyptian fish farms over five sampling periods, representing different seasonal conditions. E. coli was isolated and identified using selective culture methods and biochemical tests. Molecular characterization was conducted via polymerase chain reaction (PCR) to detect diarrheagenic E. coli pathotypes (st, lt, eaeA, bfpA, stx1, stx2). Additionally, PCR was utilized to screen for β-lactamase and carbapenemase resistance genes. Water parameters, including temperature and pH, were recorded, and their correlation with bacterial prevalence, virulence, and antibiotic resistance profiles were analyzed. A high prevalence of E. coli (92.68%) was observed, with a significant correlation between bacterial occurrence and elevated water temperatures. Diarrheagenic E. coli was detected in 82.1% of samples, with enterotoxigenic E. coli (ETEC) being the most common pathotype. Some isolates harbored multiple virulence genes, indicating hybrid strains. Resistance genes such as blaTEM, blaCTX-M, and blaOXA-48 were widely distributed, particularly during warmer months and at neutral pH levels. Groups with elevated water temperatures exhibited a higher prevalence of antibiotic-resistant isolates, often harboring multiple resistance genes. This study highlights the significant role of environmental stressors in influencing the prevalence, pathogenicity, and antibiotic resistance profiles of E. coli in aquaculture systems. The findings emphasize the need for continuous monitoring and improved biosecurity measures to mitigate the risks associated with MDR E. coli in aquaculture, ensuring food safety and protecting public health.

Phenotype Detection and Drug Resistance Analysis of Carbapenem-Resistant Gram-Negative Bacilli

BACKGROUND

The increasing prevalence of infections caused by carbapenem-resistant organisms (CRO) represents a global health issue. Therefore, a rapid and accurate method for detecting these microbes in any clinical microbiology laboratory is crucial for the prevention and control of their transmission, as well as for clinical treatment. This study aimed to evaluate the phenotypic detection methods, PBA-EDTA, mCIM, PCR, and immunocolloidal gold kit for CRO.

METHODS

We collected 99 samples from the inpatients in Sun Yat-Sen University Cancer Center (SYSUCC) from March 2019 to February 2022 and classified the drug resistance and genotype of various strains by various enzyme-type experiments.

RESULTS

Out of 99 multidrug-resistant Gram-negative bacilli resistant to carbapenems, 58 (58.59%) were identified as carbapenemase-positive using the mCIM test. The carbapenemase genotypes included 19 NDM strains, 4 KPC strains, 1 IMP strain, and 5 OXA-23 strains. Enzyme detection revealed 21 strains positive for metallo-β-lactamase, 50 for serine-β-lactamase, and 2 positive for both, with a total positive rate of 73.74%. 26 strains were negative for enzyme detection, and mCIM showed limited effectiveness in detecting strains coproducing NDM and KPC. The immunocolloidal gold assay had a sensitivity of 96.9% and specificity of 98.5%.

CONCLUSION

This study used an immunocolloidal gold kit for carbapenemase detection, providing results within 15 min. This cost-effective method can quickly assist in identifying carbapenemase genotypes and holds potential as a new rapid detection and diagnostic tool for CRE in clinical and lab settings.

Isolation and Genomic Analysis of Escherichia coli Phage AUBRB02: Implications for Phage Therapy in Lebanon

BACKGROUND/OBJECTIVES

Escherichia coli (E. coli), a prevalent Gram-negative bacterium, is a frequent cause of illness. The extensive use of antibiotics has led to the emergence of resistant strains, complicating antimicrobial therapy and emphasizing the need for natural alternatives such as phages.

METHODS

In this study, a novel Escherichia coli phage, AUBRB02, was isolated from sewage and characterized through whole-genome sequencing, host range assays, and biofilm elimination assays. The phage's stability and infectivity were assessed under various pH and temperature conditions, and different E. coli strains.

RESULTS

Phage AUBRB02 has an incubation period of 45 min, a lysis period of 10 min, and a burst size of 30 phages/infected cell. It is stable across pH 5.0-9.0 and temperatures from 4 °C to 60 °C. Treatment with AUBRB02 significantly reduced post-formation E. coli biofilms, as indicated by lower OD values compared with the positive control. The whole genome sequencing revealed a genome size of 166,871 base pairs with a G + C (Guanine and Cytosine content) content of 35.47%. AUBRB02 belongs to the Tequatrovirus genus, sharing 93% intergenomic similarity with its closest RefSeq relative, and encodes 262 coding sequences, including 10 tRNAs.

CONCLUSIONS

AUBRB02 demonstrates high infectivity and stability under diverse conditions. Its genomic features and similarity to related phages highlight its potential for phage therapy, offering promising prospects for the targeted treatment of E. coli infections.

Bacterial Extracellular Vesicles and Antimicrobial Peptides: A Synergistic Approach to Overcome Antimicrobial Resistance

Antimicrobial resistance is already a major global health threat, contributing to nearly 5 million deaths annually. The rise of multidrug-resistant pathogens has made many infections increasingly difficult to treat. This growing threat has driven the search for alternative therapeutic approaches. Among the most promising candidates are bacterial extracellular vesicles (BEVs) and antimicrobial peptides (AMPs), which offer unique mechanisms of action, potential synergistic effects, and the ability to bypass conventional resistance pathways. This review summarizes the current research on synergistic effects of BEVs and AMPs to overcome antimicrobial resistance.

Antibiotic resistance and virulence patterns of O25 and O16 serogroups in uropathogenic Escherichia coli

OBJECTIVE

This study investigates antibiotic resistance patterns, virulence factors, and phylogenetic groups of O25 and O16 serogroups in uropathogenic Escherichia coli (UPEC) isolates from kidney transplant recipients (KTPs) and non-KTPs. The presence of serogroups O25 and O16, resistance genes (e.g., blaCTX-M, blaTEM), and virulence factors (e.g., fimH, PAI) were determined using PCR. Phylogenetic groups were identified via quadruplex PCR, and genetic diversity was assessed using ERIC-PCR.

RESULTS

A total of 111 E. coli isolates were examined in the present study. The O-serotyping results indicated that 18% and 3.6% of isolates were positive for O25 and O16 serogroup, respectively. In serogroup O25, the highest resistance rates were observed for nalidixic acid and cotrimoxazole, whereas in serogroup O16, the highest resistance rates were against cotrimoxazole and ampicillin-sulbactam. ESBL production was identified in 30% of O25 and 25% of O16 isolates. O25 isolates belonged to phylogenetic group B2, whereas O16 isolates were grouped in B1. ERIC-PCR revealed significant genetic diversity among isolates. The O25 serogroup is prevalent and closely associated with high antibiotic resistance and virulence, suggesting its critical role in UTI pathogenesis in transplant patients. These findings underscore the importance of monitoring resistance patterns and developing targeted therapeutic and preventive strategies for managing UPEC infections.

Colonization with extended-spectrum β-lactamase and carbapenemase-producing Enterobacterales in Ethiopia: A systematic review and meta-analysis

BACKGROUND

The human intestinal tract contains many commensals. However, during an imbalance of the normal microbiota following exposure to antibiotics, extended-spectrum β-lactamase- and carbapenemase-producing Enterobacterales emerge. Individuals colonized with these bacteria may develop subsequent infections themselves. Therefore, this review aimed to estimate the colonization rate of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacterales in Ethiopia.

METHODS

The protocol was registered (PROSPERO ID: CRD42024550137). A systematic literature search was conducted in electronic databases, including PubMed, Google Scholar, and Hinari, to retrieve potential studies. The quality of the included studies was assessed using the Joanna Briggs Institute critical appraisal tool. The data were extracted from the eligible studies using Microsoft Excel 2019 and analyzed using STATA version 11. Heterogeneity between studies was checked using I2 test statistics. Publication bias was assessed using funnel plots and Egger's test. A random-effects model of DerSimonian-Laird method was employed to estimate the outcomes.

RESULTS

A total of 15 studies with 4713 participants were included in the meta-analysis. The overall pooled colonization rates of extended-spectrum β-lactamase-producing and carbapenemase-producing Enterobacterales in Ethiopia were 28.5% (95% CI: 16.4-40.5%, I2 =  95.9%, p <  0.001) and 4.4% (95% CI: 0.9-7.9%, I2 =  0.0%, p =  0.64), respectively. The majority of the extended-spectrum β-lactamase producers were E. coli (20.6%, 95% CI: 9.3-31.9%, I2 =  94.4%, p < 0.001), followed by Klebsiella spp. (11.1%, 95% CI: 7.7-14.6%, I2 =  20.2%, p =  0.245). Similarly, the predominant carbapenemase producers were E. coli (2.7%, 95% CI: -1.3-6.7, I2 =  0.0%, p = 0.941) and Klebsiella spp. (2.1%, 95% CI: -1.7-5.9%, I2 =  0.0%, p = 0.999). Furthermore, the pooled estimate of multidrug resistance among extended-spectrum β-lactamase producers was 71.7% (95% CI: 55.25-88.05%, I2 =  92.9%, p < 0.001).

CONCLUSION AND RECOMMENDATIONS

Approximately one-quarter of Ethiopians are colonized with ESBL-PE, while about one in 25 is colonized with CPE. These findings were obtained from studies with a moderate-to-low risk of bias. However, the results for ESBL-PE showed significant variability, indicating high heterogeneity among the studies. This colonization may lead to subsequent extraintestinal infections. Therefore, proactive action from all stakeholders is required to combat the unrecognized spread of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacterales in humans.

Comparative genomics of clinical hybrid Escherichia coli strains in Norway

The global rise of hybrid Escherichia coli (E. coli) is a major public health concern, as enhanced virulence from multiple pathotypes complicates the traditional E. coli classification system and challenges clinical diagnostics. Hybrid strains are particularly concerning as they can infect both intestinal and extraintestinal sites, complicating treatment and increasing the risk of severe disease. This study analyzed virulence-associated genes (VAGs) in 13 E. coli isolates from fecal samples of patients with symptoms of gastrointestinal (GI) infection in Norwegian hospitals and clinics. Whole genome sequencing (WGS) was conducted using Oxford Nanopore's MinION and Illumina's MiSeq platforms. Eleven strains harbored molecular diagnostic markers of atypical enteropathogenic E. coli (aEPEC), enteroinvasive E. coli (EIEC), Shiga toxin-producing E. coli (STEC), enterotoxigenic E. coli (ETEC), or typical enteropathogenic E. coli (tEPEC). Two of those isolates were identified as triple intestinal hybrids with molecular diagnostic markers for aEPEC, EIEC, and STEC. Notably, two isolates lacked any IPEC-specific molecular diagnostic markers, yet were suspected of causing the patient's GI infection. Furthermore, genes associated with extraintestinal pathogenic E. coli (ExPEC)-including adhesins, toxins, protectins, siderophores, iron acquisition systems, and invasins-were identified in all the isolates. Thus, most of the isolates were classified as hybrid aEPEC/ExPEC, STEC/ExPEC, tEPEC/ExPEC, or aEPEC/EIEC/STEC/ExPEC. These findings emphasize the genomic plasticity of E. coli and highlight the need to revise the classification system for enteric pathogens.

Emerging threats: Antimicrobial resistance in extended-spectrum beta-lactamase and carbapenem-resistant Escherichia coli

Antimicrobial resistance (AMR) in Escherichia coli strains, particularly those producing Extended-Spectrum Beta-Lactamase (ESBL) and Carbapenemase (CR-Ec), represents a serious global health threat. These resistant strains have been associated with increased morbidity, mortality, and healthcare costs, as they limit the effectiveness of standard antibiotic therapies. The prevalence of ESBL- and CR-Ec-producing strains continues to rise, driven by the overuse and misuse of antibiotics in healthcare and agricultural settings, and facilitated by global interconnectedness through international travel, trade, and food distribution. This review article examines the molecular mechanisms behind ESBL and CR resistance, focusing on the key genes involved in these processes, such as blaCTX-M, blaKPC, and blaNDM, and the clinical challenges posed by these strains. Additionally, the public health impact, including the spread of infections in hospital and community environments, is highlighted. The discussion emphasizes the urgent need for improved diagnostic tools, robust surveillance systems, and innovative therapeutic strategies. Emerging treatments, including phage therapy and novel antibiotic combinations, show promise in addressing these challenges and offer potential breakthroughs in combating resistant strains. Lastly, the review calls for stronger antimicrobial stewardship and policy reforms to mitigate the spread of resistant E. coli strains and protect global public health. Effective intervention at multiple levels, from diagnostics to policy, is critical to controlling the threat posed by AMR.

Incidence of extended spectrum beta-lactamase (ESBL) producing Escherichia coli isolated from women with urinary tract infections in Jordan

Background and Objectives

Urinary tract infections are one of the world's major health problems. In addition, clinical disorders may result from the presence of bacteria or fungi in urine. The aim of this study was to isolate Escherichia coli (E. coli) strains from midstream urine samples, and to determine molecular characterization of encoded Extended Spectrum Beta-Lactamase (ESBL) genes.

Materials and Methods

Collected urine samples were streaked on MacConkey, blood and EMB agar plates, then identifying E. coli isolates by using antibiotic susceptibility tests. ESBL production was measured using double disc diffusion. Furthermore, uniplex PCR was performed to identify two ESBL genes (bla CTX and bla TEM).

Results

Among 412 isolates, 198 (48.1%) were E. coli strains, followed by Staphylococcus saprophyticus, Klebsiella sp., Serratia sp., Enterococci sp. and Proteus sp. with frequency of 132 (32.0%), 51 (12.4%), 15 (3.6%), 10 (2.4%), and 6 (1.5%) respectively. Female participants who were between the ages of 40 and 49 years old, married, and pregnant were more likely to develop urinary tract infections (UTIs). E. coli species were present in 189 (95.5) of the recurrent UTIs. Regarding antimicrobial susceptibility testing of E. coli isolates, the highest percentage of resistance and susceptible rates were found for nalidixic acid (75.8%) and gentamicin (64.1%) respectively. Among the E. coli isolates, 25 (12.6%) were ESBL-producers. The bla CTX-M gene was genetically confirmed in 20 (10.1%) of the isolates.

Conclusion

E. coli is the most common cause of UTI and ESBL production leads to increased resistance to common antibiotics and complicates treatment strategies.

Bioactive Compounds as Alternative Approaches for Preventing Urinary Tract Infections in the Era of Antibiotic Resistance

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide. They occur in the urinary system when a microorganism, commonly present on the perineal skin or rectum, reaches the bladder through the urethra, and adheres to the luminal surface of uroepithelial cells, forming biofilms. The treatment of UTIs includes antibiotics, but their indiscriminate use has favored the development of multidrug-resistant bacteria strains, which represent a serious challenge to today's microbiology. The pathogenesis of the infection and antibiotic resistance synergistically contribute to hindering the eradication of the disease while favoring the establishment of persistent infections. The repeated requirement for antibiotic treatment and the limited therapeutic options have further contributed to the increase in antibiotic resistance and the occurrence of potential relapses by therapeutic failure. To limit antimicrobial resistance and broaden the choice of non-antibiotic preventive approaches, this review reports studies focused on the bacteriostatic/bactericidal activity, inhibition of bacterial adhesion and quorum sensing, restoration of uroepithelial integrity and immune response of molecules, vitamins, and compounds obtained from plants. To date, different supplementations are recommended by the European Association of Urology for the management of UTIs as an alternative approach to antibiotic treatment, while a variety of bioactive compounds are under investigation, mostly at the level of in vitro and preclinical studies. Although the evidence is promising, they are far from being included in the clinical practice of UTIs.

Bacteriophage Treatment Induces Phenotype Switching and Alters Antibiotic Resistance of ESBL Escherichia coli

Background/Objectives: Bacteriophage therapy represents a promising strategy to combat multidrug-resistant pathogens, such as Escherichia coli. In this study, we explored the effects of a bacteriophage infection on an Extended Spectrum Beta-Lactamase (ESBL) positive E. coli isolate. Methods: We used next generation sequencing, proteomics and phenotypic screens to investigate the effect of bacteriophage infections on E. coli metabolism and resistance phenotypes. Results: The bacteriophage infection led to notable alterations in colony morphology, indicating profound changes in bacterial metabolism. Proteomic analysis revealed significant shifts in protein expression, with 65 proteins upregulated and 246 downregulated post-infection. The downregulated proteins were involved in various metabolic pathways, including nucleic acid, protein and lipid metabolism, and iron acquisition. Bacteriophage treatment also led to increased bacterial membrane permeability. Altogether, these alterations in bacterial metabolism and membrane permeability may lead to a general reduction in antibiotic resistance. Indeed, the bacteriophage-infected E. coli exhibited increased sensitivity to various classes of antibiotics, including beta-lactams, fluoroquinolones, trimethoprim-sulfamethoxazole, and aminoglycosides. Conclusions: Our findings highlight the potential of bacteriophage therapy as an adjunct to existing antibiotics, enhancing their efficacy against resistant strains.

Gram Negative Biofilms: Structural and Functional Responses to Destruction by Antibiotic-Loaded Mixed Polymeric Micelles

Biofilms are a well-known multifactorial virulence factor with a pivotal role in chronic bacterial infections. Their pathogenicity is determined by the combination of strain-specific mechanisms of virulence and the biofilm extracellular matrix (ECM) protecting the bacteria from the host immune defense and the action of antibacterials. The successful antibiofilm agents should combine antibacterial activity and good biocompatibility with the capacity to penetrate through the ECM. The objective of the study is the elaboration of biofilm-ECM-destructive drug delivery systems: mixed polymeric micelles (MPMs) based on a cationic poly(2-(dimethylamino)ethyl methacrylate)-b-poly(ε-caprolactone)-b-poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA35-b-PCL70-b-PDMAEMA35) and a non-ionic poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) (PEO100-b-PPO65-b-PEO100) triblock copolymers, loaded with ciprofloxacin or azithromycin. The MPMs were applied on 24 h pre-formed biofilms of Escherichia coli and Pseudomonas aeruginosa (laboratory strains and clinical isolates). The results showed that the MPMs were able to destruct the biofilms, and the viability experiments supported drug delivery. The biofilm response to the MPMs loaded with the two antibiotics revealed two distinct patterns of action. These were registered on the level of both bacterial cell-structural alterations (demonstrated by scanning electron microscopy) and the interaction with host tissues (ex vivo biofilm infection model on skin samples with tests on nitric oxide and interleukin (IL)-17A production).

Kaempferol restores the susceptibility of ESBLs Escherichia coli to Ceftiofur

Introduction

The development of extended-spectrum-beta-lactamase (ESBLs) Escherichia coli (E. coli) has become a global threat to public health. An alternative strategy to alleviate this is identifying potential natural compounds to restore antibiotic activity against ESBLs E. coli. This study aimed to find a possible compound to restore ESBLs E. coli sensitivity to ceftiofur.

Methods

The synergistic effect of kaempferol and ceftiofur against ESBLs E. coli was investigated by checkerboard assays, time-kill, growth curves, and scanning electronic microscope. The impact of kaempferol with ceftiofur on the biofilm of ESBLs E. coli was evaluated by crystal violet staining and laser scanning confocal microscopy and this study also assessed the effect of kaempferol on the initial adhesion and aggregation of E. coli (SY20) by examining motility, adhesion, and surface characteristics. The RT-qPCR was used to determine the effect of kaempferol on the expression of genes related to the LuxS/AI-2 quorum sensing system in ESBLs E. coli, and the effect of kaempferol on AI-2 signaling molecules was determined by molecular docking and bioassay. The impact of kaempferol on the activity of blaCTX-M-27 protein was determined by RT-qPCR, molecular docking, and nitrofen experiments, the results were further verified by transcriptome analysis. The mouse infection model was established, and the inhibitory mechanism of kaempferol with ceftiofur on bacteria in vivo was further verified by HE staining and immunohistochemistry.

Results and discussion

Kaempferol with ceftiofur exerts synergistic antibacterial and bactericidal effects on ESBLs E. coli by influencing β-lactamase activity, biofilm formation, and LuxS/AI-2 QS system. In vivo, kaempferol protected the small intestinal villi from the damage of ESBLs E. coli. Furthermore, kaempferol fully restores the activity of ceftiofur in animal infection models by relieving the TLR4/NF-κb pathway. In conclusion, the sensitivity of ESBLs E. coli to ceftiofur in vitro and in vivo could be enhanced by kaempferol, which showed that kaempferol may be a kind of antibiotic adjuvant.

Comparative analysis of the gut microbiota composition and diversity in Erinaceus amurensis from the Wandashan Mountain range area based on metagenomics

This study aimed to preliminarily explore the composition and diversity of intestinal bacteria in Erinaceus amurensis during breeding period, aiding in the field rescue and population conservation efforts of Erinaceus amurensis. This also provides foundational data for further research on the prevention and screening of Emerging Zoonotic Infectious Diseases and the experimental animalization of wild Erinaceus amurensis. Between April and July 2023, we collected 13 fresh fecal samples from Erinaceus amurensis at the Sishan Forest Farm in Jidong County, Heilongjiang Province, situated within the Wandashan Mountain range. Utilizing metagenomic sequencing technology, we conducted a comparative analysis of the gut microbiota composition and diversity in wild Erinaceus amurensis across different genders and between adult and fetal individuals within the same habitat. Our results revealed significant differences (P < 0.01) in the classification and diversity of gut microbiota between genders and between adult and fetal Erinaceus amurensis. Specifically, the dominant bacterial groups in the gut of Erinaceus amurensis were Pseudomonas, Proteobacteria, and Enterobacteriaceae. In male and female Erinaceus amurensis, the dominant bacterial groups were Pseudomonas, Bacteroides, and Firmicutes, with variations in bacterial abundance and diversity. While male and female Erinaceus amurensis exhibited similar microbial compositions, they displayed significant differences in specific bacterial classifications. The dominant bacterial group in fetal Erinaceus amurensis was Proteobacteria, which demonstrated lower diversity and abundance compared to the adult group. Furthermore, the types and abundance of pathogenic or opportunistic pathogens in the gut of fetal Erinaceus amurensis and male Erinaceus amurensis were higher than those in female Erinaceus amurensis. The analysis of experimental results indicates that Erinaceus amurensis in this region either have or are at risk of developing inflammation related to the intestinal and urinary tracts, as well as skin-related issues. Consequently, it is advised that forestry and wildlife conservation personnel in this area prioritize treatment against these specific pathogens when conducting rescue operations for Erinaceus amurensis in the wild.

Natural Solutions to Antimicrobial Resistance: The Role of Essential Oils in Poultry Meat Preservation with Focus on Gram-Negative Bacteria

The increase in antimicrobial resistance (AMR) is a major global health problem with implications on human and veterinary medicine, as well as food production. In the poultry industry, the overuse and misuse of antimicrobials has led to the development of resistant or multi-drug resistant (MDR) strains of bacteria such as Salmonella spp., Escherichia coli and Campylobacter spp., which pose a serious risk to meat safety and public health. The genetic transfer of resistance elements between poultry MDR bacteria and human pathogens further exacerbates the AMR crisis and highlights the urgent need for action. Traditional methods of preserving poultry meat, often based on synthetic chemicals, are increasingly being questioned due to their potential impact on human health and the environment. This situation has led to a shift towards natural, sustainable alternatives, such as plant-derived compounds, for meat preservation. Essential oils (EOs) have emerged as promising natural preservatives in the poultry meat industry offering a potential solution to the growing AMR problem by possessing inherent antimicrobial properties making them effective against a broad spectrum of pathogens. Their use in the preservation of poultry meat not only extends shelf life, but also reduces reliance on synthetic preservatives and antibiotics, which contribute significantly to AMR. The unique chemical composition of EOs, that contains a large number of different active compounds, minimizes the risk of bacteria developing resistance. Recent advances in nano-encapsulation technology have further improved the stability, bioavailability and efficacy of EOs, making them more suitable for commercial use. Hence, in this manuscript, the recent literature on the mechanisms of AMR in the most important Gram-negative poultry pathogens and antimicrobial properties of EOs on these meat isolates was reviewed. Additionally, chemical composition, extraction methods of EOs were discussed, as well as future directions of EOs as natural food preservatives. In conclusion, by integrating EOs into poultry meat preservation strategies, the industry can adopt more sustainable and health-conscious practices and ultimately contribute to global efforts to combat AMR.

Eleutherin and Isoeleutherin Activity against Staphylococcus aureus and Escherichia coli Strain's: Molecular Docking and Antibacterial Evaluation

Naphthoquinones eleutherin and isoeleutherin have demonstrated promising antibacterial activity, probably due to their quinone structure, which can generate reactive oxygen species. The study examines the activities of pathogens, such as Staphylococcus aureus and Escherichia coli, associated with antimicrobial resistance and explores their potential mechanisms of action. The MIC, IC50, and MBC were determined. PharmMapper 2017 server and GOLD 2020.1 software were utilized for molecular docking to identify protein targets and interaction mechanisms. The docking predictions were verified by redocking, focusing on structures with RMSD below 2 Å. The molecular docking revealed a significant affinity of eleutherin for the peptide, transcriptional regulator QacR, and regulatory protein BlaR1 with better interactions with BlaR1 than the crystallographic ligand (benzylpenicillin). Isoeleutherin demonstrated specific interactions with methionine aminopeptidase, indicating specificity and affinity. In summary, the difference in naphthoquinones activities may be related to structural differences. Eleutherin exhibits potential as a therapeutic adjuvant to reverse bacterial resistance in S. aureus, suggesting this molecule interferes with the antibiotic resistance mechanism. The absence of homologous proteins or variations in the structure of the target proteins could be the cause of the inactivity against E. coli.

Antibacterial properties enhancement tropical fruit waste biopolymer hydrogel loaded Nephelium Lappaceum leaf extract for sanitizing applications

Current alcohol-based sanitizers present safety concerns and are not suitable for all applications. To address the issue, biopolymer hydrogels offer a safer, sustainable alternative due to biocompatibility, biodegradability, and customizable properties. In present study, carboxymethyl cellulose (CMC) was prepared from Durian fruit rind, a tropical fruit byproduct rich in polysaccharides and combined with the synthetic polymer Carbopol to form a hydrogel with homogenization technique. Rambutan (Nephelium lappaceum) leaf extract (RLE) as an antibacterial agent was analyzed for functional, morphological, antibacterial, and structural properties. Phytochemical analysis of RLE confirmed the presence of antibacterial compounds, while Minimum Inhibitory Concentrations (MIC) were 33.3 μg/mL for Escherichia coli and 28.5 μg/mL for Staphylococcus aureus. Additionally, Scanning Electron Microscopy showed significant disruptions in bacterial cell walls. Hydrogel incorporated RLE was produced with improved properties confirmed through viscosity, FT-IR, Disc-diffusion assay and spread plate method analysis. In general, Rambutan leaf extract significantly improves the antibacterial properties of biopolymer-based hydrogels, hence offering a promising, eco-friendly alternative to alcohol-based sanitizers.

Antimicrobial Potential of Probiotic Strains From Bulgarian Cheese and Shallot Yogurt Against Staphylococcus saprophyticus

The escalating incidence of hospital infections due to antibiotic resistance necessitates the identification of alternative therapeutic agents such as probiotics. This study was designed to isolate and evaluate the efficacy of probiotics against Staphylococcus saprophyticus, a prevalent etiological agent of urinary tract infections (UTIs). A total of 100 S. saprophyticus strains were isolated from clinical samples and subjected to antibiotic susceptibility testing via the disc diffusion method. Concurrently, probiotic bacteria were isolated from Bulgarian cheese and shallot yogurt, and their antibacterial activity against S. saprophyticus strains was assessed. The inhibitory potential of probiotic supernatants was evaluated using microtiter plate assays, with the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) determined at a 1/2 dilution. Cytotoxicity was evaluated using the MTT assay, and high-performance liquid chromatography (HPLC) was employed to analyze the concentrations of organic acids produced by the probiotics. The results revealed that all S. saprophyticus strains were resistant to tetracycline and doxycycline but susceptible to other antibiotics. Lactobacillus rhamnosus strains M and B demonstrated notable antibacterial and antibiofilm activity against S. saprophyticus isolates. These probiotics exhibited susceptibility to most antibiotics and lacked virulence factors, suggesting their safety for therapeutic use. The organic acids produced by the probiotics were identified as lactic acid, acetic acid, and formic acid. In conclusion, L. rhamnosus strains M and B exhibit potent antimicrobial properties against S. saprophyticus, indicating their potential as therapeutic agents for UTIs. Further research is warranted to validate these findings and explore the possibility of these probiotics in clinical applications.

Determinants of Antibiotic Resistance and Virulence Factors in the Genome of Escherichia coli APEC 36 Strain Isolated from a Broiler Chicken with Generalized Colibacillosis

Objective: Multidrug-resistant, highly pathogenic Escherichia coli strains are the primary causative agents of intestinal and extraintestinal human diseases. The extensive utilization of antibiotics for farm animals has been identified as a contributing factor to the emergence and dissemination of E. coli strains that exhibit multidrug resistance and possess high pathogenic potential. Consequently, a significant research objective is to examine the genetic diversity of pathogenic E. coli strains and to identify those that may pose a threat to human health. Methods: In this study, we present the results of genome sequencing and analysis, as well as the physiological characterization of E. coli strain APEC 36, which was isolated from the liver of a broiler chicken with generalized colibacillosis. Results: We found that APEC 36 possess a number of mechanisms of antibiotic resistance, including antibiotic efflux, antibiotic inactivation, and antibiotic target alteration/replacement/protection. The most widely represented group among these mechanisms was that of antibiotic efflux. This finding is consistent with the strain's documented resistance to multiple antibiotics. APEC 36 has an extremely rare variant of the beta-lactamase CTX-M-169. Notwithstanding the multitude of systems for interfering with foreign DNA present in the strain, seven plasmids have been identified, three of which may possess novel replication origins. Additionally, qnrS1, which confers resistance to fluoroquinolones, was found to be encoded in the genome rather than in the plasmid. This suggests that the determinants of antibiotic resistance may be captured in the genome and stably transmitted from generation to generation. Conclusions: The APEC 36 strain has genes for toxins, adhesins, protectins, and an iron uptake system. The obtained set of genetic and physiological characteristics allowed us to assume that this strain has a high pathogenic potential for humans.

Diarrheagenic Escherichia coli in Stool Specimens Collected from Patients Attending Primary Healthcare Facilities in Ethiopia: Whole-Genome Sequencing-Based Molecular Characterization

The diarrheagenic Escherichia coli (DEC) is the major cause of diarrheal diseases in Africa, including Ethiopia. However, the genetic diversity of E. coli pathotypes found in Ethiopia has not been studied well. This study aimed to characterize potential DEC belonging to enteropathogenic (EPEC), Shiga toxin-producing (STEC), enteroaggregative (EAEC), enterotoxigenic (ETEC), and enteroinvasive (EIEC) E. coli pathotypes from stool specimens of patients attending primary healthcare units (n = 260) in Addis Ababa and Hossana using whole-genome sequencing. Real-time PCR assays were used to identify DEC isolates belonging to EPEC, STEC, EAEC, ETEC, and EIEC pathotypes, which were then subjected to whole-genome sequencing on the Illumina platform. Twenty-four whole-genome nucleotide sequences of DEC strains with good enough quality were analyzed for virulence-associated genes (VAGs), antibiotic resistance genes (ARGs), phylogenetic groups, serogroups, and sequence types. The majority (62.5%) of DEC isolates belonged to the phylogenetic group B1. The identified DEC isolates belonged to 21 different serogroups and 17 different sequence types. All tested DEC isolates carried multiple VAGs and ARGs. The findings highlight the high diversity in the population structure of the studied DEC isolates, which is important for designing targeted interventions to reduce the diarrheal burden in Ethiopia.

The epidemiology of antibiotic-resistant clinical pathogens in Uganda

Background

Antibiotic resistance (ABR) is a global challenge, and its control depends on robust evidence primarily derived from surveillance systems.

Methods

We utilised a national surveillance data set to demonstrate how such evidence can be systematically generated. In doing so, we characterised the ABR profiles of priority clinical pathogens, identified associated factors, and drew inferences on antibiotic usage in Uganda.

Results

Of the 12 262 samples collected between 2019-21, we analysed 9033 with complete metadata. ABR was steadily increasing at a rate of 0.5% per year, with a surge in 2021 and the highest and lowest levels of penicillin and carbapenems detected in the northern (odds ratio (OR) = 2.26; P < 0.001) and the northeast (OR = 0.28; P < 0.001) regions of Uganda respectively. ABR was commonly observed with Escherichia coli (OR = 1.18; P < 0.001) and Klebsiella pneumoniae (OR = 1.25; P < 0.001) among older and male patients (61-70 years old) (OR = 1.88; P = 0.005). Multi-drug resistance (MDR) and ABR were disproportionately higher among bloodstream infections than respiratory tract infections and urinary tract infections, often caused by Acinetobacter baumannii. Co-occurrence of ABR suggests that cephalosporins such as ceftriaxone are in high use all over Uganda.

Conclusions

ABR is indeed a silent pandemic, and our results suggest it is increasing at 0.5% per year, with a notable surge in 2021 likely due to coronavirus disease 2019 (COVID-19). Of concern, ABR and MDR are mainly associated with bloodstream and surgical wound infections, with a gender and age dimension. However, it is encouraging that carbapenem resistance remains relatively low. Such evidence is critical for contextualising the implementation and evaluation of national action plans.

Analysis of Antibiotic Resistance Genes (ARGs) across Diverse Bacterial Species in Shrimp Aquaculture

There is little information available on antibiotic resistance (ABR) within shrimp aquaculture environments. The aim of this study was to investigate the presence of antibiotic resistance genes (ARGs) in shrimp farming operations in Atacames, Ecuador. Water samples (n = 162) and shrimp samples (n = 54) were collected from three shrimp farming operations. Samples were cultured and a subset of isolates that grew in the presence of ceftriaxone, a third-generation cephalosporin, were analyzed using whole-genome sequencing (WGS). Among the sequenced isolates (n = 44), 73% of the isolates contained at least one ARG and the average number of ARGs per isolate was two, with a median of 3.5 ARGs. Antibiotic resistance genes that confer resistance to the β-lactam class of antibiotics were observed in 65% of the sequenced isolates from water (20/31) and 54% of the isolates from shrimp (7/13). We identified 61 different ARGs across the 44 sequenced isolates, which conferred resistance to nine antibiotic classes. Over half of all sequenced isolates (59%, n = 26) carried ARGs that confer resistance to more than one class of antibiotics. ARGs for certain antibiotic classes were more common, including beta-lactams (26 ARGs); aminoglycosides (11 ARGs); chloramphenicol (three ARGs); and trimethoprim (four ARGs). Sequenced isolates consisted of a diverse array of bacterial orders and species, including Escherichia coli (48%), Klebsiella pneumoniae (7%), Aeromonadales (7%), Pseudomonadales (16%), Enterobacter cloacae (2%), and Citrobacter freundii (2%). Many ARGs were shared across diverse species, underscoring the risk of horizontal gene transfer in these environments. This study indicated the widespread presence of extended-spectrum β-lactamase (ESBL) genes in shrimp aquaculture, including blaCTX-M, blaSHV, and blaTEM genes. Increased antibiotic resistance surveillance of shrimp farms and identification of aquaculture operation-level risk factors, such as antibiotic use, will likely be important for mitigating the spread of ARGs of clinical significance.

The A226D Mutation of OmpC Leads to Increased Susceptibility to β-Lactam Antibiotics in Escherichia coli

Bacterial resistance to antibiotics can lead to long-lasting, hard-to-cure infections that pose significant threats to human health. One key mechanism of antimicrobial resistance (AMR) is to reduce the antibiotic permeation of cellular membranes. For instance, the lack of outer membrane porins (OMPs) can lead to elevated AMR levels. However, knowledge on whether mutations of OMPs can also influence antibiotic susceptibility is limited. This work aims to address this question and identified an A226D mutation in OmpC, a trimeric OMP, in Escherichia coli. Surveillance studies found that this mutation is present in 50 E. coli strains for which whole genomic sequences are available. Measurement of minimum inhibition concentrations (MICs) found that this mutation leads to a 2-fold decrease in MICs for β-lactams ampicillin and piperacillin. Further survival assays confirmed the role this mutation plays in β-lactam susceptibility. With molecular dynamics, we found that the A226D mutation led to increased overall flexibility of the protein, thus facilitating antibiotic uptake, and that binding with piperacillin was weakened, leading to easier antibiotic penetration. This work reports a novel mutation that plays a role in antibiotic susceptibility, along with mechanistic studies, and further confirms the role of OMPs in bacterial tolerance to antibiotics.

Multidrug-Resistant Escherichia coli Accumulated by Freshwater Bivalves: An Underestimated Risk for Public Health?

As bioindicators, freshwater bivalves are crucial for the assessment of the contamination impact on different levels of biological integration. Escherichia coli is used as a bioindicator of water fecal contamination, representing a critical global concern, especially with the rise of multidrug-resistant (MDR) strains. Phylogenetic diversity, pathotypic characterization, and antibiotic resistance profiles of E. coli isolated from freshwater bivalves (Anodonta anatina) were assessed. Samples were collected from the Tua River in Northern Portugal, from two different sites, Chelas and Barcel, representing different degrees of contamination. Antimicrobial susceptibility testing was performed by the disk diffusion method, and characterizations of the phylogenetic groups and pathotypes were assessed by PCR-multiplex and real-time PCR-multiplex, respectively. Results showed that 60% of isolates were characterized as MDR, including resistance to carbapenems, considered the last resort against multidrug-resistant bacteria. Within this study, it was also possible to verify the antimicrobial resistance (AMR) profile differences between the two sampling sites, with bivalve isolates from the Chelas site showing a higher percentage of antibiotic resistance. Among the E. coli isolates, the highest prevalence (55%) was observed in group B1, followed by group D or E (15%), group A (10%), and group E or Clade I (10%). None of the isolates were classified as diarrheagenic E. coli (DEC). This work highlights the potential transmission of antimicrobial-resistant bacteria through bivalves in the food chain. The 'One Health' approach is crucial for combating antimicrobial resistance, namely in edible freshwater species, emphasizing active surveillance to protect human, animal, and environmental health against the spread of antibiotic-resistant bacteria in aquatic environments.

Activity of Synthetic Peptide KP and Its Derivatives against Biofilm-Producing Escherichia coli Strains Resistant to Cephalosporins

Bacterial resistance to β-lactam antibiotics, particularly new generation cephalosporins, is a major public health concern. In Escherichia coli, resistance to these antibiotics is mainly mediated by extended-spectrum β-lactamases (ESBL), which complicates a range of health-threatening infections. These infections may also be biofilm-related, making them more difficult to treat because of the higher tolerance to conventional antibiotics and the host immune response. In this study, we tested as potential new drug candidates against biofilm-forming ESBL-producing E. coli four antimicrobial peptides previously shown to have antifungal properties. The peptides proved to be active in vitro at micromolar concentrations against both sensitive and ESBL-producing E. coli strains, effectively killing planktonic cells and inhibiting biofilm formation. Quantitative fluorescence intensity analysis of three-dimensional reconstructed confocal laser scanning microscopy (CLSM) images of mature biofilm treated with the most active peptide showed significant eradication and a reduction in viable bacteria, while scanning electron microscopy (SEM) revealed gross morphological alterations in treated bacteria. The screening of the investigated peptides for antibacterial and antibiofilm activity led to the selection of a leading candidate to be further studied for developing new antimicrobial drugs as an alternative treatment against microbial infections, primarily associated with biofilms.

Comparison of Crohn's disease-associated adherent-invasive Escherichia coli (AIEC) from France and Hong Kong: results from the Pacific study

Association between ileal colonization by Adherent-Invasive Escherichia coli (AIEC) and Crohn's disease (CD) has been widely described in high-incidence Western countries but remains unexplored in Asian countries with a fast increase in CD incidence. In the PACIFIC study, we compared the characteristics of AIEC pathobionts retrieved from ileal biopsies of CD patients enrolled in France (FR) and Hong Kong (HK). The prevalence of AIEC was similar in France (24.5%, 25/102) and Hong Kong (30.0%, 18/60) (p = 0.44). No difference was observed between the two populations of AIEC regarding adhesion and invasion levels. When tested for antibiotic resistance, the proportion of AIEC strains resistant to ampicillin, piperacillin, tobramycin, and gentamicin was significantly higher in HK AIEC strains compared to French strains. AIEC strains from FR or HK population were both able to persist in the mice intestine (DSS-treated CEABAC10 mice model). Moreover, genomic analysis of 25 FR and 17 hK AIEC strains using next-generation sequencing revealed the co-existence of several virulence factors associated with enteric E. coli pathotypes, although no single virulence factor was significantly associated with either country of origin or AIEC status. In vitro, all AIEC strains (FR and HK) were sensitive to the EcoActive™ phage cocktail, suggesting that it could be a promising option to target AIEC in CD across the world.