Uropathogenic Escherichia coli endeavors: an insight into the characteristic features, resistance mechanism, and treatment choice

Arafi, Vahid; Hasani, Alka; Sadeghi, Javid; Varshochi, Mojtaba; Poortahmasebi, Vahdat; Hasani, Akbar; Hasani, Roqaiyeh

doi:10.1007/s00203-023-03553-5

Cited by 4 publications

(1 citation statement)

References 138 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Antibiotic resistance mechanisms can range from enzymatic degradation or inactivation of antimicrobial agents to alteration of the antimicrobial target sites [ 4 ]. In addition, more defensive strategies, such as extracellular matrix production or surface remodeling, can decrease the binding and uptake of antimicrobial agents [ 5 , 6 ]. Bacteria utilize their surface structures as protective barriers to increase resistance against antibiotics, detergents, antimicrobial peptides, and various host defense factors such as lysozymes, beta-lysin, leukocyte proteins, bile salts, and digestive enzymes [ 7 , 8 , 9 , 10 , 11 ].…”

Section: Introductionmentioning

confidence: 99%

The Two Faces of Bacterial Membrane Vesicles: Pathophysiological Roles and Therapeutic Opportunities

2023

View full text Add to dashboard Cite

Bacterial membrane vesicles (MVs) are nanosized lipid particles secreted by lysis or blebbing mechanisms from Gram-negative and -positive bacteria. It is becoming increasingly evident that MVs can promote antimicrobial resistance but also provide versatile opportunities for therapeutic exploitation. As non-living facsimiles of parent bacteria, MVs can carry multiple bioactive molecules such as proteins, lipids, nucleic acids, and metabolites, which enable them to participate in intra- and interspecific communication. Although energetically costly, the release of MVs seems beneficial for bacterial fitness, especially for pathogens. In this review, we briefly discuss the current understanding of diverse MV biogenesis routes affecting MV cargo. We comprehensively highlight the physiological functions of MVs derived from human pathogens covering in vivo adaptation, colonization fitness, and effector delivery. Emphasis is given to recent findings suggesting a vicious cycle of MV biogenesis, pathophysiological function, and antibiotic therapy. We also summarize potential therapeutical applications, such as immunotherapy, vaccination, targeted delivery, and antimicrobial potency, including their experimental validation. This comparative overview identifies common and unique strategies for MV modification used along diverse applications. Thus, the review summarizes timely aspects of MV biology in a so far unprecedented combination ranging from beneficial function for bacterial pathogen survival to future medical applications.

show abstract

Section: Introductionmentioning

confidence: 99%

The Two Faces of Bacterial Membrane Vesicles: Pathophysiological Roles and Therapeutic Opportunities

2023

View full text Add to dashboard Cite

show abstract

Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases

Irankhah,

Khorsand,

Naghibzadeh

et al. 2024

J. Bioinform. Comput. Biol.

View full text Add to dashboard Cite

Accurate knowledge of the genome, virus and bacteria that have invaded our bodies is crucial for diagnosing many human diseases. The field of bioinformatics encompasses the complex computational methods required for this purpose. Metagenomics employs next-generation sequencing (NGS) technology to study and identify microbial communities in environmental samples. This technique allows for the measurement of the relative abundance of different microbes. Various tools are available for detecting bacterial species in sequenced metagenomic samples. In this study, we focus on well-known taxonomic classification tools such as MetaPhlAn4, Centrifuge, Kraken2, and Bracken, and evaluate their performance at the species level using synthetic and real datasets. The results indicate that MetaPhlAn4 exhibited high precision in identifying species in the simulated dataset, while Kraken2 had the best area under the precision-recall curve (AUPR) performance. Centrifuge, Kraken2, and Bracken showed accurate estimation of species abundances, unlike MetaPhlAn4, which had a higher L2 distance. In the real dataset analysis with samples from an inflammatory bowel disease (IBD) research, MetaPhlAn4, and Kraken2 had faster execution times, with differences in performance at family and species levels among the tools. Enterobacteriaceae and Pasteurellaceae were highlighted as the most abundant families by Centrifuge, Kraken2, and MetaPhlAn4, with variations in abundance among ulcerative colitis (UC), Crohn’s disease (CD), and control non-IBD (CN) groups. Escherichia coli (E. coli) has the highest abundance among Enterobacteriaceae species in the CD and UC groups in comparison with the CN group. Bracken overestimated E. coli abundance, emphasizing result interpretation caution. The findings of this research can assist in selecting the appropriate short-read classifier, thereby aiding in the diagnosis of target diseases.

show abstract

Comprehensive Analysis of Virulence Genes, Antibiotic Resistance, Biofilm Formation, and Sequence Types in Clinical Isolates of Klebsiella pneumoniae

Nazari,

Hemmati,

Asghari

2024

Canadian Journal of Infectious Diseases and Medical Microbiolog

View full text Add to dashboard Cite

Background: The rise in multidrug‐resistant pathogens poses a formidable challenge in treating hospital‐acquired infections, particularly those caused by Klebsiella pneumoniae. Biofilm formation is a critical factor contributing to antibiotic resistance, enhancing bacterial adherence and persistence. K. pneumoniae strains vary in virulence factors, influencing their pathogenicity and resistance profiles. This study aimed to comprehensively analyze virulence factors, antibiotic resistance patterns, and biofilm formation in clinical isolates of K. pneumoniae from Hamadan hospitals. Moreover, the study explored the molecular epidemiological relationships among isolates using multilocus sequence typing (MLST) to uncover the genetic diversity associated with resistance and virulence.Materials and Methods: Between December 2022 and April 2024, 402 K. pneumoniae isolates were collected from clinical samples, including urine, tracheal aspirates, blood, wounds, and abscesses, in teaching hospitals in Hamadan. Initial culturing was performed on blood agar and MacConkey agar, and isolates were identified using biochemical tests. Antimicrobial susceptibility testing followed CLSI, employing the Kirby–Bauer disk diffusion method with 10 antibiotics. Biofilm formation was assessed using the microtiter plate method, and virulence genes were detected by PCR. MLST analysis was conducted on 10 selected isolates based on their virulence gene profiles and resistance patterns.Result: Of the 456 clinical isolates analyzed, 402 (88.15%) were identified as K. pneumoniae, predominantly isolated from tracheal samples (251/402, 62.44%), followed by urine (105/402, 26.12%), blood (30/402, 7.46%), wounds (15/402, 3.73%), and abscesses (1/402, 0.25%). Antibiotic resistance rates revealed high resistance to cefepime (356/402, 88.55%), imipenem (345/402, 85.82%), and ceftazidime (305/402, 75.87%), while resistance to amikacin (165/402, 41.04%) and piperacillin–tazobactam (75/402, 18.65%) was comparatively lower. Biofilm formation varied among the isolates, with 17/402 (4.22%) forming strong biofilms, 104/402 (25.87%) moderate biofilms, 180/402 (44.78%) weak biofilms, and 101/402 (25.12%) showing no biofilm production. Virulence gene analysis indicated high prevalence rates for mrkD (396/402, 98.50%), fimH1 (351/402, 87.31%), and entB (402/402, 100%), while genes like irp-1 (151/402, 37.56%) and irp-2 (136/402, 33.83%) were less common, and hylA and cnf-1 were absent. MLST analysis of 10 selected isolates identified sequence types ST147 (5/10, 50%), ST11 (3/10, 30%), and ST15 (2/10, 20%).Conclusion: K. pneumoniae demonstrates notable biofilm‐associated antibiotic resistance, supported by a significant association with XDR strains, along with a diverse array of virulence gene profiles. The study underscores the importance of understanding molecular epidemiology for effective management of hospital infections, emphasizing the need for targeted surveillance and infection control measures.

show abstract

Uropathogenic Escherichia coli endeavors: an insight into the characteristic features, resistance mechanism, and treatment choice

Cited by 4 publications

References 138 publications

The Two Faces of Bacterial Membrane Vesicles: Pathophysiological Roles and Therapeutic Opportunities

The Two Faces of Bacterial Membrane Vesicles: Pathophysiological Roles and Therapeutic Opportunities

Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases

Comprehensive Analysis of Virulence Genes, Antibiotic Resistance, Biofilm Formation, and Sequence Types in Clinical Isolates of Klebsiella pneumoniae

Contact Info

Product

Resources

About