Antibiotics-Basel最新文献

Background: Machine learning models have been shown to be a time-saving and cost-effective tool for peptide-based drug discovery. In this regard, different graph learning-driven frameworks have been introduced to exploit graph representations derived from predicted peptide structures. Such graphs are always derived by applying a Euclidean distance threshold between amino acid pairs, despite the fact that there is no evidence other than intuitive reasoning that supports the Euclidean distance as the most suitable.

Objective: In this work, we examined the use of different distance functions to derive graph representations from predicted peptide structures to train deep graph learning-based models to predict antiviral peptides.

Methods: To this end, we first analyzed how differently the closeness of the amino acids is characterized by different distance functions. Then, we studied the similarity between the graphs derived with several distance functions, as well as between them and random graphs. Finally, we trained several models with the best graph representations and analyzed how different they are regarding their predictions. Comparisons regarding state-of-the-art models were also performed.

Results and conclusion: We demonstrated that only using Euclidean distance thresholds is not sufficient criterion to build graphs representing structural features of predicted peptide structures, since other distance functions enabled building dissimilar graphs codifying different chemical spaces, which were useful in the construction of better discriminative models.

Background: Carbapenem-resistant Acinetobacter baumannii (CRAB) remains a major challenge in healthcare settings due to its persistence on inanimate surfaces and resistance to conventional cleaning methods. Bacteriophages (phages) represent a promising biocontrol option owing to their high specificity and lytic activity. Methods: This study evaluated the use of a personal hand-held vibrating mesh nebulizer (VMN) as a rapid and localized delivery platform for phage aerosols. Using two lytic phages (ϕ2, Podovirus; ϕ11, Myovirus), we assessed phage stability under different storage conditions, viability during VMN operation, and surface decontamination efficacy under varying spray parameters. Results: In saline, both phages showed optimal long-term stability at 4 °C, whereas storage at -20 °C resulted in a progressive reduction in infectivity exceeding 3 logs over the storage period. VMN aerosolization did not compromise viability. A 3 min spray achieved >99.9% surface reduction: ϕ2 was effective at 1 × 10⁷ PFU/mL, whereas ϕ11 required 1 × 10⁸ PFU/mL. Importantly, residual ϕ2 activity persisted for at least 24 h, preventing detectable recolonization under the assay conditions, while ϕ11 protection was limited to 6 h. Conclusions: These findings establish the hand-held sprayer as a practical, low-cost, and flexible approach to deliver viable phage aerosols, providing an effective complement to large-scale disinfection systems and offering a targeted strategy to enhance infection control in healthcare environments.

Background: In China, Carbapenem-resistant Klebsiella pneumoniae (CRKP) is dominated by sequence type 11 (ST11) harbouring KPC-2, with KL64 displacing KL47 and KL25 emerging. ST859 (ST11 variant) has caused outbreaks, but its epidemiology is unclear. Materials and Methods: A total of 99 non-duplicate CRKP isolates were collected from June to December 2024. Antimicrobial susceptibility was determined by broth microdilution. The genomic sequences of the strains were obtained using next-generation sequencing technology. Resistance genes, virulence loci, and plasmid replicons were identified with Kleborate, Abricate, and MOB-suite, respectively. Results: ST11 accounted for 63.64% and ST859 for 15.15%. All ST859 were KL19, while ST11 were mainly KL25 (60.32%) and KL64 (26.98%). 76.8% co-harbored carbapenemase and extended-spectrum beta-lactamase (ESBL) genes, with KPC-2 and CTX-M-65 being the predominant types. Susceptibility rates were 100% to tigecycline, and 78.79% to ceftazidime/avibactam. ST859 CRKP isolates exhibited higher phenotypic resistance to tetracycline and colistin than ST11 CRKP isolates (p < 0.05), and carrying LAP-2, QnrS1, QnrS10, and tet(A) more frequently. ST11-KL25 showed higher resistance to amikacin, gentamicin, and chloramphenicol, with increased prevalence of CTX-M-65, TEM-1, rmtB, catA2, and dfrA14 compared to ST11-KL64 (p < 0.05). IncF was the most prevalent replicon and both ST859 and ST11 CRKP carry conjugative resistance plasmids, and the host range is predominantly Enterobacterales. Conclusions: ST859-KL19 ranks second to ST11 with higher resistance to tetracyclines and colistin. ST11-KL25 may have already displaced ST11-KL64 as the predominant capsular type in Shanghai, with distinct resistance profiles between KL variants. Long-term, multicenter surveillance is urgently needed to delineate the evolutionary trajectory and clinical impact of these emerging clones.

Background: The emergence of antibiotic-resistant bacteria is one of the top health concerns. Escherichia coli is a Gram-negative bacterium that commonly causes severe infections. However, this research exposed its antibiotic-producing potential.

Methods: Rifampicin-resistant mutants of E. coli C91 were generated to activate cryptic BGCs. Mutants (C91-R1, R2 and R3) were tested for antimicrobial production using agar-well diffusion assays. Metabolite profiling was performed by LC-MS/MS. Siderophore production was tested by construction of a Δycao deletion mutant. Growth of this mutant was assessed under iron-limited conditions versus iron-rich conditions using dipyridyl. qRT-PCR was used to analyze gene expression entB, mcmA and mchF. Genome mining was performed using antiSMASH and BAGEL4.

Results: Compared to the wild type, Mutant C91-R1(S531L) displayed clear antibacterial activity against Staphylococcus aureus. LC-MS/MS revealed unique metabolites, including a novel peak at m/z 410.5, specific to the mutant C91-R1. A reduction in siderophore production of 61% was demonstrated in the Δycao mutant, and downregulation of entB, mcmA and mchF. Conclusions: Genome mining predicted non-ribosomal peptide, thiopeptide and polyketide BGCs. E. coli C91 offers antibiotic-producing potential that can be activated through ribosome-engineering-type approaches. Moreover, E. coli C91-R1 has unique metabolites and is considered as a promising candidate for novel antibiotic discovery.

Drug-resistant Klebsiella pneumoniae and related Enterobacterales represent an escalating global public health threat, increasingly limiting therapeutic options in both healthcare- and community-associated infections. This review summarizes how resistance in K. pneumoniae emerges from the synergy of intrinsic barriers and acquired determinants. Key molecular mechanisms include reduced permeability via porin remodeling (notably OmpK35/OmpK36), multidrug efflux (e.g., AcrAB-TolC and OqxAB), and enzymatic drug inactivation driven by extended-spectrum beta-lactamases and carbapenemases (e.g., KPC, OXA-48-like enzymes, and metallo-beta-lactamases). We also highlight clinically meaningful pathways underlying polymyxin/colistin resistance, including mgrB inactivation and PhoPQ/PmrAB-mediated lipid A modification. In addition to stable genetic resistance, adaptive programs can shape transient tolerance and persistence, including stress responses that modulate gene expression under antibiotic and host-imposed pressures. The ability of these organisms to form biofilms, particularly on medical devices, further complicates treatment and eradication. Finally, we discuss therapeutic implications and current options and limitations-including novel beta-lactam/beta-lactamase inhibitor combinations and siderophore cephalosporins-and emphasize the importance of aligning therapy and surveillance with the underlying resistance mechanisms and circulating high-risk lineages.

To address the challenges in wound healing, clinical management increasingly demands targeted, adaptive, responsive, and patient-centered strategies. This is especially true for wounds characterized by delayed healing and a high risk of infection. Advances in regenerative medicine and biomaterial technologies are fostering the development of multifunctional approaches that integrate tissue regeneration, antibacterial/antibiofilm activity, immunomodulation, and real-time monitoring. This paper surveys emerging platforms, including both natural and synthetic scaffolds, hydrogels enriched with platelet-derived growth factors, glycosaminoglycan mimetics, bioactive peptides (such as GHK-Cu and antimicrobial peptides), nanoscaffolds, and stimuli-responsive systems. The paper also explores cutting-edge technologies such as water-powered, electronics-free dressings that deliver localized electrical stimulation; biodegradable bioelectric sutures that produce self-sustained mechano-electrical signals; and sensory bandages that monitor pH, moisture, temperature, and bacterial contamination in real-time while enabling on-demand drug release with pro-regenerative, antibacterial, and other therapeutic functionalities. Further therapeutic approaches include natural matrices, exosomes, gene editing, 3D bioprinting, and AI-assisted design. Particular attention is paid to orthopedic applications and orthopedic implant infection. A brief section addresses the still unresolved challenge of articular cartilage regeneration. Interdisciplinary innovation, integrating insights from molecular biology through engineering, plays a central role in translating novel strategies into tailored, clinically effective wound management solutions.

Streptococcus agalactiae are bacteria that can cause a range of infections, some of them life-threatening. Currently, antimicrobial resistance has become a global problem that puts public health at risk. Despite the widespread use of β-lactams, penicillin remains the first-line antimicrobial for the treatment of invasive S. agalactiae infections. However, reduced susceptibility and resistance to penicillin have been identified in several countries. Penicillin-binding proteins, mainly PBP2X, have been associated with reduced susceptibility to β-lactams in streptococci. The aim of this review is to summarize currently published data on penicillin-binding proteins in S. agalactiae and penicillin susceptibility, highlighting the increasing number of strains with reduced susceptibility and resistance to penicillin commonly used in the prophylaxis and treatment of invasive infections by this pathogen. Data on invasive S. agalactiae strains with high levels of penicillin resistance have been found in Japan, the United States, Canada, and Africa. The data on antibiotic resistance are alarming and require increased monitoring of strains with reduced penicillin susceptibility, as well as preventive control measures to avoid the spread of resistant mutant strains.

Background: Difficult-to-treat resistant Pseudomonas aeruginosa (DTR-PA) infections are associated with high morbidity and mortality, but data on prognostic factors remain limited. Given the limited real-world data on outcomes of DTR-PA infections, we aimed to identify clinical predictors of mortality and response to therapy in this setting. Methods: We conducted a single-center retrospective cohort study of 51 patients with DTR-PA infections. The primary endpoint was 30-day all-cause mortality; secondary endpoints were clinical and microbiological cure at end of therapy. An exploratory analysis evaluated 30-day infection-related mortality. Logistic regression models (univariable, multivariable and Firth bias-reduced) were used to identify independent predictors. Results: Median age was 64 years (IQR 22); 63% were male and 71% were in the ICU at infection onset. Sepsis occurred in 80% and septic shock in 45%. Thirty-day all-cause mortality was 49% (25/51). According to multivariable analysis, septic shock was an independent predictor of mortality (aOR 5.52, 95% CI 1.04-29.27; p = 0.045) as younger age (aOR 1.06, 95% CI 1.00-1.12; p = 0.052), whereas targeted therapy with ceftazidime/avibactam or ceftolozane/tazobactam is a protective factor (aOR 0.15, 95% CI 0.02-1.17; p = 0.070) did not reach significance in the final model. Clinical cure occurred in 33% (17/51) and was negatively associated with device burden and bloodstream infection, whereas microbiological cure (45%, 23/51) was more likely with targeted therapy and absence of sepsis. The exploratory analysis of infection-related mortality (35%) showed similar predictors. Conclusions: DTR-PA infections are associated with high mortality. Septic shock and older age predict death, while the use of novel β-lactam/β-lactamase inhibitors is associated with improved outcomes. Early recognition of severe illness and timely administration of active therapy may improve survival in these infections.

Ventilator-associated pneumonia (VAP) remains the most frequent ICU-acquired infection and a major driver of antimicrobial exposure. Historically, clinicians treated patients for 10-14 days or longer, particularly when multidrug-resistant organisms were suspected. Current evidence from randomized trials and meta-analyses now supports shorter-course therapy (~7 days) for most immunocompetent patients with VAP who demonstrate clinical improvement. Mortality and treatment failure are not increased when compared with longer regimes. The REGARD-VAP trial demonstrated the non-inferiority of individualized ≤7-day therapy compared with conventional longer courses. This remained true even in cohorts rich in non-fermenting Gram-negative bacilli (NF-GNB) and carbapenem-resistant organisms while markedly reducing antibiotic-related toxicity. North American and European guidelines recommend 7-8 days as the default duration, with individualized extension for slow clinical response, bacteremia, uncontrolled foci, or profound immunosuppression. Additionally, biomarker-guided discontinuation, particularly serial procalcitonin (PCT), may reduce antibiotic days when used to enrich clinical assessment. This narrative review synthesizes guideline recommendations, trial evidence, biomarker-guided stewardship, and pathogen- and patient-specific scenarios to provide a practical framework for intensivists: treat until infection is controlled and the patient is improving, usually about 1 week, and extend therapy only with clear justification.

Background:Stenotrophomonas maltophilia is an intrinsically multidrug-resistant, biofilm- forming, non-fermenter increasingly implicated in hospital-acquired infections. Evidence from non-cystic fibrosis populations, especially in the Middle East, remains sparse. Methods: We conducted a retrospective observational cohort study at a tertiary academic center (Al-Khobar, Saudi Arabia) spanning 1 May 2001-30 April 2023. Hospitalized adults (≥18 years) with culture-confirmed, clinically diagnosed S. maltophilia infection and ≥72 h of antibiotic therapy were included. The primary outcome was all-cause mortality (14-day, 30-day, 1-year). Secondary outcomes were clinical response, microbiological eradication, and infection recurrence. Predictors of 30-day mortality were assessed using multivariable logistic regression; 14-day mortality was analyzed by Kaplan-Meier/log-rank according to susceptibility-guided versus alternative therapy. Results: Of 539 patients with positive cultures, 436 met the inclusion criteria. Mean age was 60.5 ± 19.3 years; 62.2% were male. Most infections were hospital-acquired (92.9%); pneumonia composed 64.7% and bloodstream infection 15.4%. Polymicrobial growth occurred in 55.5% (predominantly Gram-negative co-isolation). Susceptibility was 95.1% to trimethoprim-sulfamethoxazole, 76.4% to levofloxacin, and 43.6% to ceftazidime. Mortality at 14 days, 30 days, and 1 year was 22.8%, 37.9%, and 57.2%, respectively. On multivariable modelling, intensive care unit (ICU) admission, leukocytosis, neutrophilia, anemia, and thrombocytopenia independently predicted 30-day mortality. Susceptibility-guided therapy was associated with improved 14-day survival (log-rank p = 0.033). Conclusions: In this large, long-running non-cystic fibrosis cohort, host acuity and early alignment of treatment to susceptibility data were dominant drivers of outcome. High polymicrobial burden and limited reliably active agents underscore the need for meticulous stewardship, robust infection prevention, and cautious interpretation of S. maltophilia antimicrobial susceptibility testing.