bims-fagtap 2025-11-23 papers

bims-fagtap

Biomed News

on Phage therapies and applications

Issue of 2025–11–23
34 papers selected by
Luca Bolliger, lxBio

Pathogen-Phage Geomapping to Overcome Resistance.
Resolution of acute rejection in a bilateral double-lung transplanted cystic fibrosis patient following phage intervention.
Inactivating conditions of therapeutic mycobacteriophages.
Bacteriophage density influences the rate of resistance evolution.
Advances in combating antimicrobial resistance in MRSA: a comprehensive review on nanotechnology and phage therapy.
Directed evolution of phages in biofilms enhances Pseudomonas aeruginosa control through improved lipopolysaccharide recognition.
Host-specificity and therapeutic potential of novel Escherichia coli-targeting bacteriophages for bovine mastitis control.
The gut microbiome as a major source of drug-resistant infections: emerging strategies to decolonize and target the gut reservoir.
KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family.
Disarming Salmonella virulence with 32H-hilE anti-virulence bacteriophage.
Eliminating the type I restriction endonuclease from Pseudomonas aeruginosa PAO1 for optimized phage isolation.
Optimizing phage-antibiotic combinations: impact of administration order against daptomycin non-susceptible (DNS) MRSA clinical isolates.
Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates.
A review of technological advances in the management of bacterial, fungal, viral, and Acanthamoeba keratitis.
ABCD-type phage cocktail targeting distinct LPS receptor sites demonstrates superior efficacy against multidrug-resistant Salmonella.
Novel lytic phages improve the antibiofilm activity of dalbavancin, daptomycin, and fosfomycin against vancomycin-resistant enterococci.
Beyond traditional antibacterial agents: Novel approaches to combat resistant pathogens.
Carbon nanomaterials: Exploring new frontiers in wound healing therapy.
Stage-Responsive Multifunctional Microneedle Patches for Enhanced Biofilm Penetration and Accelerated Healing of Bacterial Infected Skin Wounds.
Harnessing Artificial Intelligence to Transform Clinical Trials and Cancer Care: Opportunities and Challenges.
Advancing chronic wound care with near-infrared spectroscopy imaging: clinical applications, measurement parameters, and insights into healing dynamics.
Effectiveness of bilayered dermal substitutes for wound healing in adults: a systematic review protocol.
Dual-layer microneedles for immunomodulation and infection-responsive therapy in diabetic foot ulcers.
Advances in nanomaterials-assisted drug delivery, diagnosis, and action towards drug-resistant Mycobacterium.
Insights into the molecular determinants of host specificity in Pseudomonas aeruginosa-infecting phages: a structural and functional analysis of tail fibre proteins.
From Design to Closure: Artificial Intelligence Transforming Clinical Research.
Comparative assessment of annotation tools reveals critical antimicrobial resistance knowledge gaps in Klebsiella pneumoniae.
Cold Atmospheric Plasma Therapy for Diabetic Foot Ulcers: A Systematic Review and Meta-Analysis of Randomised Controlled Trials.
Complete genome sequence of lytic Pseudomonas aeruginosa phage vB_PaeS_Tums_P6.
Bionic meta microneedle photonic crystal patch for advanced wound care.
Efficacy and Safety of Negative Pressure Wound Therapy in Diabetic Foot Ulcers: A Cross-Sectional Analysis of Overlapping Meta-Analyses.
A retrospective comparative study of helium-neon laser combined with ultrasonic debridement in improving healing of chronic non-healing wounds.
Anti-staphylococcal chitosan-alginate-lyophilized platelet-rich fibrin wound dressings for infected wound healing.
Janus Hydrogel Microparticles with Tea Polyphenol/Melanin Nanoparticles Integration from Microfluidics for Wound Healing.

bioRxiv. 2025 Oct 01. pii: 2025.10.01.679739. [Epub ahead of print]

Pathogen-Phage Geomapping to Overcome Resistance.

Camilla Do, Keiko C Salazar, Justin R Clark, Austen L Terwilliger, Paul Ruchhoeft, Paul Nicholls, Anthony W Maresso.

The rise of antibiotic resistance has renewed interest in bacteriophages as therapeutic alternatives. However, co-evolution of phage and bacteria will naturally give rise to phage-resistant pathogens, complicating phage therapy efforts. A critical bottleneck in the production of phage therapeutics is the discovery of virulent phages against resistant pathogens. Conventional methods for discovery are time-consuming, biased, and laborious, limiting the potential for identifying suitable phage candidates. To overcome these limitations, we combined small-volume environmental sampling with 16S rRNA sequencing to identify reservoirs where bacterial hosts co-exist with their phage predators. This strategy, which we term geographical phage mapping (geΦmapping), pinpoints ecological "hotspots" for targeted phage hunting. We further developed a portable phage hunting device (ΦHD) that generates highly enriched phage concentrates directly from these reservoirs. By integrating geΦmapping with high-throughput enrichment, we constructed the RΦ library, a diverse collection of novel phages targeting resistant pathogens.

DOI: https://doi.org/10.1101/2025.10.01.679739
ASM Case Rep. 2025 Sep;pii: e00058-24. [Epub ahead of print]1(5):

Resolution of acute rejection in a bilateral double-lung transplanted cystic fibrosis patient following phage intervention.

Marco Pardo-Freire, Mireia Bernabéu-Gimeno, Benjamin K Chan, Paul E Turner, Isabel Sánchez-Romero, Myriam Aguilar-Pérez, Marta Erro-Iribarren, Pilar Domingo-Calap.

   Background: Antimicrobial resistance is a major threat to human health worldwide, requiring investigation into alternative therapeutics such as phage therapy. Phages have been used to treat numerous multidrug-resistant infections recently, particularly in people with cystic fibrosis (CF) who are predisposed to infection from Pseudomonas aeruginosa.
Case Summary: Here, we report the use of phage therapy to treat a chronic P. aeruginosa infection in a 44-year-old woman with CF who underwent bilateral lung transplantation. This individual experienced acute rejection and deteriorating lung function, possibly worsened as a consequence of a P. aeruginosa infection. Phage therapy using phage vB_Pae_10 was administered via nebulizer alongside standard antimicrobials in two 10-day courses. Clinical and microbiological assessments indicated an initial reduction in bacterial load along with an improvement in lung function. Phage therapy was well-tolerated with no adverse events reported. The patient showed sustained clinical improvement, including mucus clearance, enhanced pulmonary function, and resolution of acute rejection.
Conclusion: This case underscores the potential of phage therapy to complement traditional treatments in managing chronic bacterial infections in CF patients, though further studies are needed to optimize treatment protocols and understand the role of phages in modulating the bacterial population.

Keywords:  antimicrobial resistance; cystic fibrosis; lung transplantation; phage therapy

DOI:  https://doi.org/10.1128/asmcr.00058-24
bioRxiv. 2025 Sep 30. pii: 2025.09.30.679648. [Epub ahead of print]

Inactivating conditions of therapeutic mycobacteriophages.

Andrew Wiggins, Umar N Chaudhry, Fabiana Bisaro, Addison Lueck, Alan A Schmalstig, Graham F Hatfull, David B Hill, Miriam Braunstein.

There is a need for new therapies to treat drug resistant nontuberculous mycobacteria (NTM) disease. Bacteriophages (phages), which are viruses that infect and kill bacteria, are actively being explored as an alternative approach for treating mycobacterial diseases. Several compassionate-use cases of phage therapy for drug resistant NTM infections exhibit favorable outcomes. To further the development of phage therapy it is important to recognize and avoid conditions that negatively impact phage activity during phage production, storage, formulation, or treatment. Conversely, there is a need to inactivate free phages in certain preclinical phage therapy experiments. In this study, we investigated three mycobacteriophages BPsΔ 33 HTH-HRM10, Muddy, and ZoeJΔ 45 from compassionate-use NTM treatment cases for their sensitivity to a variety of conditions that included temperature, acid pH, detergents, mucus, and phage inactivating buffers. Several conditions resulted in dramatic and rapid reductions in the level of active phage while others had no effect. We also observed different sensitivities between the phages. The results provide valuable information to support further investigation and development of these phages as therapeutics.

DOI: https://doi.org/10.1101/2025.09.30.679648
bioRxiv. 2025 Oct 05. pii: 2025.10.05.680490. [Epub ahead of print]

Bacteriophage density influences the rate of resistance evolution.

Tuan Phan, Anuja Shrestha, Jacob Schow, Craig R Miller, Tracey L Peters, James T Van Leuven.

The antagonistic relationship between bacteria and bacteriophages (phages) drives genetic changes that result in phage resistance. Phage resistance mutations arise in natural microbial communities and during the treatment of diseases with phages (phage therapy), making it important to understand the dynamics of resistance acquisition. It is well-established that when bacteria are challenged with phages in dense liquid cultures, bacterial populations quickly become dominated by phage-resistant variants. However, these conditions-well-mixed liquid cultures with high phage concentrations-are not necessarily common in microbial ecosystems. We developed a simplified mathematical model of phage resistance evolution to explore how phage and host concentration impact the dynamics of resistance evolution. The model was parameterized with microbial growth data from two pathogens and their phages: Pseudomonas aeruginosa and Paenibacillus larvae . Our analyses revealed two fundamental discoveries about resistance evolution. First, phage resistance evolution is predictably governed by a core set of parameters that exhibited high resolution across all bacterial strains: intrinsic growth rate of susceptible bacteria, resistance acquisition rate, fitness cost of resistance, and phage adsorption rate. Second, competitive interactions and fitness costs are the primary drivers of resistance patterns rather than intrinsic mutation rates. We observed three distinct growth patterns-delayed growth, two phase growth, and complete suppression-corresponding to specific parameter regimes as initial phage concentration increased. Two phase growth patterns emerged when competitive dynamics remained balanced, enabling coexistence of susceptible and resistant populations. Complete suppression patterns occurred when low proliferation thresholds combined with extreme competitive asymmetries created unsustainable conditions for resistant bacteria. These findings demonstrate that phage resistance evolution is fundamentally an ecological process where competitive context determines outcomes independently of mutation capacity, with important implications for phage therapy design.

DOI: https://doi.org/10.1101/2025.10.05.680490
Antonie Van Leeuwenhoek. 2025 Nov 17. 118(12): 196

Advances in combating antimicrobial resistance in MRSA: a comprehensive review on nanotechnology and phage therapy.

Deepak Chandra Joshi, Mayuri Bapu Chavan, Sunita Walia Tiwari, Suprabha Devi.

   AIM: Methicillin-resistant Staphylococcus aureus (MRSA) is a global public health concern owing to its resistance to conventional antibiotics. To overcome this challenge, innovative strategies such as nanotechnology and phage therapy have emerged as promising alternatives to conventional antimicrobial treatments.
METHODS: This review explores the dual approach of using nanoparticles (NPs) and bacteriophages to treat MRSA. NPs, such as silver, gold, and zinc oxide, exhibit antimicrobial effects through mechanisms including membrane disruption, the generation of reactive oxygen species (ROS), and biofilm degradation. Phage therapy uses bacteriophages for the targeted lysis of MRSA. Additionally, CRISPR-Cas9 gene editing targeting the mecA gene and efflux pump inhibition strategies are discussed as adjunctive therapies for MRSA infections.
RESULTS: Studies have shown that synergistic nanocomposites can enhance the efficacy of existing antibiotics against resistant strains. Engineered phages have demonstrated expanded host ranges, improved biofilm degradation, and resistance evasion to these mechanisms. ROS production by nanoparticles leads to oxidative stress and bacterial death. Blocking bacterial efflux pumps increases intracellular drug retention and improves therapeutic outcomes.
DISCUSSION: The combination of nanotechnology and phage therapy offers a complementary approach, with nanotechnology providing broad-spectrum activity and phages providing specificity and adaptability to the host. Challenges such as nanoparticle toxicity, environmental impact, and potential phage resistance require interdisciplinary research efforts and improved regulatory frameworks.
CONCLUSION: Integrating advanced nanotechnology and phage therapy into healthcare systems could transform the MRSA treatment landscape. Future research guided by systems biology and personalized medicine principles will be crucial for mitigating antimicrobial resistance and ensuring equitable access to novel therapeutics.

Keywords:  Efflux pumps; MRSA; Nanomaterials; Nanotechnology; Phage therapy; Silver nanoparticles

DOI:  https://doi.org/10.1007/s10482-025-02208-3
Nat Commun. 2025 Nov 20. 16(1): 10219

Directed evolution of phages in biofilms enhances Pseudomonas aeruginosa control through improved lipopolysaccharide recognition.

Luciana Meneses, Lucie Valentová, Sílvio B Santos, Jelena Erdmann, Aurélie Crabbé, Pavel Plevka, Susanne Häussler, Diana P Pires, Tom Coenye, Joana Azeredo.

Pseudomonas aeruginosa is a leading cause of chronic lung infections in cystic fibrosis (CF) patients. While bacteriophages hold potential as a treatment for antibiotic-resistant infections, the complex structure and heterogeneity of P. aeruginosa biofilms pose significant challenges to phage therapy. In this study, we investigate the adaptive evolution of the Pbunavirus phage PE1 to biofilms formed by a CF-derived P. aeruginosa isolate. Our findings reveal that biofilm-adapted PE1 mutants exhibit enhanced efficacy in controlling biofilms in vitro under conditions mimicking the CF lung environment. This improvement is attributed to the mutants' increased ability to recognize the diverse populations within the biofilm. Using a combination of cryo-EM, lipopolysaccharide (LPS) profiling, and adsorption assays, we demonstrate that mutations in tail fiber and baseplate genes of the phage improve adsorption and enable recognition of truncated LPS variants. This study highlights the critical role of biofilm heterogeneity in limiting phage effectiveness, identifies mechanisms to overcome this barrier, and pinpoints specific genomic targets for engineering phages tailored for therapeutic applications in CF patients.

DOI: https://doi.org/10.1038/s41467-025-65014-5
Sci Rep. 2025 Nov 20. 15(1): 41071

Host-specificity and therapeutic potential of novel Escherichia coli-targeting bacteriophages for bovine mastitis control.

Diderich Jacob, Antoine Céline, Cornet Thomas, Toussaint Cédric, Saulmont Marc, Helleputte Thibault, Thiry Damien.

  E. coli mastitis is a major production disease in dairy cattle and requires alternative treatments to antibiotics. In this context, phages are of growing interest, but their host specificity remains a challenge in therapy. This study aimed to characterize eight newly isolated phages for the control of E. coli mastitis, to assess their efficacy in milk and to investigate their specificity. Physicochemical characterization of the phages was performed, followed by in vitro stability and lytic activity assays in raw and heat-treated milks. Genome sequencing of phages and bacteria was performed to investigate phage attachment. Phage stability was maintained across physiological pH and temperature ranges, as well as in raw milk. Phage lytic activity demonstrated bacterial decreases below detection level, but regrowth occurred in raw milk after 5 h of incubation with 3/8 phages. A narrow host range was linked to the diversity of the bacterial collection and to the presence of two receptor-binding proteins among Tevenvirinae. Indeed, structural analysis of the proteins revealed a variable region in the long tail fiber and a conserved short tail fiber. In conclusion, phage specificity was mainly associated with the long tail fiber and milk components didn't hinder the efficacy of phages to control bovine mastitis, although resistance should be investigated.

Keywords:   Escherichia coli (E. coli); Bacteriophage; Bovine mastitis; Host-specificity; Milk; Receptor-binding protein

DOI:  https://doi.org/10.1038/s41598-025-25008-1
Front Cell Infect Microbiol. 2025 ;15 1692582

The gut microbiome as a major source of drug-resistant infections: emerging strategies to decolonize and target the gut reservoir.

Ishrya Sharma, Drishya Sudarsanan, Shannon Moonah.

  Infections caused by antimicrobial-resistant bacteria represent a significant global health crisis that continues to worsen, creating an urgent need for alternative treatment and prevention strategies. A major source of drug-resistant bacteria is the human gut. The gut microbiota consists of bacteria that are frequently exposed to antibiotics, leading to selective pressure that promotes the development of resistant strains such as carbapenem-resistant Enterobacterales (CRE) and vancomycin-resistant enterococci (VRE). These drug-resistant bacteria can spread from the gut to other body sites, leading to hard-to-treat and potentially life-threatening infections such as bacteremia, surgical site infections, and urinary tract infections. Targeting the gut reservoir is essential in the fight against antimicrobial resistance. In this review, we focus on emerging non-antibiotic strategies aimed at eliminating drug resistant bacteria from the gut before they cause invasive infections, with particular emphasis on clinical evidence. Approaches discussed include fecal microbiota transplantation, bacteriophage therapy, antimicrobial peptides, probiotics, and dietary interventions. Optimizing these strategies, while continuing to explore newer approaches, will be essential to combat the growing threat of drug-resistant infections.

Keywords:  antibiotic resistance; antimicrobial pepides; bacteria; bacteriophage; dietary interventions; fecal micriobiota transplantation; gut microbiome; probiotics

DOI:  https://doi.org/10.3389/fcimb.2025.1692582
Nucleic Acids Res. 2025 Nov 13. pii: gkaf1122. [Epub ahead of print]53(21):

KlebPhaCol: a community-driven resource for Klebsiella research identified a novel phage family.

Daniela Rothschild-Rodriguez, Kai S Lambon, Simran Krishnakant Kushwaha, Sofya K Garushyants, Moritz Ertelt, Agnieszka Latka, Ana Rita Costa, Anna Mantzouratou, Claire King, Dimitri Boeckaerts, Elizabeth Sheridan, Eugene V Koonin, Francesca Merrick, Francis Drobniewski, Ilaria De Angelis, Kordo Saeed, Macy Martin, J Mark Sutton, Matthew E Wand, Michael Andrew, Morgen Hedges, Stan J J Brouns, Pieter-Jan Haas, Sophie T Lawson, Stephen M E Fordham, Yan-Jiun Lee, Yi Wu, Yves Briers, Peter Braun, Peter R Weigele, Franklin L Nobrega.

The growing threat of multidrug-resistant Klebsiella pneumoniae, coupled with its role in gut colonisation, has intensified the search for new treatments, including bacteriophage therapy. Despite increasing documentation of Klebsiella-targeting phages, clinical applications remain limited, with key phage-bacteria interactions still poorly understood. A major obstacle is fragmented access to well-characterised phage-bacteria pairings, restricting the collective advancement of therapeutic and mechanistic insights. To address this gap, we created the Klebsiella Phage Collection (KlebPhaCol), an open resource comprising 52 phages and 74 Klebsiella isolates, characterised at phenotypic and genomic levels. These phages span six families-including a novel family, Felixviridae, associated with the human gut-and target 20 sequence types (including ST258, ST11, and ST14) and 19 capsular-locus types (including KL1 and KL2), across 6 Klebsiella species. Freely accessible at www.klebphacol.org, KlebPhaCol invites the scientific community to both use and contribute to this resource, fostering collaborative research and a deeper understanding of Klebsiella-phage interactions beyond therapeutic use.

DOI: https://doi.org/10.1093/nar/gkaf1122
Microbiol Res. 2025 Nov 10. pii: S0944-5013(25)00355-6. [Epub ahead of print]303 128396

Disarming Salmonella virulence with 32H-hilE anti-virulence bacteriophage.

Jinwoo Kim, Haejoon Park, Young Hyun Jung, Ho Jae Han, Doyeon Kim, Sangryeol Ryu, Minsik Kim.

  As the development of new antibiotics struggles with the continuous emergence of drug-resistant bacteria, targeting bacterial virulence factors instead of viability has been proposed as one of the alternative approaches to combat the pathogens. Here, we genetically engineered the temperate phage SPC32H to serve as a delivery vehicle for key negative regulators of Salmonella virulence to inhibit Salmonella infection. Negative regulator genes associated with Salmonella pathogenicity island 1 (SPI1), hilE, csrA, and lrp, were inserted into the phage SPC32H genome and expressed under a strong constitutive promoter. When Salmonella cells lysogenized by the engineered phages were exposed to the virulence-inducing condition, the expression of key positive regulators and major virulence factors associated with SPI1 was significantly reduced. Furthermore, in a murine early-intervention model, oral administration of the engineered phage 32H-hilE shortly after a lethal Salmonella challenge led to a significant increase in survival. No noticeable side effects were observed in mice treated with the engineered phage alone. These results suggest the relevance of the engineered phages that suppress the Salmonella virulence network as alternative anti-Salmonella agents without resistance concerns. This proof-of-concept study of anti-virulence phages could open a new avenue for controlling pathogenic bacteria using engineered temperate phages as vectors of anti-virulence factors.

Keywords:  Anti-virulence; Engineered phage; Gene delivery; Phage therapy; Salmonella; Temperate phage

DOI:  https://doi.org/10.1016/j.micres.2025.128396
Microbiology (Reading). 2025 Nov;171(11):

Eliminating the type I restriction endonuclease from Pseudomonas aeruginosa PAO1 for optimized phage isolation.

Ellie J Tong, Kate A Bickerton, Alina J Creber, Steven L Porter, Ben Temperton.

  Phage therapy is a promising treatment for multidrug-resistant bacterial infections. Due to their high host specificity, phages must be matched to the target clinical strains. Efficiently identifying appropriate phages and producing sufficient titres for clinical use requires comprehensive phage libraries and multiple propagation hosts. An idealized system would use a highly promiscuous bacterial host to isolate a broader range of phages and streamline optimized phage production. Anti-phage defences constrain bacterial host promiscuity, such as restriction-modification systems that recognize and cleave foreign DNA. Here, the type I restriction endonuclease, HsdR, was deleted from Pseudomonas aeruginosa PAO1 to make a more promiscuous phage isolation and propagation host. Removal of this endonuclease more than doubled the efficiency of phage propagation on solid media, improved yields from hard-to-propagate phages in liquid bulk-ups and yielded seven times more phages from freshwater samples than wild-type PAO1 - an important step in producing an optimized P. aeruginosa strain for isolating and propagating phages for clinical phage therapy.

Keywords:  Pseudomonas aeruginosa; anti-phage defence; hsdR; phage isolation; phage therapy; restriction-modification

DOI:  https://doi.org/10.1099/mic.0.001634
Antimicrob Agents Chemother. 2025 Nov 18. e0069925

Optimizing phage-antibiotic combinations: impact of administration order against daptomycin non-susceptible (DNS) MRSA clinical isolates.

Callan R Bleick, Sean R Van Helden, Andrew D Berti, Rita Richa, Susan M Lehman, Arnold S Bayer, Michael J Rybak.

  The rise of bacterial resistance has driven the exploration of novel therapies, such as bacteriophage-antibiotic cocktails (PACs), which have shown in vitro promise against resistant pathogens, including daptomycin non-susceptible-methicillin-resistant Staphylococcus aureus (DNS-MRSA) strains. While daptomycin has been a cornerstone for treating MRSA bacteremia and vancomycin-refractory infective endocarditis, the emergence of DNS-MRSA presents a significant challenge due to high morbidity, mortality, and rapid intrinsic resistance development. Phages, Intesti13 and Sb-1, were selected for their unique host range and activity against sixteen DNS-MRSA strains. Synergy with antibiotics was assessed via growth suppression curves and 24-hour time-kill assays (TKAs) across varying administration sequences and minimum inhibitory concentration (MIC) increments. Selected regimens were further assessed in an ex vivo simulated endocardial vegetation (SEV) model, with pharmacokinetic analyses confirming target antibiotic concentrations. In the ex vivo SEV model, simultaneous PAC administration using daptomycin ± phage showed superior bactericidal activity over sequential treatments in isolate C6 (P < 0.01). Similarly, in the same model, C2 reached detection limits within 48 h and remained suppressed for 120 h (P < 0.0037). Sequential outcomes varied by phage-antibiotic order and antibiotic choice. Simultaneous and phage-first regimens outperformed antibiotic-first, especially in 24 h TKAs, but showed variability at lower MICs and between in vitro and ex vivo settings. This study highlights PAC's potential for DNS-MRSA treatment, emphasizing the importance of administration timing. The observed differences across clinical strains emphasize the need for strain-specific evaluations and a deeper understanding of phage-antibiotic interactions to optimize therapy. Future research must focus on expanding phage diversity, refining protocols, and clinically validating sequential strategies to enhance PAC efficacy.

Keywords:  DNS; MRSA; PACs; administration timing; antibiotic resistance; bacteriophage therapy; combination therapy; order effects; phage-antibiotic interactions

DOI:  https://doi.org/10.1128/aac.00699-25
Nat Commun. 2025 Nov 19. 16(1): 9903

Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates.

Pooja Ghatbale, Alisha Blanc, Andrew Sue, Jesse Leonard, Monica Bates, Andrew G Garcia, Joshua Hensley, Danielle Devequi Gomes Nunes, Nicole Hitchcock, Job Shiach, Roberto Bardaró, Govind Sah, Chandrabali Ghose, Katrine L Whiteson, Robert T Schooley, Richard Allen White, Ana G Cobián Güemes, Justin R Meyer, David T Pride.

Resistance to antibiotics is approaching crisis levels for organisms such as the ESKAPEE pathogens (includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli) that often are acquired in hospitals. These organisms sometimes have acquired plasmids that confer resistance to most if not all beta-lactam antibiotics. We have been developing alternative means for dealing with antibiotic resistant microbes that cause infections in humans by developing viruses (bacteriophages) that attack and kill them. One of these pathogens, K. pneumoniae, has one of the highest propensities for antimicrobial resistance. We identified many phages that have lytic capacity against limited numbers of clinical isolates, and through experimental evolution over the course of 30 days, were able to vastly expand the host ranges of these phages to kill a broader range of clinical K. pneumoniae isolates including MDR (multi-drug resistant) and XDR (extensively-drug resistant) isolates. Most interestingly, they were capable of inhibiting growth of clinical isolates both on solid and in liquid medium over extended periods. That we were able to extend the host ranges of multiple naïve antibiotic resistant K. pneumoniae through experimental phage evolution suggests that such a technique may be applicable to other antibiotic-resistant organisms to help stem the tide of antibiotic resistance and offer further options for medical treatments.

DOI: https://doi.org/10.1038/s41467-025-66062-7
Clin Exp Optom. 2025 Nov 16. 1-11

A review of technological advances in the management of bacterial, fungal, viral, and Acanthamoeba keratitis.

Tanzina Akter, Shyam Mishra Baishnab, Meseret Damtie, Srikanth Dumpati, Teshome Belachew Eshete, Suleman Irfan, Mukesh Kumar, Manjulatha Sara, Umme Laila Urmi, Mark Willcox.

  Microbial keratitis is a major cause of monocular blindness worldwide. Trauma and contact lens wear are major risk factors. Bacteria are a major cause, but fungi, viruses, and Acanthamoeba can also cause the disease. Therapeutic options are dwindling with the rise of antimicrobial resistance in all of these microbes, but especially bacteria. Infection with resistant strains results in worse clinical outcomes. New antimicrobial therapies are being developed but most have yet to be either used to treat ocular infections or become commercially available. For bacterial keratitis, antimicrobial peptides (AMPs) are a potential new option, as are bacteriophages and even bacteria that eat other bacteria or maggot secretions. For fungal keratitis, ocular natamycin, with oral ketoconazole or voriconazole treatments, offer improved outcomes for severe cases. For viral keratitis, AMPs again offer hope as new therapeutics, as do RNA interference and CRISPR-Cas systems. The recent release of a commercially available polyhexamethylene biguanide eye drop is a step forward, but new therapies that can kill both Acanthamoeba trophozoites and cysts are still needed. Beyond antibiotics, photoactivated chromophores for keratitis-corneal collagen cross-linking and photodynamic therapy have been successfully used. Therapies for large ulcers or scarring include corneal gluing, tissue scaffolds such as amniotic membrane or conjunctival flaps, and tissue replacement through penetrating or lamellar keratoplasty.

Keywords:  Antibiotics; bacteriophage; keratitis; microbial keratitis; surgical techniques

DOI:  https://doi.org/10.1080/08164622.2025.2579169
J Hazard Mater. 2025 Nov 10. pii: S0304-3894(25)03355-2. [Epub ahead of print]500 140435

ABCD-type phage cocktail targeting distinct LPS receptor sites demonstrates superior efficacy against multidrug-resistant Salmonella.

Yibao Chen, Xiaoqian Wang, Qing Zhang, Zhipeng Zhang, Zhengjie Liu, Xiaonan Zhao, Lulu Li, Ming Hu, Qianghua Lv, Yanbo Luo, Xiaohui Xu, Bent Petersen, Yumei Cai, Thomas Sicheritz-Pontén, Martha R J Clokie, Yuqing Liu.

  The narrow host range of phages poses a limitation in addressing multidrug-resistant bacteria, whereas phage cocktail therapy, targeting multiple bacterial receptors, broadens the phage host spectrum. This study establishes a comprehensive Salmonella phages repository through nationwide surveillance in China, isolating 242 phages classified into 29 genera, with genome sizes ranging from 5.4 to 350.3 Kb. Based on LPS specificity, phages were categorized into four types A-D. Here, we developed an ABCD-Type phage cocktail targeting four distinct LPS recognition sites, demonstrating superior efficacy versus single phages or phage cocktail with different receptors (CCR-Type). In vitro, ABCD-Type phage cocktail treatment sustained bactericidal activity > 36 h versus CCR's 8 h, effectively controlling Salmonella in lettuce, milk, and Galleria mellonella infection models. Moreover, ABCD-Type phage cocktail effectively cleared Salmonella biofilms and showed promising results in the treatment of animal infections, significantly reducing bacterial loads in infected chicks and improving their survival rates. Resistant mutants predominantly harbored mutations in the btuB gene and LPS biosynthesis genes. These mutants showed increased antibiotic sensitivity and attenuated virulence. Collectively, these findings underscore the therapeutic potential of Salmonella phages, specifically ABCD-Type phage cocktail formulations which contain the phages PJNS014, PJNS023, PJNS036, and PJNS038, for controlling Salmonella infections. This work provides a foundation for developing advanced phage-based therapeutics.

Keywords:  Antibiotic alternatives; Biofilm clearance; LPS receptor; Phage cocktail therapy; Salmonella phages

DOI:  https://doi.org/10.1016/j.jhazmat.2025.140435
Microbiol Spectr. 2025 Nov 19. e0181825

Novel lytic phages improve the antibiofilm activity of dalbavancin, daptomycin, and fosfomycin against vancomycin-resistant enterococci.

Rima Fanaei Pirlar, Alvaro Irigoyen-von-Sierakowski, Jeroen Wagemans, Yu Ning, Rob Lavigne, Andrej Trampuz, Svetlana Karbysheva.

  Periprosthetic joint infections (PJI) caused by Enterococcus spp., especially vancomycin-resistant strains (VRE), are challenging to treat due to biofilm tolerance and limited antibiotic options. Bacteriophages offer a promising adjunct through targeted and biofilm-disrupting activity. This study evaluated two novel lytic phages, alone and combined with last-line antibiotics, for their ability to eradicate VRE biofilms in vitro. Two novel lytic phages, CUB-FM (E. faecium) and CUB-FS (E. faecalis), were isolated from hospital sewage and characterized via whole-genome sequencing and transmission electron microscopy. Antibiofilm efficacy of phages alone and in combination with dalbavancin, daptomycin, and fosfomycin was assessed against biofilm-embedded VRE strains using isothermal microcalorimetry. Synergy was defined as a combined effect exceeding the sum of individual activities. Genomic analysis confirmed both phages as strictly lytic and free of lysogeny, virulence, or resistance genes. TEM classified CUB-FM within Salasmaviridae and CUB-FS within Herelleviridae. Both exhibited dose-dependent antibiofilm activity, with optimal efficacy at 10¹² (CUB-FM) and 10⁸ PFU/mL (CUB-FS). While antibiotic monotherapies showed limited antibiofilm effects, phage-antibiotic combinations markedly enhanced activity. CUB-FM with dalbavancin achieved the strongest suppression against E. faecium (tMax22.3 h vs. 5.2 h control, P < 0.001), and CUB-FS with dalbavancin or fosfomycin at ≥10 × MIC completely eradicated E. faecalis biofilms. Daptomycin-phage combinations produced additive to synergistic effects. Novel phages CUB-FM and CUB-FS exhibit potent antibiofilm activity and synergize with last-line antibiotics against VRE. Phage-antibiotic combinations, particularly with dalbavancin and fosfomycin, represent a promising strategy for treating biofilm-associated enterococcal PJIs.IMPORTANCEVancomycin-resistant enterococci (VRE) are increasingly implicated in biofilm-associated periprosthetic joint infections, where treatment options are limited, and clinical outcomes are poor. Conventional antibiotics often fail due to reduced biofilm penetration and bacterial tolerance, highlighting the need for novel therapeutic strategies. Our study introduces two newly characterized lytic phages, CUB-FM and CUB-FS, which demonstrated strong antibiofilm activity and synergistic interactions with last-line antibiotics. Notably, phage-antibiotic combinations achieved either additive or synergistic effects, with dalbavancin and fosfomycin-phage therapy leading to a complete eradication of E. faecalis biofilms. These findings provide proof of concept that combining phages with antibiotics enhances efficacy against multidrug-resistant Enterococcus biofilms, offering a translational pathway for personalized, adjunctive therapies in complex orthopedic infections. By bridging the gap between genomic phage safety validation and functional synergy testing, this work supports further preclinical and clinical development of phage-antibiotic strategies for refractory implant-associated infections.

Keywords:  VRE; antibiotics; bacteriophages; biofilms; enterococci; periprosthetic joint infection

DOI:  https://doi.org/10.1128/spectrum.01818-25
Eur J Med Chem. 2025 Nov 10. pii: S0223-5234(25)01127-4. [Epub ahead of print]302(Pt 2): 118362

Beyond traditional antibacterial agents: Novel approaches to combat resistant pathogens.

Wei Zong, Shengjie Xie, Hongtao Chu, Shuang Han, Xunan Zhang.

  As bacterial infections caused by antibiotic-resistant strains become increasingly prevalent, traditional antibacterial therapies face mounting challenges. These resilient pathogens not only complicate the treatment of common infections but also undermine the efficacy of therapies for major diseases. This growing threat underscores the urgent need for innovative therapeutic strategies. In recent years, the combinatorial use of antibacterial agents has emerged as a promising approach to enhance efficacy and combat resistant bacteria. This review first provides an overview of antibacterial classifications and their mechanisms of action against bacterial infections. It then explores two combined treatment strategies: antibacterial-antibacterial combinations and antibacterial-non-antibacterial pairings, alongside a drug delivery technology: antibacterial-loaded liposomes. Furthermore, we highlight emerging frontiers in antimicrobial strategies, including CRISPR-Cas technologies, AI-driven discovery platforms, nanomaterials beyond liposomes, microbiota-based therapies, and immunotherapeutic approaches. Finally, we offer a forward-looking perspective on the challenges and opportunities shaping the future of antibacterial development in the biomedical field.

Keywords:  Antibacterial agents; Antibiotic-resistant bacteria; Combination therapy; Liposomes

DOI:  https://doi.org/10.1016/j.ejmech.2025.118362
Bioeng Transl Med. 2025 Nov;10(6): e70071

Carbon nanomaterials: Exploring new frontiers in wound healing therapy.

Pegah Madaninasab, Mahsa Mohammadzadeh, Sheyda Labbaf.

  This comprehensive review explores the therapeutic potential of carbon nanomaterials, including carbon nanotubes, graphene, carbon dots, and other related materials, in wound healing applications. These materials offer a cutting-edge approach by modulating critical cellular processes, addressing current challenges in wound care, and advancing tissue regeneration techniques. The article thoroughly examines recent developments in carbon nanomaterials, highlighting their integration into wound care strategies and the ongoing efforts to overcome limitations such as biocompatibility, toxicity, and long-term safety. Unlike previous reviews, this work not only acknowledges recent advancements but also provides a critical analysis of the still existing barriers and novel strategies for effectively translating these materials from research to clinical applications. By emphasizing both the potential and the challenges, the review aims to present a unique perspective on the future of carbon nanomaterials in wound healing, paving the way for more efficient and personalized treatment options.

Keywords:  biomedical applications; carbon nanomaterials; e‐skin; therapeutic potential; wound healing

DOI:  https://doi.org/10.1002/btm2.70071
ACS Appl Mater Interfaces. 2025 Nov 17.

Stage-Responsive Multifunctional Microneedle Patches for Enhanced Biofilm Penetration and Accelerated Healing of Bacterial Infected Skin Wounds.

Yuemin Wang, Kai Xu, Xinyu He, Xinran Kang, Chongxu Tang, Chao Niu, Zhiqiang Li, Jie Weng, Jianshu Li, Xingyu Chen.

  Biofilms, formed by microorganisms and surrounding substances, hinder traditional drug delivery and delay wound healing. Microneedles, with their excellent mechanical properties, minimally invasive nature, and ability to penetrate biofilms for rapid drug delivery, offer a promising solution for biofilm eradication. In this study, we developed an intelligent, responsive bilayer microneedle system (CurMN@RRH) based on photodynamic therapy to accelerate wound healing caused by bacterial infections. Cur@ZIF-8 nanoparticles are synthesized in a one-pot process and embedded in gelatin and hyaluronic acid to form the microneedle tips. The microneedle substrate consists of ROS-responsive boronate-ester-based hydrogels (TSPBA-PVA), loaded with the antioxidant glutathione (GSH). In the early stages of wound healing, the acidic environment triggered by bacterial infection prompts the release of curcumin from Cur@ZIF-8 nanoparticles, which generates hydroxyl radicals under blue light to promote bacterial death. In later stages, the CurMN@RRH microneedles release GSH, clearing excessive reactive oxygen species and reducing inflammation, thus accelerating healing. Both in vitro and in vivo experiments demonstrate that the intelligent CurMN@RRH microneedles exhibited strong antibacterial, anti-inflammatory, and antioxidant properties, promoted cell proliferation, and accelerated tissue wound healing. This approach offers a novel strategy for treating bacterial infection-induced wounds.

Keywords:  bacterial biofilm; infected wounds; microneedles; photodynamic therapy; smart-responsive

DOI:  https://doi.org/10.1021/acsami.5c20107
Cancer J. 2025 Nov-Dec 01;31(6):pii: e0796. [Epub ahead of print]31(6):

Harnessing Artificial Intelligence to Transform Clinical Trials and Cancer Care: Opportunities and Challenges.

Jennifer H Benbow, Edward S Kim.

  Artificial intelligence (AI) is working toward the reality of speeding up oncology drug development, offering the ability to cut years off the pipeline while maintaining patient safety and personalized care. Machine learning (ML) models analyze historical and real-world data to optimize eligibility criteria, simulate in silico cohorts, flag protocol risks, and recommend real-time adaptations. Natural language processing enhances patient screening by extracting patient data from electronic health records to match diverse patient populations to trials faster than traditional methods. AI-driven analysis of data from electronic wearables and imaging enables early toxicity and efficacy signals, allowing providers real-time monitoring. However, the same code that accelerates technology can also amplify bias, increase data security issues, hallucinate unsafe recommendations, and raise legal and ethical alarms. Safeguards, including transparent model reporting, bias mitigation, robust cybersecurity, clinician oversight, and education for providers and patients, are essential. Harnessed responsibly, AI can transform clinical trials and oncology care without sacrificing empathy, accountability, and patient-centered values.

Keywords:  Artificial Intelligence; clinical trials; drug discovery; machine learning; natural language processing; precision medicine

DOI:  https://doi.org/10.1097/PPO.0000000000000796
Wounds. 2025 Oct;37(10): 384-392

Advancing chronic wound care with near-infrared spectroscopy imaging: clinical applications, measurement parameters, and insights into healing dynamics.

Alisha Oropallo, Alex G Ortega-Loayza, Holly Korzendorfer, Francis James, Peggy Dotson, Anna Khimchenko, Vickie R Driver, Sharon Eve Sonenblum.

BACKGROUND: Chronic wound management is a global health care challenge affecting patient morbidity and quality of life while presenting a substantial economic burden. A critical limitation in effective wound care is the inability to accurately assess microvascular tissue health in real time. This review of near-infrared spectroscopy (NIRS) imaging and its use in wound care emphasizes relevant clinical end points and explores key measurement parameters assessed via NIRS imaging.
OBJECTIVE: To identify, describe, and illustrate NIRS imaging modalities and measurement parameters, and their clinical applications.
RESULTS: Clinical studies demonstrated that NIRS imaging can effectively detect poor wound healing early, facilitating timely interventions. Changes in parameters such as oxygenated hemoglobin, deoxygenated hemoglobin, and tissue oxygen saturation have shown strong correlations with wound healing progress, enabling clinicians to make more informed decisions.
CONCLUSION: NIRS imaging advances wound management by providing real-time, noninvasive, and objective data on tissue oxygenation and perfusion. NIRS imaging may objectively complement the standard percentage area reduction assessments during the wound treatment process.
JBI Evid Synth. 2025 Nov 19.

Effectiveness of bilayered dermal substitutes for wound healing in adults: a systematic review protocol.

Lauren Middleton, Elias Awwad, Elizabeth Concannon, Edoardo Aromataris.

   OBJECTIVE: The objective of this systematic review will be to evaluate the effectiveness of the bilayered dermal substitute, Biodegradable Temporising Matrix (BTM), compared with other wound management options in improving clinical outcomes for adults with wounds requiring surgical intervention.
INTRODUCTION: Dermal substitutes provide physiological wound cover for major burns, traumatic wounds, necrotizing fasciitis, diabetes, oncological resections, and previously non-graftable wound beds. Bilayered dermal substitutes such as BTM are designed to provide immediate coverage to an area of skin loss, with subsequent skin grafting to restore structure and function.
ELIGIBILITY CRITERIA: This review will consider studies on adult patients (18 years or older) with wounds of any etiology or severity requiring surgical intervention. Studies will be considered if they evaluate surgical treatment for wounds using BTM, with or without negative pressure wound therapy, compared with any other surgical technique.
METHODS: This review will adhere to the JBI methodology for systematic reviews of effectiveness. The following databases will be searched for published studies: PubMed, Embase (Ovid), and CINAHL Ultimate (EBSCOhost). Unpublished studies, gray literature, conference presentations, and posters will also be considered. The searches will be conducted from database inception till the present, with no language limitations. Two independent reviewers will screen titles and abstracts against the eligibility criteria, followed by full-text screening. Eligible studies will be critically appraised at the outcome/result level for methodological quality using JBI's standardized critical appraisal instruments. Data will be extracted and pooled in statistical meta-analysis. The results will be reported in tables, visual format, and narrative format.
REVIEW REGISTRATION: PROSPERO CRD42024595778.

Keywords:  Biodegradable Temporising Matrix; collagen-chondroitin silicone bilayer; dermal substitute; wound healing

DOI:  https://doi.org/10.11124/JBIES-24-00464
Mater Today Bio. 2025 Dec;35 102490

Dual-layer microneedles for immunomodulation and infection-responsive therapy in diabetic foot ulcers.

Li Chen, Mengyi Zhan, Li Zhang, Zhuohang Xiong, Chi Zhang, Xuanxuan Zhang, Zhengyang Yang, Lixin Ma, Yibin Cheng, Huanhuan Chen.

  Diabetic foot ulcers (DFU) are a refractory form of chronic wound characterized by persistent infection and impaired healing. Distinct from other hard-to-treat infections, DFU are aggravated by neuropathy, vasculopathy, and immune dysfunction, which hinder microbial clearance and tissue repair. Their management is further challenged by antibiotic overuse, rising resistance, and the limited efficacy of current therapies. To address these issues, we developed the dual-layer microneedles (IGR MNs) platform that integrated a nitroreductase (NTR)-responsive fluorescent probe for real-time infection monitoring with near-infrared (NIR)-triggered photothermal therapy. The microneedle tips were loaded with liposome-encapsulated antibacterial and immunomodulatory agents for controlled, on-demand release, while the base layer incorporated the infection-responsive probe for spatially precise detection. The IGR MNs overcame the limitations of conventional single-layer microneedles by simultaneously enabling diagnosis and therapy. In vivo evaluations in diabetic wound models demonstrated efficient infection detection, reduced local inflammation, enhanced collagen deposition and neovascularization, and significantly accelerated wound closure. This antibiotic-free strategy enables targeted biofilm disruption and immunomodulation, providing a clinically translatable approach for managing refractory, infected diabetic wounds.

Keywords:  Diabetic foot ulcers; Immunomodulation; Infection-responsive therapy; Microneedles; Wound healing

DOI:  https://doi.org/10.1016/j.mtbio.2025.102490
Prog Biophys Mol Biol. 2025 Nov 18. pii: S0079-6107(25)00057-4. [Epub ahead of print]

Advances in nanomaterials-assisted drug delivery, diagnosis, and action towards drug-resistant Mycobacterium.

Parikshana Mathur, Pinky Choudhary, Rajkuberan Chandrasekaran, Ragini Singh, Hemant Kumar Daima.

  Threatening impact of tuberculosis (TB) on public health remains significant even after the global initiatives and emergence of multi-drug resistance (MDR) strains have made the situation complicated. Herein, the exploitation of the same medications for several decades, ineffective drug administration, and insufficient patient follow-up are some of the variables that have fuelled the resistance. As a result, the twenty-first century has seen the greatest number of multi-drug resistance TB cases. Nevertheless, nanotechnology has emerged as a promising tool against drug-resistant Mycobacterium tuberculosis, the bacterium responsible for TB. This seminal review highlights the most important findings from nanomaterials-related research to detect and counter TB. First, a deeper understanding of the essential molecular mechanisms underlying drug-resistance and drug-tolerance in Mycobacterium pathogen is provided along with biofilm formation and intracellular survival mechanisms. It is followed by detailed discussion about innovative nanomaterial-based drug delivery for antituberculosis medications, and different types of nanomaterials for direct antimicrobial actions. Then, nanotechnology-assisted diagnosis techniques and anti-biofilm possibilities for drug-resistant M. tuberculosis are elaborated. Finally, the challenges and perspectives related to nanomaterials-based theranostic for TB drug-resistance and treatment are provided with concluding remarks.

Keywords:  Tuberculosis (TB); antibiotics; diagnostic; drug delivery; nanotoxicity; point-of-care

DOI:  https://doi.org/10.1016/j.pbiomolbio.2025.11.001
BMC Biol. 2025 Nov 18. 23(1): 342

Insights into the molecular determinants of host specificity in Pseudomonas aeruginosa-infecting phages: a structural and functional analysis of tail fibre proteins.

Aleksandra Zalewska, Agata Jurczak-Kurek, Magdalena Kwiatek, Heejoon Myung, Marcin Górniak.

   BACKGROUND: Bacteriophages and bacteria frequently occupy the same ecological niches, driving complex and dynamic host-virus interactions. In Pseudomonas aeruginosa, phages from the Migulavirinae subfamily, tail fibre proteins (TFPs) are crucial to host recognition. These proteins, located within the phage tail structure, are subject to frequent recombination and may play a key role in shaping host range. This study investigates the molecular basis of host specificity in Litunavirus and Luzseptimavirus phages, focusing on the structure and variation of their TFPs.
RESULTS: Host spectrum analysis divided phages into three categories; however, contrary to expectations, no direct correlation was found between TFP recombination history and host range, most likely because subsequent single amino acid changes in the pyocin knob regions, critical for adsorption, altered the host spectrum after the recombination event. Notably, phages sharing highly similar pyocin knob 2 domain architectures displayed identical host spectra, suggesting a strong link between this region and host specificity. Despite high sequence variability, all TFPs adopted a conserved trimeric fold with five regions: N-terminal, GrpE-like, GDSL-like with a carbohydrate-binding module, pyocin knob, and C-terminal. Structural similarities to bacterial PilA and pyocins were noted. Variation in the pyocin knob region, especially substitutions involving polar residues, was partially correlated with host range, likely via hydrogen bonding with the O-antigen. The GrpE-like domain resembled type IV pili, suggesting a role in reversible attachment, while the GDSL-like domain may support enzymatic processing of the O-antigen.
CONCLUSIONS: Our findings support a multi-step adsorption mechanism of Migulavirinae phages, initiated by random encounters with the bacterial surface, followed by specific, stable interactions between the pyocin knob region and the bacterial lipopolysaccharide (LPS) O-antigen. Final stabilization involves additional interactions with the LPS core region. While the GrpE-like domain may contribute to transient stabilization near the surface, its structural similarity to PilA suggests a possible evolutionary convergence rather than a direct pilus-binding function. Despite high sequence variability, TFPs maintain conserved structural features, allowing for modular adaptations that precisely adjust host specificity. Importantly, the lack of a direct link between TFP recombination and host range suggests that factors beyond recombination influence phage host specificity.

Keywords:   Pseudomonas aeruginosa ; Bacteriophages; Host spectrum; Phage adsorption; Phage-host interactions; Protein modelling; Receptor-binding protein; Tail fibre proteins

DOI:  https://doi.org/10.1186/s12915-025-02445-y
Cureus. 2025 Oct;17(10): e94895

From Design to Closure: Artificial Intelligence Transforming Clinical Research.

Kanika Vats, Mohammad Mazhar Alam.

  Clinical research is essential as it advances medical innovation, from developing new treatments and improving existing ones for additional disease indications to creating better processes and the availability of medical devices, yet traditional trial methods are often slow, costly, and full of challenges. Over the past decade, the use of artificial intelligence (AI) and machine learning (ML) has evolved across all phases of the clinical research cycle, from study design and planning to initiation, conduct, and closure. This editorial explores how AI can create new opportunities to enhance patient recruitment, optimize trial design, improve dose adherence and participant retention, strengthen safety monitoring, and enable advanced data analysis. It also highlights key challenges associated with the use of AI/ML, including selection bias, privacy, ethical considerations, and regulatory compliance. Since these tools generate outputs based on trained datasets, issues like data drift must be carefully managed to ensure ongoing accuracy and reliability. By recognizing both opportunities and challenges of using AI/ML across all stages of clinical research, we have proposed potential solutions to help overcome these challenges and promote responsible adoption of this new technological era. Responsible deployment and rigorous validation are essential; although hybrid approaches combine AI-driven insights with human oversight, these technologies can improve trial efficiency, improve patient outcomes, and accelerate development of novel therapies, while ensuring that accountability, safety, and ethical integrity remain firmly with humans. This editorial provides a roadmap for integrating responsible use of AI into clinical trials, ensuring ethical integrity, regulatory alignment, and trust, so that AI ultimately strengthens trial outcomes and benefits the patients these studies are designed to serve.

Keywords:  artificial intelligence (ai); clinical research; clinical trial; data monitoring; digital health; machine learning; participant recruitment; safety monitoring; trial design; trial efficiency

DOI:  https://doi.org/10.7759/cureus.94895
Sci Rep. 2025 Nov 18. 15(1): 40495

Comparative assessment of annotation tools reveals critical antimicrobial resistance knowledge gaps in Klebsiella pneumoniae.

Kristina Kordova, Caitlin Collins, Julian Parkhill.

Bacterial antimicrobial resistance (AMR) poses a significant public health threat. The increase of both global awareness and affordable whole genome sequencing has yielded an ever-growing collection of bacterial genome sequence datasets and corresponding antibiotic resistance metadata. This enables the use of computational techniques, including machine learning (ML), to predict phenotypes and discover novel AMR-associated variants. With the great variety of resistance mechanisms to interrogate and the number of datasets that can be mined, there is a need to identify where novel AMR marker discovery is most necessary. Multiple databases and annotation pipelines exist to annotate AMR variants known to be associated with resistance to specific antibiotics or antibiotic classes, however, the completeness of these databases varies, and for some antibiotics, even the most complete databases remain insufficient for accurate classification. Here, we build predictive ML models using only those known markers, which we call "minimal models" of resistance. We predict the binary resistance phenotypes of 20 major antimicrobials in the genomically diverse pathogen Klebsiella pneumoniae, allowing us to identify their shortcomings in phenotype prediction, thereby highlighting opportunities for novel marker discovery. We provide a critical review of the differences in annotation tools and databases commonly used in bacterial AMR studies, and outline guidance for the establishment of a standard dataset for the development and benchmarking of ML models of AMR.

DOI: https://doi.org/10.1038/s41598-025-24333-9
Int J Low Extrem Wounds. 2025 Nov 20. 15347346251395904

Cold Atmospheric Plasma Therapy for Diabetic Foot Ulcers: A Systematic Review and Meta-Analysis of Randomised Controlled Trials.

Duda Matija, Damjanović Ivan, Crkvenac Gregorek Andrea, Vrkic Kirhmajer Majda, Robert Likic.

  Aims/hypothesisDiabetic foot ulcers are a common and serious complication of diabetes, frequently resulting in infection, amputation, and increased mortality. Cold atmospheric plasma (CAP) is a new treatment modality that combines antimicrobial activity with promotion of tissue regeneration. We aimed to systematically review and meta-analyse randomized controlled trials to determine whether cold atmospheric plasma therapy, when added to standard wound care, improves healing outcomes and safety in patients with diabetic foot ulcers (DFUs).MethodsFollowing PRISMA 2020 guidelines, we included randomized controlled trials in adults with DFUs comparing adjunctive CAP plus standard care versus standard care. Non-RCTs, non-CAP energy modalities, CAP without concomitant standard care, and studies without a concurrent control were excluded. The primary outcome was final fractional wound area (final/baseline; unitless proportion, 0-1). Secondary outcomes were ≥50% wound-size reduction by week 3, bacterial load, and adverse events.ResultsThree RCTs (107 participants; 126 ulcers) showed that CAP reduced final fractional wound area (mean difference -0.29 proportion units, 95% CI -0.47 to -0.11; p = 0.002; I2 = 22%). The proportion achieving ≥50% wound-size reduction by week 3 was higher with CAP (RR 2.39, 95% CI 1.46-3.91; p < 0.001; I2 = 0%). Bacterial load declined over time in both groups with no sustained between-group difference; immediate post-application reductions were observed with CAP within sessions. No serious treatment-related adverse events were reported.Conclusions/interpretationAdjunctive cold atmospheric plasma improved early healing of diabetic foot ulcers and showed a favourable short-term safety profile, with no sustained advantage in infection control over standard care. Larger, longer randomized trials are warranted to assess complete closure and recurrence outcomes and to define optimal treatment parameters.RegistrationPROSPERO registration ID CRD4201113940.

Keywords:  cold atmospheric plasma; diabetic foot ulcer; meta-analysis; systematic review; wound healing

DOI:  https://doi.org/10.1177/15347346251395904
3 Biotech. 2025 Dec;15(12): 414

Complete genome sequence of lytic Pseudomonas aeruginosa phage vB_PaeS_Tums_P6.

Haniyeh Kamyab, Narges Torkashvand, Ahmad Reza Shahverdi, Mohammad Reza Khoshayand, Mohammad Sharifzadeh, Zargham Sepehrizadeh.

  The genomic characterization of phages is fundamental to the development of an effective phage therapy strategy for clinically important bacteria. This study is aimed at isolating and characterizing vB_PaeS_TUMS_P6, a new lytic Pseudomonas phage. The whole-genome sequencing revealed that it contains a Linear dsDNA genome of 73,885 bp with a G + C content of 53.5% and 106 predicted coding sequences. Genes related to virulence or lysogeny behavior were not found in the genome, so it is potentially safe in regard to therapeutic applications. Genomic and phylogenetic analysis indicated that vB_PaeS_TUMS_P6 is a member of the genus Luzseptimavirus, belonging to Schitoviridae family. The present study provides some basic information for further research on treatment of P. aeruginosa infections.
Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-025-04528-7.

Keywords:  Genome sequencing; Multidrug resistance; NGS; Phage therapy

DOI:  https://doi.org/10.1007/s13205-025-04528-7
Talanta. 2025 Nov 15. pii: S0039-9140(25)01609-1. [Epub ahead of print]299 129118

Bionic meta microneedle photonic crystal patch for advanced wound care.

Chengxin Luan, Meng Wei, Linlin Dong, Li Tang, Bingbing Gao.

  Chronic wounds remain difficult to manage due to unstable adhesion, uncontrolled therapy, and the absence of real-time monitoring. Here, we present a bionic meta microneedle photonic crystal patch that integrates robust tissue adhesion, spatiotemporal drug delivery, and optical biosensing in a single platform. The patch combines drug-loaded biodegradable microneedles with a micropillar-inspired interface to establish a tissue-mimetic three-dimensional contact, ensuring secure attachment on moist and dynamic skin surfaces. Embedded photonic crystal structures function as high-sensitivity optical sensors, enabling continuous, noninvasive monitoring of wound parameters infection-related metabolites. In a chronic wound mouse model, the patch significantly accelerated healing by inhibiting bacterial proliferation, attenuating inflammation, and promoting tissue regeneration, outperforming conventional dressings. This bioinspired hybrid system demonstrates strong translational potential for precision and multifunctional wound care by uniting adhesion, therapy, and dynamic sensing in one device.

Keywords:  Chronic wound healing; Drug delivery; Microneedle-micropillar patch; Photonic crystal sensors; Real-time monitoring

DOI:  https://doi.org/10.1016/j.talanta.2025.129118
Diabetes Metab Syndr Obes. 2025 ;18 4099-4112

Efficacy and Safety of Negative Pressure Wound Therapy in Diabetic Foot Ulcers: A Cross-Sectional Analysis of Overlapping Meta-Analyses.

Ying Du, Tiangang Zhai, Zhujun Sheng, Weinan Xie, Zhiwei Jia, Tianlin Wen, Xiyan Zhao, Xiaolin Tong.

   Objective: Negative pressure wound therapy (NPWT) is a key intervention for diabetic foot ulcers (DFUs). However, the body of meta-analytic evidence is fraught with conflicting findings, creating significant clinical uncertainty. This study was designed to harmonize the discordant evidence, identify the most methodologically robust meta-analysis, and formulate a clear, evidence-based recommendation for the clinical use of NPWT.
Methods: We conducted a comprehensive search of the PubMed, Embase, and Cochrane Library databases to identify all pertinent meta-analyses. The methodological quality of each included review was rigorously assessed using the Assessment of Multiple Systematic Reviews (AMSTAR) instrument. The Jadad decision algorithm was then employed to systematically select the most reliable and robust evidence.
Results: Eight meta-analyses met the inclusion criteria, with AMSTAR scores ranging from 6 to 9. The formal application of the Jadad decision algorithm identified the meta-analysis by Deng et al as the definitive source of best available evidence. This meta-analysis demonstrated that NPWT significantly improved wound healing rates (risk ratio = 1.46) and decreased amputation rates (risk ratio = 0.69) relative to conventional therapy, while also shortening granulation tissue formation time without increasing adverse events.
Conclusion: The highest-quality evidence, harmonized through this appraisal, confirms that NPWT is a safe and effective adjunctive therapy for DFUs. Its demonstrated ability to accelerate healing while reducing amputations provides a strong evidence base for consideration as a key component of standard clinical practice.

Keywords:  diabetic foot ulcer; meta-analysis; negative pressure wound therapy; systematic review; vacuum-assisted closure

DOI:  https://doi.org/10.2147/DMSO.S565993
Am J Transl Res. 2025 ;17(10): 7838-7846

A retrospective comparative study of helium-neon laser combined with ultrasonic debridement in improving healing of chronic non-healing wounds.

Wanjun Yang, Lei Zhao, Hongwei Zhu, Siyuan Chen, Canyu Yang.

   OBJECTIVE: To evaluate the clinical value of ultrasonic debridement alone, helium-neon (He-Ne) laser therapy alone, and their combined use in the treatment of chronic non-healing wounds.
METHODS: A total of 272 patients with chronic non-healing wounds treated at Panzhihua Central Hospital between October 2023 and December 2024 were retrospectively selected and assigned to three groups according to treatment modality: a combined group (n=90, He-Ne laser and ultrasonic debridement), an ultrasonic debridement group (n=95, ultrasonic debridement alone), and a He-Ne laser group (n=87, He-Ne laser alone). Clinical indicators, including wound healing, Pressure Ulcer Scale for Healing (PUSH) scores, microbiological parameters, and visual analog scale (VAS) scores were assessed before treatment and at 4, 8, and 12 weeks after treatment. Adverse reactions during treatment and recurrence rates within six-month of follow-up were collected.
RESULTS: The combined group achieved better efficacy compared with the single-treatment groups at all assessment time points. At 12 weeks after treatment, the combined group demonstrated higher complete healing rates than the single-treatment groups (P<0.05). The combined group demonstrated higher wound area reduction rates, lower PUSH scores, lower bacterial infection rates, lower VAS scores, shorter average hospitalization stay, fewer treatment sessions, lower six-month recurrence rates, and lower adverse reaction rates compared with the single-treatment groups (P<0.05).
CONCLUSION: The combined application of He-Ne laser therapy and ultrasonic debridement provides significant advantages in managing chronic non-healing wounds. This approach effectively promotes wound healing, enhances bacterial clearance, alleviates pain, shortens treatment cycles, lowers recurrence risk, and reduces treatment-related adverse reactions.

Keywords:  He-Ne laser; Ultrasonic debridement; chronic non-healing wounds; combined treatment

DOI:  https://doi.org/10.62347/NTOP9738
J Biomater Sci Polym Ed. 2025 Nov 19. 1-20

Anti-staphylococcal chitosan-alginate-lyophilized platelet-rich fibrin wound dressings for infected wound healing.

Archa Mini Abhilash, Abhirami Dinesan, Vivek Vinod, Raja Biswas, Jayakumar Rangasamy.

  Staphylococcus aureus (S. aureus) is a common cause of wound infections, resulting in symptoms such as redness, swelling, pain, and formation of pus. This group of bacteria has evolved resistance to several antibiotics used in human therapies, making it difficult to treat. Additionally, their ability to form biofilm on wound surfaces shields the bacteria from the host immune system and antibiotics, thereby hindering the healing process. To address this issue, we have developed and characterized a chitosan-alginate composite dressing incorporating lysostaphin (LST) and lyophilized platelet-rich fibrin (LPRF) to treat S. aureus infections and enhance wound healing. LST exhibits potent antibacterial activity against various strains of S. aureus, whereas LPRF promotes slow and sustained release of growth factors, namely PDGF, IGF and EGF. The prepared dressings were porous and FT-IR analysis confirms the incorporation of LST and LPRF into the chitosan-alginate dressing. Swelling and degradation studies of the prepared dressings showed better swelling ratio and controlled degradation. The prepared dressing is biocompatible and showed L929 cell attachment. Furthermore, the in vitro antibacterial and anti-biofilm activity of CA-LPRF-LST dressing was studied against S. aureus and clinical isolates of MRSA, which showed inhibition and biofilm disruption. Based on these in vitro studies, the developed CA-LPRF-LST dressing demonstrates promising antibacterial properties against S. aureus and biocompatibility by L929, suggesting its potential as for further investigation as a treatment for wound infections and healing.

Keywords:  Staphylococcal wound infections; chitosan-alginate dressing; lyophilized platelet rich fibrin; lysostaphin; wound healing

DOI:  https://doi.org/10.1080/09205063.2025.2588215
Small Sci. 2025 Nov;5(11): 2500322

Janus Hydrogel Microparticles with Tea Polyphenol/Melanin Nanoparticles Integration from Microfluidics for Wound Healing.

Zhiqiang Luo, Danqing Huang, Yuanjin Zhao.

  Massive bioactives show outstanding performance in promoting wound healing, while their combined application remains challenging in avoiding mutual interference. Herein, Janus hydrogel microparticles co-loaded with tea polyphenol-magnesium and melanin nanoparticles for synergistically antioxidant and antibacterial wound treatment are proposed. The tea polyphenol-magnesium nanoparticles are prepared by the self-assembly of tea polyphenol molecule and magnesium ion, while melanin nanoparticles are harvested from black hair. These two kinds of nanoparticles are, respectively, embedded into the hemisphere of Janus microparticles by microfluidics technology. The in vitro tests reveal that the resultant Janus microparticles have high biocompatibility and show enhanced antioxidant performance and synergistical antibacterial activity. Additionally, when the Janus microparticles are applied to the treatment of diabetic wounds, they promote the wound healing by scavenging reactive oxygen species, killing bacteria, reducing inflammation, decreasing matrix metalloproteinase-9 secretion, and enhancing tissue remolding. Therefore, it is believed that the Janus microparticles with melanin and tea polyphenol-Mg nanoparticles are highly promising candidate for clinical wound healing.

Keywords:  Janus; melanin; microfluidics; particles; tea polyphenol; wounds

DOI:  https://doi.org/10.1002/smsc.202500322