bims-fagtap 2025-06-29 papers

bims-fagtap

Biomed News

on Phage therapies and applications

Issue of 2025–06–29
eighteen papers selected by
Luca Bolliger, lxBio

Current Applications and the Future of Phage Therapy for Periprosthetic Joint Infections.
Current Clinical Laboratory Challenges to Widespread Adoption of Phage Therapy in the United States.
The Current Landscape of Phage-Antibiotic Synergistic (PAS) Interactions.
[Phage therapy for multidrug-resistant Acinetobacter baumannii].
Synergistic efficacy of phages along with vancomycin for eradication of vancomycin-resistant Enterococcus faecalis biofilms.
Phage Host Prediction Using Deep Neural Network with Multi-source Protein Language Models and Squeeze-and-Excitation Attention Mechanism.
Proteomic analysis reveals phage-driven metabolic shifts and biofilm disruption in methicillin-resistant Staphylococcus aureus (MRSA).
Multi-omics characterization of a lytic phage targeting Listeria monocytogenes.
Isolation and complete genome sequence of a novel Mycobacterium phage MS619.
Advances in Local Drug Delivery for Periodontal Treatment: Present Strategies and Future Directions.
Clinical trial landscape for pneumonia: Evolving agents against bacterial pathogens.
Gut Microbiome in Pulmonary Arterial Hypertension-An Emerging Frontier.
Antimicrobial Smart Dressings for Combating Antibiotic Resistance in Wound Care.
Research Progress of Multifunctional Hydrogels in Promoting Wound Healing of Diabetes.
Advancements in AI for Computational Biology and Bioinformatics: A Comprehensive Review.
AI Revolutionizing Cell and Genetic Engineering: Innovations and Applications.
Rapid microbial evaluation of acute exacerbations of bronchiectasis using FilmArray Pneumonia plus Panel in a real-world setting.
Microrobots for Antibiotic-Resistant Staphylococcus aureus Skin Colony Eradication.

Antibiotics (Basel). 2025 Jun 06. pii: 581. [Epub ahead of print]14(6):

Current Applications and the Future of Phage Therapy for Periprosthetic Joint Infections.

Arian Ocean Abedi, Armita Armina Abedi, Tristan Ferry, Mustafa Citak.

  Periprosthetic joint infections (PJI) present significant challenges in orthopedic surgery, largely due to the complexity of treating antibiotic-resistant infections. Phage therapy, which utilizes bacteriophages to target bacterial pathogens, offers a promising supplement to traditional antimicrobial methods. This review discusses the current applications of phage therapy in the management of PJI, exploring its underlying mechanisms, clinical outcomes, and practical considerations. We also explore advances in phage therapy technology, including the development of phage cocktails, bioengineered phages, and combination therapies with antibiotics, which enhance the specificity and effectiveness of treatments. Furthermore, we address the future potential of phage therapy to be integrated into standard treatment protocols, focusing on ongoing innovations and research areas.The regulatory and ethical aspects of phage therapy in clinical settings are also discussed. By offering a comprehensive evaluation of both the current state and prospects of phage therapy, this review aims to inform clinical practice and stimulate further research into this innovative treatment modality for PJI management.

Keywords:  antimicrobial resistance; bacteriophage; periprosthetic joint infection; phage therapy

DOI:  https://doi.org/10.3390/antibiotics14060581
Antibiotics (Basel). 2025 May 29. pii: 553. [Epub ahead of print]14(6):

Current Clinical Laboratory Challenges to Widespread Adoption of Phage Therapy in the United States.

Ahnika Kline, Ana G Cobián Güemes, Jennifer Yore, Chandrabali Ghose, Daria Van Tyne, Katrine Whiteson, David T Pride.

  The resurgence of phage therapy in Western societies has been in direct response to recent increases in antimicrobial resistance (AMR) that have ravaged many societies. While phage therapy as a concept has been around for over 100 years, it has largely been replaced by antibiotics due to their relative ease of use and their predictability in spectrum of activity. Now that antibiotics have become less reliable due to greater antibiotic resistance and microbiome disruption, phage therapy has once again become a viable and promising alternative, but it is not without its challenges. Much like the development of antibiotics, with deployment of phage therapeutics there will be a simultaneous need for diagnostics in the clinical laboratory. This review provides an overview of current challenges to widespread adoption of phage therapy with a focus on adoption in the clinical diagnostic laboratory. Current barriers include a lack of standard methodology and quality controls for phage susceptibility testing and selection, the absence of phage-antibiotic synergy testing, and the absence of standard methods to assay phage activity on biofilms. Additionally, there are a number of lab-specific administrative and regulatory barriers to widespread phage therapy adoption including the need for pharmacokinetic (PK) and pharmacodynamic (PD) assays, methods to account for changes in phages after passaging, an absence of regulatory guidance on what will be required for agency approvals of phages and how broad that approval will apply, and the increased need for lab personnel or automation to account for the work of testing large phage libraries against bacteria isolates.

Keywords:  antibiotic alternatives; antibiotic–phage synergy; bacteriophage therapy; clinical microbiology laboratory; synergy testing

DOI:  https://doi.org/10.3390/antibiotics14060553
Antibiotics (Basel). 2025 May 27. pii: 545. [Epub ahead of print]14(6):

The Current Landscape of Phage-Antibiotic Synergistic (PAS) Interactions.

Brittany S I Supina, Jonathan J Dennis.

  Background: In response to the urgent need for new antibiotics targeting high-priority MDR pathogens, bacteriophages (phages) have emerged as promising non-traditional antimicrobial agents. Phages are viruses that infect bacteria and induce cell lysis through mechanisms distinct from those of antibiotics, making them largely unaffected by most antibiotic resistance mechanisms. Importantly, phages have been shown to work cooperatively with an array of clinically useful antibiotics, and phage-antibiotic synergy (PAS) represents a sophisticated strategy that may improve treatment outcomes. However, the interactions between phages and antibiotics are diverse, ranging from synergistic to antagonistic, and understanding the mechanisms underlying these interactions is crucial for developing effective PAS treatments. In this review, we summarize the potential evolutionary and molecular mechanisms that drive PAS and the current landscape of phage-antibiotic interactions. Conclusions: Towards the development of robust PAS strategies, we review in vitro methods for assessing PAS and considerations for choosing and employing candidate phage-antibiotic combinations.

Keywords:  antagonism; antibiotics; bacteriophages; novel therapeutics; phage therapy; phages; synergy

DOI:  https://doi.org/10.3390/antibiotics14060545
Sheng Wu Gong Cheng Xue Bao. 2025 Jun 25. 41(6): 2256-2274

[Phage therapy for multidrug-resistant Acinetobacter baumannii].

Jia Wu, Jun Wang.

  Acinetobacter baumannii is a Gram-negative opportunistic pathogen widely distributed in hospital settings. It can survive for a long time and cause a variety of infections, including pneumonia, septicemia, urinary tract infections, and meningitis. The bacterium demonstrates extensive resistance, particularly to critical antibiotics like carbapenems and polymyxins, posing a serious threat to the recovery of severely ill patients. Carbapenem-resistant A. baumannii has been designated as a pathogen of critical priority on the World Health Organization (WHO) Bacterial Pathogen Priority List, requiring urgent development of new therapeutic agents. Phages, as a novel biological control approach, exhibit substantial potential in combating A. baumannii infections due to their specific ability to infect and lyse bacteria. This review highlights the application and potential of phages and phage-derived enzymes against multidrug-resistant A. baumannii, considering the epidemiological trends of A. baumannii in China, with the aim of providing innovative insights and strategies for phage therapy of drug-resistant bacterial infections.

Keywords:  Acinetobacter baumannii; multidrug-resistant; phage; phage-derived enzymes

DOI:  https://doi.org/10.13345/j.cjb.250114
World J Virol. 2025 Jun 25. 14(2): 95826

Synergistic efficacy of phages along with vancomycin for eradication of vancomycin-resistant Enterococcus faecalis biofilms.

Minakshi Sahu, Ranjeet Kumar Vishwakarma, Subhash Lal Karn, Gopal Nath.

   BACKGROUND: The upsurge of antibiotic resistance is a significant challenge to public health, and the dry pipeline of new antibiotics has prompted the discovery of alternative treatment approaches. Enterococcus faecalis (E. faecalis) isolates are often multidrug-resistant, posing challenges to antibiotic therapy. Bacteriophage therapy is being explored as an alternative method to treat the growing population of antibiotic-resistant infections. Nevertheless, many inherent limitations of phages diminish their therapeutic utility, notably the restricted host range and quick development of mutants. The specific types and quantities of bacteriophages and antibiotics may be crucial in generating the optimal phage-antibiotic synergy.
AIM: To optimize the doses, order, and timing to optimize the synergy of phages and vancomycin on different bacteria states.
METHODS: A volume of 180 μL of E. faecalis bacteria in the logarithmic growth phase, with a concentration of approximately 1 × 108 colony forming units (CFUs)/mL, was introduced onto a microtitre plate. Subsequently, 20 μL of phage suspension (1 × 106 PFUs/mL), vancomycin (16 µg/mL), or a combination of both was introduced into the designated wells in the specified sequence and incubated at 37 °C for 48 hours. The number of live bacteria was counted at different time points using standardized CFU counting protocols.
RESULTS: The biofilm model demonstrated that combining phages with vancomycin can eradicate the biofilm. Sequential therapy, involving phage application 8 hours before the antibiotic at a concentration of 108 PFUs/mL, proved the most efficient in eliminating the biofilms and killing the planktonic form of E. faecalis.
CONCLUSION: The combination of phage ɸEFP01 at a higher concentration with a subinhibitory concentration of vancomycin yields a synergistic antibacterial outcome on E. faecalis strain resistant to vancomycin.

Keywords:  Bacteriophage; Biofilm; Enterococcus faecalis; Multiple drug resistance; Phage-antibiotic synergy

DOI:  https://doi.org/10.5501/wjv.v14.i2.95826
IEEE J Biomed Health Inform. 2025 Jun 24. PP

Phage Host Prediction Using Deep Neural Network with Multi-source Protein Language Models and Squeeze-and-Excitation Attention Mechanism.

Peng Gao, Long Xu, Yuan Bai, Qiuzhen Lin, Junkai Ji, Lijia Ma.

Phage therapy (PT) has become a promising alternative for treating infections with the increase of antimicrobial resistance. PT utilizes phages to bind to specific receptors on bacterial surfaces via receptor-binding proteins (RBPs), enabling precise destruction of targeted hosts. In PT, a key issue is the phage host prediction (PHP), which tries to match therapeutic phages to pathogenic hosts. However, traditional PHP methods are often hindered by the time-consuming and expensive wet-lab experiments, while recent computational methods neglect the evolutionary diversity and local feature patterns of RBPs. In this article, we propose a novel deep neural network (called PHPRBP) for PHP based on phage RBPs. In PHPRBP, we first utilize pre-trained protein language models (i.e., ESM2 and ProtT5) to learn the multi-source embedding representations from these RBPs, revealing diverse and complementary features. Then, we employ an adaptive synthetic technique to augment minority class samples, addressing the data scarcity issue. Subsequently, we design a deep neural network architecture, which uses a convolutional neural network to capture local sequence features, and applies a squeeze-and-excitation attention mechanism to enhance the contribution of important features. Finally, a fully connected network is used for host prediction. Experimental results show that PHPRBP outperforms the state-of-the-arts in host prediction at both genus and species levels. The data and code of PHPRBP are available at https://github.com/a1678019300/PHPRBP.

DOI: https://doi.org/10.1109/JBHI.2025.3582652
World J Microbiol Biotechnol. 2025 Jun 25. 41(7): 230

Proteomic analysis reveals phage-driven metabolic shifts and biofilm disruption in methicillin-resistant Staphylococcus aureus (MRSA).

Khulood Hamid Dakheel, Raha Abdul Rahim, Jameel R Al-Obaidi, Nurhanani Razali, Vasantha Kumari Neela, Tan Geok Hun, Khatijah Yusoff.

  Methicillin-resistant Staphylococcus aureus (MRSA) biofilms pose a severe risk to public health, showing resistance to standard antibiotics, which drives the need for novel antibacterial strategies. Bacteriophages have emerged as potential agents against biofilms, especially through their phage-encoded enzymes that disrupt the biofilm matrix, enhancing bacterial susceptibility. In this study, two bacteriophages, UPMK_1 and UPMK_2, were propagated on MRSA strains t127/4 and t223/20, respectively. Biofilms formed by these strains were treated with phages at specified concentrations, followed by protein extraction and analysis. Comparative proteomic profiling was performed using one-dimensional and two-dimensional SDS-PAGE, with protein identification facilitated by MALDI-TOF/TOF MS spectrometry, to observe biofilm degradation effects. Proteomic analysis revealed that phage treatment induced significant changes in biofilm protein expression, particularly with upregulated ribosome-recycling factors and elongation factors linked to enhanced protein synthesis, reflecting a reactivation of amino acid metabolism in the treated biofilms. This was marked by upregulated intracellular proteases like CIpL, which play a role in protein refolding and degradation, critical for phage progeny production and biofilm disruption. Phage treatment demonstrated notable effects on the metabolic and protein synthesis pathways within MRSA biofilms, suggesting that phages can redirect bacterial cellular processes to favour biofilm breakdown. This indicates the potential of bacteriophages as a viable adjunct to traditional antimicrobial approaches, particularly in combating antibiotic-resistant infections like MRSA. The study underscores the efficacy of bacteriophages as anti-biofilm agents, offering a promising strategy to weaken biofilms and combat antibiotic resistance through targeted disruption of bacterial metabolic pathways and biofilm integrity.

Keywords:  Bacteriophages therapy; Biofilm disruption; Phage-encoded enzymes; Protein synthesis

DOI:  https://doi.org/10.1007/s11274-025-04397-5
mSystems. 2025 Jun 25. e0058725

Multi-omics characterization of a lytic phage targeting Listeria monocytogenes.

Stevan Cucić, Leena Putzeys, Maarten Boon, Dion Lepp, Rob Lavigne, Cezar M Khursigara, Hany Anany.

  Listeria monocytogenes is a foodborne pathogenic bacterium that can persist in food-processing environments. Strictly lytic Listeria phages have shown promise as biosanitation and biocontrol agents. However, little is known about the molecular progression of phage expression and the host gene expression profile it elicits in Listeria. In this work, the P100-like phage CKA15 was characterized using a proteogenomics-based approach to identify virion-associated proteins, Illumina-based RNA-seq to analyze time-resolved host and phage transcript abundance during infection, and ONT-cappable-seq to experimentally determine the operon structure of the phage genome. We detected 29 phage-encoded putative particle-associated proteins. During infection, a progressive decrease in host transcript abundance and an increase in phage transcript abundance are observed. The progression of phage gene expression indicates a switch in functions from hypothetical at 5 min; nucleic acid metabolism at 15; structural proteins at 25; and DNA packaging, tail assembly, and lysis at 40 min post-infection. Using ONT-cappable-seq, we identified 81 phage transcription start sites (TSS) and 66 transcription termination sites (TTS). We used motif analysis to identify two classes of promoters, corresponding to early and late infection stages. Profound changes in the host transcriptome became evident 5 min post-infection. GO enrichment and KEGG pathway analysis indicate a downregulation of host transcription factor expression and an upregulation of translation, cobalamin biosynthesis, and propanediol metabolism. This research contributes to our systems-level understanding of the infection process of a strictly lytic phage infecting an important foodborne pathogen.IMPORTANCEListeria monocytogenes is an important foodborne pathogenic bacterium that contributes to significant mortality worldwide. Since bacteriophages have evolved diverse mechanisms to take over their host bacteria, studying phage interactions with pathogenic bacteria enables researchers to develop novel ways of controlling pathogenic bacteria and tools to study them. Detection of phage particle-associated proteins using mass spectrometry combined with transcriptomic techniques that determine the operon structure of the phage genome, time-resolved transcript abundance of phage, as well as host transcripts, comprises powerful approaches for phage characterization. Moreover, these analyses provide a starting point for hypothesis generation in relation to different aspects of the biology of phages infecting L. monocytogenes, including phage particle assembly, gene regulation, host takeover, and bacterial response to phage infection.

Keywords:  Listeria phage CKA15; multi-omics; phage-host interactions; proteogenomics; transcriptomics

DOI:  https://doi.org/10.1128/msystems.00587-25
Virus Genes. 2025 Jun 21.

Isolation and complete genome sequence of a novel Mycobacterium phage MS619.

Qiqi Zhao, Xinpu Shi, Mingshuai Liu, Lei Ji.

  Mycobacterium, an opportunistic pathogen, is highly prone to causing infections in humans, and its resistance to antibiotics poses a significant challenge. Phage therapy has emerged as a highly promising alternative treatment. In this study, a bacteriophage infecting Mycobacterium smegmatis was isolated from soil, named MS619, and classified within the class Caudoviricetes. Phages have an icosahedral head (60 ± 2 nm in diameter) and a long, non-contractile tail with a size of 125 ± 2 nm. The genome of MS619 was found to be a double-stranded DNA composed of 48,955 bp, containing 76 open reading frames (ORFs), related to phage packaging, structure, lysin, regulation, and replication. The BLASTN results indicated that MS619 exhibits a high-sequence identity (93%) with Mycobacterium phage Georgie2, a known bacteriophage recorded in the NCBI GenBank database. A typical holin-lysin system was identified in the MS619 genome. The topology of holin was predicted to contain two transmembrane domains, which significantly contribute to antimicrobial activity. No antibiotic resistance- or virulence factor-related genes were detected in the phage. Moreover, the bacteriophage demonstrates biofilm growth inhibition capability. This study led to the isolation of MS619, a bacteriophage exhibiting potential antibacterial efficacy against Mycobacterium infections.

Keywords:   Mycobacterium smegmatis ; Biological characteristics; Genomic analysis; Phage

DOI:  https://doi.org/10.1007/s11262-025-02170-2
Biomolecules. 2025 Jun 19. pii: 903. [Epub ahead of print]15(6):

Advances in Local Drug Delivery for Periodontal Treatment: Present Strategies and Future Directions.

Mayuka Nakajima, Mayuko Yanagawa, Honoka Takikawa, Truong Tran Thien, Lorena Zegarra-Caceres, Chunyang Yan, Koichi Tabeta.

  Periodontitis is a highly prevalent, irreversible inflammatory disease characterized by the destruction of tooth-supporting tissues, eventually leading to tooth loss. Conventional treatment involves the mechanical removal of the subgingival biofilm, which is a major cause of gingival inflammation. However, the inaccessibility of deep-seated polymicrobial biofilms limits its effectiveness. Despite the adjunct use of systemic antimicrobials, their low site-specific bioavailability and systemic side effects remain concerns. Local drug administration offers a targeted alternative. However, the dynamic oral environment, which is characterized by continuous salivary and gingival crevicular fluid flow, poses challenges in maintaining therapeutic drug levels. Drug delivery systems (DDSs) provide technical solutions to overcome these limitations. With advancements in materials science and nanotechnology, diverse local DDS (LDDS) formulations tailored for periodontal applications have been developed. While traditionally focused on infection control, the application of LDDSs has expanded beyond antimicrobial therapy. Increasing attention has been paid to LDDS-based regenerative strategies, which aim to overcome the limitations of conventional regenerative therapies. This review aims to provide a comprehensive overview of the current and emerging DDS strategies in periodontal therapy, focusing on their applications in infection management and bone regeneration and discussing their limitations and prospects for clinical translation.

Keywords:  antibiofilm therapy; bone regeneration; local drug delivery systems; nanotechnology; periodontitis

DOI:  https://doi.org/10.3390/biom15060903
Int J Infect Dis. 2025 Jun 25. pii: S1201-9712(25)00189-4. [Epub ahead of print] 107965

Clinical trial landscape for pneumonia: Evolving agents against bacterial pathogens.

Du Feng, Huixin Jiang, Hao Deng, Gengda Huang, Yue Zhu, Rong Xiao, Gengjia Chen, Chengzhi Zhou.

  Pneumonia remains a significant global health challenge, exacerbated by the escalating crisis of antimicrobial resistance. Through a comprehensive analysis of clinical trials spanning three decades, this study reveals the evolving landscape of anti-pneumonia drug development. Through analysis of clinical trial volumes and therapeutic mechanisms, our findings demonstrate a substantial increase in early-phase clinical trials over the past decade, reflecting intensified efforts to combat growing antimicrobial resistance, while research focusing on DNA topoisomerase inhibition has declined after an initial development surge. Although carbapenems serve as a cornerstone in pneumonia treatment, they face increasing risks of resistance-related mortality, particularly in hospital-acquired pneumonia (HAP) dominated by drug-resistant pathogens. Given the varying pathogen susceptibility across different age groups, we conducted age-stratified analyses. While traditional mechanisms like cell wall synthesis inhibition remain dominant, innovative approaches are emerging to enhance drug delivery and antimicrobial action, exemplified by phage therapy, non-ionic silver nanoparticles, and antibody-drug conjugates. This landscape analysis not only synthesizes historical and current therapeutic trends but also highlights promising directions for combating resistance, emphasizing the urgent need for novel agents in the post-antibiotic era.

Keywords:  Antimicrobial resistance; Clinical trial landscape; Pneumonia

DOI:  https://doi.org/10.1016/j.ijid.2025.107965
Infect Dis Rep. 2025 Jun 09. pii: 66. [Epub ahead of print]17(3):

Gut Microbiome in Pulmonary Arterial Hypertension-An Emerging Frontier.

Sasha Z Prisco, Suellen D Oliveira, E Kenneth Weir, Thenappan Thenappan, Imad Al Ghouleh.

  Pulmonary arterial hypertension (PAH) is an irreversible disease characterized by vascular and systemic inflammation, ultimately leading to right ventricular failure. There is a great need for adjunctive therapies to extend survival for PAH patients. The gut microbiome influences the host immune system and is a potential novel target for PAH treatment. We review the emerging preclinical and clinical evidence which strongly suggests that there is gut dysbiosis in PAH and that alterations in the gut microbiome may either initiate or facilitate the progression of PAH by modifying systemic immune responses. We also outline approaches to modify the intestinal microbiome and delineate some practical challenges that may impact efforts to translate preclinical microbiome findings to PAH patients. Finally, we briefly describe studies that demonstrate contributions of infections to PAH pathogenesis. We hope that this review will propel further investigations into the mechanisms by which gut dysbiosis impacts PAH and/or right ventricular function, approaches to modify the gut microbiome, and the impact of infections on PAH development or progression.

Keywords:  gut microbiome; inflammation; pulmonary arterial hypertension

DOI:  https://doi.org/10.3390/idr17030066
Pharmaceuticals (Basel). 2025 May 30. pii: 825. [Epub ahead of print]18(6):

Antimicrobial Smart Dressings for Combating Antibiotic Resistance in Wound Care.

Alina-Georgiana Cristea Hohotă, Elena-Lăcrămioara Lisă, Simona Iacob Ciobotaru, Ionut Dragostin, Claudia Simona Ștefan, Iuliu Fulga, Andra Monica Anghel Ștefan, Maria Dragan, Ionela Daniela Morariu, Oana-Maria Dragostin.

  Wound healing is a complex, tightly regulated process essential for maintaining skin barrier function. Chronic wounds, often complicated by biofilm-forming bacteria and elevated oxidative stress, pose significant challenges in clinical management. The rise of antibiotic-resistant bacteria has further exacerbated the problem, limiting therapeutic options and complicating wound treatment. Traditional wound care approaches frequently fail to provide real-time accurate insights into wound status, leading to delayed or suboptimal treatments. Recent advancements in modern and smart wound dressings, which integrate various biosensors, different new drug delivery systems, and wireless communication technology, offers promising solutions for monitoring wound progression over time. These innovations enable early detection of adverse events such as bacterial infections and inflammation, facilitating more effective, on-demand treatment. This review highlights the current state of antibiotic-embedded wound dressings, discusses their limitations, and explores the potential of next-generation wound dressings incorporating microelectronic sensors for real-time monitoring and adaptive therapeutic responses to support healing and combat antimicrobial resistance.

Keywords:  antimicrobial resistance; antimicrobials; wound dressings; wound infection

DOI:  https://doi.org/10.3390/ph18060825
Int J Nanomedicine. 2025 ;20 7549-7578

Research Progress of Multifunctional Hydrogels in Promoting Wound Healing of Diabetes.

Jiansong He, Jiemei Chen, Taotao Liu, Fuli Qin, Weipeng Wei.

  Diabetic wound healing represents a crucial and complex subject in clinical medicine, because of its physiological mechanism and pathological state, the conventional treatment methods are often limited. In recent years, multifunctional hydrogels have emerged as a focal point in the research field regarding the healing of diabetic wounds. This is attributed to their outstanding biocompatibility, the capacity for controlling drug release, and the traits of facilitating cell migration and proliferation. This paper reviews the fundamental materials, modification strategies for functionality, the principles underlying drug release, and the latest application advancements of multifunctional hydrogels in the context of facilitating the healing process of diabetic wounds. By introducing bioactive molecules and utilizing 3D bioprinting technology, researchers continue to optimize the properties of hydrogels to adapt to various wound conditions, which demonstrates great promise in the use of wound dressings. Taking the microenvironment of diabetic wounds into consideration, strategies for antibacterial, anti-inflammatory, immunomodulatory, antioxidant, and pro-angiogenic effects are integrated with multifunctional hydrogels. This paper systematically analyzes the existing challenges and explores the future research directions, and emphasizes the potential of multifunctional hydrogels in improving wound healing of diabetes and their clinical application prospects.

Keywords:  diabetic wound; hydrogels; multi-functional; wound dressing

DOI:  https://doi.org/10.2147/IJN.S519100
Methods Mol Biol. 2025 ;2952 87-105

Advancements in AI for Computational Biology and Bioinformatics: A Comprehensive Review.

Viswanathan Nalina, Dhamodharan Prabhu, Jesudass Joseph Sahayarayan, Ramasamy Vidhyavathi.

  The field of computational biology and bioinformatics has seen remarkable progress in recent years, driven largely by advancements in artificial intelligence (AI) technologies. This review synthesizes the latest developments in AI methodologies and their applications in addressing key challenges within the field of computational biology and bioinformatics. This review begins by outlining fundamental concepts in AI relevant to computational biology, including machine learning algorithms such as neural networks, support vector machines, and decision trees. It then explores how these algorithms have been adapted and optimized for specific tasks in bioinformatics, such as sequence analysis, protein structure prediction, and drug discovery. AI techniques can be integrated with big data analytics, cloud computing, and high-performance computing to handle the vast amounts of biological data generated by modern experimental techniques. The chapter discusses the role of AI in processing and interpreting various types of biological data, including genomic sequences, protein-protein interactions, and gene expression profiles. This chapter highlights recent breakthroughs in AI-driven precision medicine, personalized genomics, and systems biology, showcasing how AI algorithms are revolutionizing our understanding of complex biological systems and driving innovations in healthcare and biotechnology. Additionally, it addresses emerging challenges and future directions in the field, such as the ethical implications of AI in healthcare, the need for robust validation and reproducibility of AI models, and the importance of interdisciplinary collaboration between computer scientists, biologists, and clinicians. In conclusion, this comprehensive review provides insights into the transformative potential of AI in computational biology and bioinformatics, offering a roadmap for future research and development in this rapidly evolving field.

Keywords:  Algorithm; Artificial intelligence; Bioinformatics; Computational biology; Machine learning

DOI:  https://doi.org/10.1007/978-1-0716-4690-8_6
Methods Mol Biol. 2025 ;2952 219-232

AI Revolutionizing Cell and Genetic Engineering: Innovations and Applications.

Salomie Jennifer Samuel Johnson.

  The integration of Artificial Intelligence (AI) into the realms of cell and genetic engineering has ushered in a transformative era of innovation and discovery. This chapter explores the myriad ways in which AI technologies are revolutionizing these fields, from data analysis and drug discovery to genomic sequencing and gene editing. AI algorithms are adept at analyzing vast datasets, uncovering intricate patterns, and predicting biological phenomena with unparalleled accuracy. In drug discovery, AI-driven platforms expedite the identification of potential therapeutics by simulating molecular interactions and predicting their efficacy. Genomic sequencing efforts benefit from AI's ability to interpret genetic variations and their implications for health and disease. Furthermore, AI-guided gene editing techniques, such as CRISPR-Cas9, enable precise and targeted modifications of the genome. Beyond the laboratory, AI facilitates personalized medicine by analyzing genetic data to tailor treatments to individual patients. This chapter underscores the pivotal role of AI in advancing cell and genetic engineering, promising a future of unprecedented scientific breakthroughs and personalized healthcare solutions.

Keywords:  Artificial intelligence (AI); Cell engineering; Data analysis; Drug discovery; Gene editing; Genetic engineering; Genomic sequencing; Precision medicine

DOI:  https://doi.org/10.1007/978-1-0716-4690-8_12
Ther Adv Respir Dis. 2025 Jan-Dec;19:19 17534666251341751

Rapid microbial evaluation of acute exacerbations of bronchiectasis using FilmArray Pneumonia plus Panel in a real-world setting.

Charles Wong, Chun Wai Tong, Hei Shun Cheng, Pui Hing Chiu, Flora Pui Ling Miu, Yiu Wing Lam, Loretta Yin Chun Yam.

   BACKGROUND: Acute exacerbations of bronchiectasis (AEB) are frequently caused by bacterial and/or viral infections. Rapid multiplex polymerase chain reaction (PCR) panels in respiratory specimens have significantly advanced microbial evaluation in patients with pneumonia. However, their clinical utility in patients with AEB remains unknown.
OBJECTIVES: To investigate the microbial characteristics of AEB using FilmArray Pneumonia plus Panel (FAPP) and explore its clinical impact in a real-world setting.
DESIGN: A cross-sectional study.
METHODS: Spontaneous sputum samples of patients hospitalized for AEB were tested using FAPP in addition to standard-of-care testing. Microbial characteristics of AEB and the clinical impact of FAPP were evaluated.
RESULTS: Among 83 patients, FAPP detected ⩾1 bacterial pathogen(s) in 68 samples (81.9%), identifying 101 bacteria, with high abundance (106 to ⩾107 copies/ml) observed in 48 patients (57.8%). The most commonly detected bacteria were Pseudomonas aeruginosa (Pa) (37/83, 44.6%), Staphylococcus aureus (21/83, 25.3%), and Haemophilus influenzae (13/83, 15.7%). Respiratory viruses were identified in 21 patients (25.3), with Influenza A and Respiratory syncytial virus being the most common. Culture detected bacteria in significantly fewer samples (n = 25 [30.1%], p < 0.001). FAPP demonstrated 100% positive percent agreement and negative predictive value for all cultured bacteria, except for Corynebacterium striatum (n = 2), which was not included in the panel. FAPP shortened the time to bacterial results (mean: 10.8 h vs 70.8 h by culture, p < 0.001), and led to antimicrobial changes in 25 patients (30.1%) before the culture results were available. In multivariate analysis, chronic Pa infection (odds ratio (OR) 14.71), underweight status (OR 5.84), and cystic bronchiectasis (OR 5.26) were independent predictors of Pa detection by FAPP.
CONCLUSION: The sputum multiplex PCR panel (FAPP) enables rapid identification of bacterial and viral pathogens in AEB, supporting early antimicrobial decision-making. Our findings highlight the potential utility of sputum multiplex PCR panels in improving the management of bronchiectasis exacerbations.

Keywords:  PCR; Pseudomonas aeruginosa; bronchiectasis; exacerbation; filmarray; sputum

DOI:  https://doi.org/10.1177/17534666251341751
ACS Appl Mater Interfaces. 2025 Jun 25.

Microrobots for Antibiotic-Resistant Staphylococcus aureus Skin Colony Eradication.

Anna Jancik-Prochazkova, Hana Michalkova, Kristyna Cihalova, Zbynek Heger, Martin Pumera.

  Self-propelled nano- and micromachines have immense potential as autonomous seek-and-act devices in biomedical applications. In this study, we present microrobots constructed with inherently biocompatible materials and propulsion systems tailored to skin-related applications. Addressing the significant treatment challenge posed by methicillin-resistant Staphylococcus aureus (MRSA) skin infections, we demonstrate that photocatalytic titanium dioxide microrobots decorated with silver or platinum can effectively and rapidly eradicate MRSA biofilms grown on skin-mimicking membranes and porcine skin tissues. These microrobots are powered by hydrogen peroxide or ultraviolet light─agents considered toxic in high concentrations but commonly used in controlled amounts for skin disinfection and naturally encountered by the skin. By examining the effects of different metal coatings on the propulsion abilities of the microrobots, we show that these chemically propelled devices can eliminate biofilms without causing significant damage to the surrounding skin tissues, as confirmed by histological analysis. This work paves the way for the use of microrobots in skin-related biomedical applications, particularly in cases where traditional antibiotics are ineffective.

Keywords:  Janus particles; biofilm; microrobots; skin infection; titanium dioxide

DOI:  https://doi.org/10.1021/acsami.5c08683