Search Results (1,372)

Bacteriophages are a key ecological factor in the legume rhizosphere, controlling bacterial populations and affecting introduced inoculant strains. Despite their importance, rhizobiophage genomic diversity remains poorly characterized. We report the complete genome of a novel predicted temperate Sinorhizobium phage, AP-202, isolated from agricultural Chernozem. This siphovirus infects the symbiont Sinorhizobium meliloti. Its 121,599 bp dsDNA genome has a strikingly low GC content (27.1%), likely reflecting adaptive evolution and a strategy to evade host defenses. The linear genome is flanked by 240 bp direct terminal repeats (DTRs), and its DNA packaging follows a T7-like strategy. Annotation predicted 178 protein-coding genes and one tRNA. Functional analysis revealed a complete lysogeny module and a divergent, two-pronged codon-usage strategy for translational control. A significant part of the proteome (74.2%) comprises hypothetical proteins, with 50 CDSs having no database homologs, underscoring its genetic novelty. Complete-genome comparison shows minimal similarity to known rhizobiophages, defining AP-202 as a distinct lineage. Phenotypic analysis indicates AP-202 acts as a selective ecological filter, with host resistance being more prevalent in agricultural than in natural soils. The AP-202 genome provides a unique model for studying phage–host coevolution in the rhizosphere and is a valuable resource for comparative genomics and soil virome research. Full article

The phage-resistant mutant (PRM) strains of Escherichia coli (E. coli) exhibited abundant genetic and phenotypic diversity. IS elements played a vital role in creating various genetic divergences and regulating gene functions under phage infection stress. Genetic variations of PRM strains derived from E. coli MG1655 and mutation frequencies of coevolved E. coli populations with phages were explored by high-throughput sequencing and resequencing. Infrequent-restriction-site PCR (IRS-PCR) and carbon utilization test revealed the genetic and phenotypic diversity of the PRM strains. Numerous and discrepant mutation sites (MSs) were observed in the PRM strains and the coevolved populations, and many MSs were related to the synthesis of flagella and LPS, which often serve as receptors in a phage invasion. The insertions of various IS elements in key gene locations were also frequently found in the PRM strains, which indicate for the first time that IS elements played a vital role in generating genetic divergence and regulating gene functions under phage infection stress. Resequencing revealed that the coevolved populations at three evolving stages had discrepant profiles of MSs, and nearly all detected MSs occurred in the coevolved populations, which led to coexisting phages that increased the mutation rates and expedited the occurrence of the defective MSs in E. coli populations. In summary, our results reveal that the widespread and abundant presence of phages may provide one important force driving bacterial genomic evolution and prompt bacterial genetic divergence via accelerated mutation and increased mutation rates in the E. coli genome. Full article

Background/Objectives: Phages show efficacy against multidrug-resistant Pseudomonas aeruginosa, but limited host ranges require combining them in cocktails. In this work, we characterized 25 P. aeruginosa phages, developed therapeutic cocktails active against diverse clinical isolates, and tested phage efficacy in a mouse incisional wound model. Methods/Results: These phages represent seven genera, and genomic and phenotypic analyses indicate that 24/25 are lytic and suitable for phage therapy. Phage host ranges on a diversity panel of 156 P. aeruginosa strains that included 106 sequence types varied from 8% to 54%, and together the 24 lytic phages were active against 133 strains (85%). All of the phages reduced bacterial counts in biofilms. A cocktail of five lytic phages, WRAIR_PAM1, covered 56% of the strain panel, protected 100% of mice from lethal systemic infection (vs. 20% survival in the saline-treated group), and accelerated healing of infected wounds. An improved five-phage cocktail, WRAIR_PAM2, was formulated by a rational design approach (using phages with broader host ranges, more complementing activity, relatively low resistance background, and compatibility in mixes). Conclusions: WRAIR_PAM2 covered 76% of highly diverse clinical isolates and demonstrated significant efficacy against topical and systemic P. aeruginosa infection, indicating that it is a promising therapeutic candidate. Full article

Rapid isolation of therapeutic bacteriophages from environmental sources is essential for personalized phage therapy, particularly when appropriate phages are unavailable in existing banks. However, comprehensive characterization of all candidate phages is resource-intensive, especially when plaque morphologies are similar and fail to discriminate between distinct phages. Here, we present an upstream screening approach that utilizes co-culture growth curve analysis to rapidly triage phage isolates during the early isolation process. We extracted seven biologically meaningful features that capture lysis kinetics, lysis efficiency, and post-lysis dynamics from bacterial growth curves and applied unsupervised clustering algorithms for phage discrimination. Validation using T-phages at a multiplicity of infection of 0.01 demonstrated superior clustering performance (Adjusted Rand Index = 0.881 ± 0.057) compared to established metrics including the Virulence Index and Centroid Index. Application to phages isolated from sewage successfully identified all three genomically distinct species present (sampling score = 1.0), enabling targeted selection of representative phages for downstream characterization. This approach reduced candidates requiring detailed analysis by two-thirds (from 21 to 7 isolates) while maintaining complete species coverage, thereby providing an efficient and scalable screening tool that reduces workload for downstream analyses and accelerates discovery of novel therapeutic phages for clinical applications. Full article

Bacteriophage therapy, which employs bacterial viruses to selectively eliminate pathogenic bacteria, has re-emerged as a promising strategy in the face of increasing antimicrobial resistance. However, its widespread clinical implementation is constrained by concerns regarding safety, standardisation, and predictable efficacy. In this review, we examine the key role of genomics in transforming phage therapy from an empirical practice into a standardised and personalised modality of contemporary medicine. We describe how whole-genome sequencing (WGS) provides a basis for safety assessment by enabling systematic screening to exclude virulence factors, antibiotic resistance genes, and markers of lysogeny. WGS also facilitates the prediction of therapeutic efficacy and supports more rational phage selection by identifying receptor-binding proteins and characterising bacterial defence systems. In clinical settings, WGS data are increasingly used to monitor the evolution of bacterial populations and to adapt phage cocktails during treatment, thereby supporting personalised, adaptive phage therapy. Looking ahead, further progress is likely to come from integrating synthetic biology and artificial intelligence to engineer phage-based therapeutics with programmable specificity and predictable properties. Together, these developments are shaping a new paradigm of phage therapy as a scientifically grounded, standardised and controlled strategy to treat infections caused by antibiotic-resistant bacteria. Full article

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

Background/Objectives: Staphylococcus (S.) aureus is a major pathogen causing bovine mastitis and is often refractory to antibiotic therapies due to virulence factors and resistance mechanisms. In this pilot study, the safety and efficacy of an intramammary phage cocktail, in naturally S. aureus-infected dairy cows, were investigated. Methods: The initial part of the study on farm 1 confirmed tolerability and safety, as there were no observed systemic side effects of treatment. The subsequent efficacy study on farm 2 included 23 with S. aureus infected udder quarters, which were randomly divided into a treatment group (n = 16) and a control group (n = 7). The quarters in the treatment group received five intramammary infusions of the phage cocktail at 12-h intervals. Results: This resulted in a bacteriological cure rate of 81.3% (13/16) for the treatment group, compared to 28.6% (2/7) in the control group (p = 0.026). Conclusions: These results indicate that phage therapy is well-tolerated and may be a promising alternative to antibiotics for treating S. aureus mastitis, although confirmation in larger-scale, multicenter studies is required. Full article

Background: Aeromonas hydrophila is a common bacterial pathogen that causes hemorrhagic septicaemia in several farmed aquaculture species. Phage therapy is considered a promising and feasible alternative to antibiotic treatment. Methods: In this study, an A. hydrophila-infecting jumbo phage Z90 was isolated from an aquaculture pond. The biological characteristics, genomic features, and in vitro and in vivo experiments were investigated to evaluate its application potential. Results: Phage Z90 was a myovirus with distinctive curled tail fibers. Additionally, phylogenetic and genomic analyses found that the phage Z90 was a novel virus belonging to the genus Ferozepurvirus of the family Chimalliviridae. One-step growth curve analysis revealed that the phage Z90 was a lytic phage, exhibiting a short latency period of 20 min and a relatively large burst size of 270 ± 42 PFU/cell. The phage Z90 particles were stable at psychrotrophic and mesophilic temperatures (10–50 °C) and a wide range of pH (pH 3–12). Genomic analysis revealed that the phage Z90 did not contain any genes encoding toxins, virulence factors, or antibiotic resistance factors. In vivo analysis demonstrated that the phage Z90 protected American eels from A. hydrophila infection, greatly increasing eel survival rates and alleviating symptoms caused by bacterial infections. The comparison of different phage administration methods suggested that phage Z90 was better administered through intraperitoneal injection than immersion in aquaculture water. Moreover, the combination of phage Z90 and ampicillin improved the bactericidal effect and reduced the treatment dosage compared to antibiotics or phage alone. Conclusions: Altogether, the findings of this study indicate that the phage Z90 can serve as a promising biocontrol agent for the treatment of A. hydrophila infection in aquaculture. Full article

Bacteriophage contamination remains a persistent and costly challenge in industrial bio-manufacturing. Traditional control strategies rely heavily on physical exclusion and chemical disinfection, yet these passive measures often fail to address the rapid evolutionary adaptation of phages and their persistence in complex fermentation environments. Recent genomic and biochemical discoveries have revealed a diverse arsenal of bacterial antiviral immune systems beyond the classical Restriction-Modification and CRISPR-Cas pathways, including cyclic oligonucleotide-based signaling systems and various abortive infection mechanisms. This review systematically summarizes the latest advances in bacterial anti-phage defense mechanisms, categorizing them into adsorption inhibition, replication interference, nucleic acid degradation, and population-level suicide defense. Furthermore, we discuss the application of synthetic biology in integrating these defense modules to construct broad-spectrum “pan-immune” microbial chassis. This active defense strategy offers a fundamental solution to phage predation and provides a theoretical basis for developing robust next-generation cell factories. Full article

Non-typhoidal Salmonella (NTS) are globally distributed zoonotic pathogens of major concern within the One Health–One Biofilm framework. Fluoroquinolone-resistant Salmonella strains are included by the World Health Organization (WHO) in the Bacterial Priority Pathogens List as high-risk agents. A key virulence determinant of Salmonella is its ability to form biofilms, which may display multidrug-resistant (MDR) characteristics and contribute to bacterial persistence and treatment failure. Animals, particularly poultry and reptiles, represent important reservoirs of Salmonella, and reptile-associated salmonellosis (RAS) may manifest as extraintestinal infections in humans. In the post-antibiotic era, there is an urgent need to identify effective alternatives to conventional therapies. This review summarizes current knowledge on Salmonella biofilms, with particular attention to their MDR potential, and discusses possible strategies for their prevention and eradication, including specific immunoprophylaxis, bacteriophage therapy, and alternative antimicrobials. The promising antimicrobials include plant-based compounds/extracts, bacteriocins, fatty acids, and synthetic/semi-synthetic substances. The integration of vaccination, phage therapy, and novel anti-biofilm compounds may provide a sustainable alternative to antibiotics in controlling Salmonella infections and aligns with the principles of the One Health approach. Full article

Bacteriophages are powerful drivers of microbial evolution and are increasingly explored as alternatives to antibiotics against multidrug-resistant pathogens such as Pseudomonas aeruginosa. Here, we describe the isolation, phenotypic characterization and genomic, structural and evolutionary analysis of Pseudomonas phage Adele, a lytic myovirus representing a novel species within the genus Pakpunavirus (family Vandenendeviridae). Phage Adele exhibits a short latent period of 20 min, a burst size of 59 ± 11 virions per infected cell and a high virulence index, efficiently lysing non-O11 Pseudomonas aeruginosa strains and reducing biofilm biomass. In vivo, Adele confers marked protection in a Galleria mellonella infection model. Phylogenetic reconstruction, synteny analysis and structural modeling demonstrate the relatedness of Vandenendeviridae to phages of the Andersonviridae and Vequintavirinae clades, pointing to a stable, ancestral virion architecture that has undergone lineage-specific elaborations, including the duplication and divergence of tail tube proteins. The tail assembly chaperone gene employs a conserved −1 programmed ribosomal frameshift. Phage Adele encodes an elaborate set of metabolic reprogramming and anti-defense systems, reflecting extensive horizontal gene transfer. The combination of a conserved structural architecture and mosaic genome establishes Adele as an exemplary system for studying modular evolution in phages, alongside its demonstrated therapeutic efficacy. Full article

Background: Periprosthetic joint infections (PJIs) of the hip and knee are one of the most severe complications in arthroplasty, often requiring prolonged antibiotic therapy and multiple revision surgeries. The increasing prevalence of multidrug-resistant organisms and biofilm-associated PJIs has renewed interest in bacteriophage therapy as a targeted, adjunctive treatment option in refractory cases. This investigation systematically reviews and discusses the current evidence regarding the application, outcomes, and safety profile of bacteriophage therapy in the management of PJIs. Methods: This systematic review was conducted in accordance with the 2020 PRISMA statement. PubMed, Google Scholar, EMBASE, and Web of Science were accessed in August 2025. No time constraints were used for the search. All clinical studies investigating bacteriophage therapy for bacterial PJIs were considered for eligibility. Results: A total of 18 clinical studies, comprising 53 patients treated with bacteriophage therapy for PJI, were included. The mean follow-up was approximately 13.6 months. Staphylococcus aureus was the most frequent pathogen (18 cases); phage cocktails were used in 33 patients and monophage preparations in 9, all combined with suppressive antibiotic therapy. Persistent or resistant joint pain was reported in only two patients (3.8%), while signs of ongoing infection despite phage therapy were observed in four patients (7.5%). Adverse events following BT were inconsistently reported. Conclusions: Bacteriophage therapy shows promise as an adjunctive treatment for hip and knee PJIs, especially in refractory or multidrug-resistant cases. Current evidence is limited and methodologically weak, underscoring the need for well-designed clinical trials to clarify efficacy, safety, and optimal integration into existing orthopaedic infection protocols. Full article

Bacteriophages, often referred to as “bacteria eaters,” have gained renewed interest as a powerful alternative to traditional antibiotics, particularly in addressing antibiotic-resistant bacterial infections. The present review summarizes data collected in Bulgaria during the 1960s, 1970s, and 1980s, drawing connections between past findings and present-day understanding of cytotoxicity and the clinical validation of bacteriophage applications. Its sections describe phage structure, mechanisms of action, and historical findings both globally and within the Bulgarian context, while also highlighting emerging trends and applications. The cited studies delve into the past through contemporary research contributions related to “Bulgarian phages”, a topic that remains underexplored in existing literature. The role of phages in medical microbiology is discussed alongside the challenges of therapeutic implementation, with particular focus on insights gained from the Bulgarian experience. In conclusion, by fostering international collaborations, investing in infrastructure, and establishing supportive policies, bacteriophage therapy can emerge as a critical tool for managing bacterial infections and reducing the global burden of antibiotic resistance in the future. Full article

Multidrug-resistant (MDR) Enterobacter cloacae is a growing public health issue worldwide, highlighting the urgent need for alternative antimicrobial strategies. This study reports on a lytic phage, designated B1, isolated from sewage, which exhibits specificity and lytic efficiency against MDR E. cloacae. Morphological observation revealed that B1 possesses an icosahedral head (~54 nm) and a short tail (~13 nm). Phage B1 showed a narrow host range, demonstrated stability within a temperature range of 4–37 °C, tolerance to pH values between 5 and 11, and showed an excellent bacteriolytic capacity with a short latent period of less than 10 min and a burst size of approximately 150 PFU/initially infected cell, indicating a rapid lytic cycle and efficient replication capability. Whole-genome sequencing revealed that the phage genome consists of 40,163 base pairs of double-stranded DNA containing 52 open reading frames (ORFs) with a GC content of 52%. Comparative genome-wide analysis using VIRIDIC revealed that B1 shares 75% to 92% similarity with Escherichia phage IMM-002 (accession: NC_048071), Citrobacter phage SH4, and Cronobacter phage Dev2 (accession: NC_023558), but shares less than 70% similarity with other Enterobacter phages. According to ICTV criteria, B1 represents a new species within the same genus as T7-like phages belonging to Autographiviridae, subfamily Studiervirinae, genus Kayfunavirus. In addition, B1 lacks lysogeny-associated or virulence genes and exhibits potent lytic activity against multidrug-resistant E. cloacae, making it a promising candidate for phage therapy. These findings opened up our understanding of the diversity of T7-like phages and provided insights into their evolutionary adaptability and therapeutic potential. Full article

Phage therapy (PT) is a promising alternative for antibiotic-resistant infections, but its immunomodulatory effects in clinical settings remain poorly understood. This exploratory observational study aimed to characterize pro- and anti-inflammatory gene response patterns in ten patients undergoing personalized PT at the Phage Therapy Unit in Wrocław. Peripheral blood mononuclear cells (PBMCs) and granulocytes were analyzed to assess changes in the expression of 22 selected immune-related genes associated with innate and adaptive immune signaling pathways. While no uniform pattern of immune gene expression was observed across the cohort, individual cases exhibited significant up- or downregulation of specific genes. Interestingly, we identified biological age as a potential determinant of the host response. Specifically, older patients showed higher activation of the innate sensing machinery in PBMCs, characterized by a higher TLR4 fold change which may reflect the “inflammaging” phenomenon. These findings suggest that chronic exposure to bacterial viruses (bacteriophages), unlike many viral infections, does not trigger a predictable, significant systemic immune activation and that immune responses to PT are highly individualized by host- and phage-related biological factors. By documenting this spectrum of real-world responses, our work provides baseline data and hypotheses to guide the rational design of future preclinical and clinical investigations. Full article