Search Results (260)

Multidrug-resistant (MDR) Escherichia coli (E. coli) at the poultry–human interface motivates evaluating strictly lytic bacteriophages as targeted biocontrol candidates. A lytic E. coli phage (GADS24) was isolated from poultry waste in Saudi Arabia. Plaque formation and host range were assessed against 10 clinical E. coli isolates. Virion morphology was examined by transmission electron microscopy (TEM). Whole-genome sequencing (Illumina) and annotation (Prokka/RAST) were followed by comparative genomics (BLASTn 2.15.0, ANI JSpeciesWS: 2014–2025 Ribocon GmbH—Version: 5.0.3, dDDH GGDC: GGDC 3.0 and phylogenetic/proteomic analyses for taxonomic placement. GADS24 formed clear plaques and lysed 5 of 10 clinical E. coli isolates tested. TEM revealed an icosahedral capsid (~72.6 nm) and a contractile tail (~131.7 nm), consistent with Tevenvirinae/Mosigvirus morphology. The dsDNA genome is 168,896 bp (GC 43.8%) with 268 predicted ORFs and two tRNA genes (tRNA-Arg and tRNA-Met); no lysogeny-related genes were detected. The closest relative was Escherichia phage JN02 (98.44% ANI; 57.8% dDDH), supporting assignment to Mosigvirus while indicating a genome-resolved distinct lineage. The genome is available in GenBank (OQ703618). GADS24 represents a genome-resolved, strictly lytic Mosigvirus with in vitro biocontrol-relevant phenotyping against E. coli, supporting follow-up development for poultry-associated infection control and deeper phage–host interaction studies. Full article

Chronic Pseudomonas aeruginosa lung infections in cystic fibrosis (CF) represent one of the most treatment-refractory bacterial diseases, sustained by biofilm formation, metabolic dormancy, and adaptive antibiotic resistance evolution. While bacteriophage (phage) therapy has emerged as a promising alternative for multidrug-resistant (MDR) pathogens, clinical studies in CF have demonstrated transient reductions in bacterial burden without achieving complete eradication. This review integrates molecular, evolutionary, and immunological findings to explain the multifactorial barriers that limit phage therapeutic efficacy in chronic CF infections. We highlight three major obstacles: (i) bacterial dormancy and persistence within biofilms that restrict phage adsorption and replication; (ii) hypermutability and extensive genotypic diversification of CF-adapted P. aeruginosa, which accelerate phage resistance evolution and necessitate broad host-range coverage; and (iii) CF-specific immune constraints—including a dysfunctional innate immune system and phage-neutralizing humoral immunity—that reduce phage bioavailability and undermine sustained bacterial clearance. Emerging strategies to overcome these challenges include the discovery of dormant-targeting phages capable of replicating in metabolically quiescent cells, evolution-informed phage training to delay resistance evolution, and synthetic phage engineering approaches designed to disrupt biofilms and expand host-range coverage. In parallel, computational or artificial intelligence (AI)-guided frameworks for phage cocktail design and cystic fibrosis transmembrane conductance regulator (CFTR) modulator-mediated restoration of host immune function together offer a more integrated therapeutic paradigm that unites phage biology and host immune context. By unifying clinical outcomes with mechanistic, evolutionary, and immunological perspectives, this review outlines a next-generation framework for phage therapy in CF aimed at achieving more durable therapeutic outcomes. Full article

Antimicrobial resistance is a growing global health threat, necessitating alternatives to conventional antibiotics. Bacteriophages, viruses that specifically target bacteria, represent a promising option, and phage-loaded electrospun fibers have recently gained attention as wound dressings for localized phage therapy. However, the influence of phage morphology and scaffold design has been largely overlooked. This study investigates how phage morphology and structure, in conjunction with scaffold design and processing conditions, may influence the biological performance of electrospun scaffolds. A bilayer scaffold was developed comprising a supportive polycaprolactone (PCL)/gelatin (70:30) layer and a polyvinyl alcohol (PVA) top layer loaded with bacteriophages. Two phage types, short-tailed podovirus APTC-SL.1 and long-tailed myovirus APTC-Efa.20, were incorporated into PVA fibers to evaluate their antibacterial activity against Staphylococcus lugdunensis and Enterococcus faecalis, respectively. The fibers were characterized using XRD, FTIR, TGA, optical microscopy, SEM, TEM, wettability analysis, and in vitro degradation tests. Biological assessments included antimicrobial testing, phage viability, and phage release. The bilayer scaffold containing short-tailed phages preserved phage viability and produced clear zones of lysis against S. lugdunensis, with ≈8.15% viability retained after electrospinning and relatively controlled release, whereas long-tailed phages showed no antibacterial activity. These results suggest that phage structure and morphology, together with electrospinning conditions and scaffold architecture, may play an important role in maintaining phage functionality in wound dressing applications, while acknowledging that host–phage interactions may also contribute to the observed differences. Full article

Bt Cry toxins remain the cornerstone of transgenic crop protection against Lepidopteran pests, yet field-evolved resistance, particularly in invasive species such as Spodoptera frugiperda and Helicoverpa armigera, can threaten their long-term efficacy. This review presents a comprehensive and unified mechanistic framework that synthesizes current understanding of Bt Cry toxin modes of action and the complex, multilayered regulatory mechanisms of field-evolved resistance. Beyond the classical pore-formation model, emerging evidence highlights signal transduction cascades, immune evasion via suppression of Toll/IMD pathways, and tripartite toxin–host–microbiota interactions that can dynamically modulate protoxin activation and receptor accessibility. Resistance arises from target-site alterations (e.g., ABCC2/ABCC3, Cadherin mutations), altered midgut protease profiles, enhanced immune regeneration, and microbiota-mediated detoxification, orchestrated by transcription factor networks (GATA, FoxA, FTZ-F1), constitutive MAPK hyperactivation (especially MAP4K4-driven cascades), along with preliminary emerging findings on non-coding RNA involvement. Countermeasures now integrate synergistic Cry/Vip pyramiding, CRISPR/Cas9-validated receptor knockouts revealing functional redundancy, Domain III chimerization (e.g., Cry1A.105), phage-assisted continuous evolution (PACE), and the emerging application of AlphaFold3 for structure-guided rational redesign of resistance-breaking variants. Future sustainability hinges on system-level integration of single-cell transcriptomics, midgut-specific CRISPR screens, microbiome engineering, and AI-accelerated protein design to preempt resistance trajectories and secure Bt biotechnology within integrated resistance and pest management frameworks. Full article

Antibiotic resistance is arguably one of the greatest threats to global health today. The worldwide emergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae underscores the urgent need for alternative treatments. Bacteriophages (phages) are considered one of the most promising alternatives to address this crisis. In this review, we summarize current knowledge of phage–host interactions and highlight recent advances in phage therapy against K. pneumoniae, including phage cocktails, antibiotic combination therapy, and treatments based on phage-derived proteins. Despite their tremendous therapeutic potential, significant challenges remain. We therefore also discuss strategies to optimize phage research and recent innovations in the field. Full article

Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the ‘low–temperature–pathogen’ model and shifts focus to mucosal barrier dysfunction and host–microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host–microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention. Full article

Bulleidia extructa strain PP_925, isolated from the periodontal pocket of a patient with periodontitis, is a Gram-positive Bacillota with an unusually compact genome of 1.38 Mb. Phylogenomic analyses place PP_925 within Erysipelotrichales and show close relatedness of Bulleidia to Solobacterium and Lactimicrobium, as well as the existence of previously undescribed related clades. The metabolic repertoire of PP_925 is strongly reduced: it retains glycolysis, the phosphotransacetylase–acetate kinase pathway, and arginine catabolism but lacks the tricarboxylic acid cycle and most de novo biosynthetic pathways for amino acids, nucleotides, fatty acids, cofactors, and vitamins, implying reliance on salvage and cross-feeding. Phylogenetic inference indicates independent peptidoglycan losses in multiple mycoplasma Erysipelotrichia-related lineages, while PP_925 has retained an ancestral Gram-positive cell wall despite extensive genomic reduction. The genome preserves systems crucial for host interaction and adaptability, including a horizontally acquired tad locus encoding type IV pili, a comG competence system, and several adherence-associated virulence factors. Defense mechanisms are diverse and include a CRISPR-Cas II-A system, a type II restriction–modification module adjacent to Gao_Qat-like genes, and the Wadjet system in a genome without prophages; CRISPR spacers indicate repeated encounters with Bacillota phages. Comparative genomics of PP_925 and related strains reveals a small core genome with lineage-specific adhesion and defense modules, indicating recent shared ancestry combined with adaptive flexibility under substantial genome reduction. Full article

Bacteriophages, viruses that target bacteria, offer a promising alternative to antibiotics in the face of escalating bacterial resistance. Despite their discovery over a century ago, their widespread adoption has been impeded by regulatory challenges, limited funding, and the dominance of antibiotics. This review evaluates the current status of phage therapy by examining a comprehensive literature search, applying predefined inclusion and exclusion criteria. The review assesses selected scientific reports and clinical studies for their safety and efficacy profiles. Our findings indicate that advancements in phage therapy involve critical steps such as rapid bacterial detection, effective isolation, production, purification of phage preparations, and understanding their interactions with the host. Clinical studies generally show promising safety profiles with fewer adverse events compared to controls, and some trials suggest efficacy even at lower phage titers. Case reports further highlight phage therapy’s potential, demonstrating high success rates and minimal adverse events, although caution is advised due to potential biases. Despite promising results, significant research gaps remain, primarily due to the limited number of large-scale, well-designed clinical trials. Full article

In this study, we characterized the holin-like protein ORF70 from the cyanophage MaMV-DC, offering valuable insights into its role in phage-mediated host cell lysis. ORF70 shares key features with class III holins, such as a hydrophobic transmembrane domain and membrane-associated localization, which are crucial for its bacteriolytic activity. Subcellular localization studies suggested its association with the membrane, supporting its classification as a holin-like protein. Overexpression of ORF70 in E. coli resulted in significant growth inhibition, increased β-galactosidase leakage, and visual confirmation of cell death through live/dead staining. Additionally, ORF70’s sensitivity to the energy toxin 2,4-dinitrophenol (DNP) further indicated its holin-like activity by promoting membrane depolarization. Transmission electron microscopy and Gram staining revealed characteristic morphological changes in E. coli cells, including membrane disruption, consistent with damage caused by holins. These results suggest that ORF70 acts as a holin-like protein that disrupts the host membrane, leading to bacterial cell death. Our study provides evidence supporting the holin-like activity of ORF70 from cyanophage MaMV-DC. This research significantly enhances our understanding of phage-host interactions and opens new avenues for developing phage-based therapies, offering promising alternatives to traditional antibiotics amidst the growing challenge of antibiotic resistance. Full article

Multi-drug-resistant Pseudomonas aeruginosa (P. aeruginosa) commonly causes infections that are difficult to treat, necessitating the development of new therapeutics. The search for more effective ways to combat the emergence of bacterial resistance has also led to research into phage-antibiotic synergy (PAS) as a potential therapeutic strategy. The aim of this study was to isolate and characterize virulent phages from water sources that are active against clinical carbapenem-resistant P. aeruginosa isolates, and to evaluate their in vivo efficacy using a Galleria mellonella larvae infection model. The biological and genomic characteristics of the isolated phages were determined using host range analysis, one-step growth curve analysis, transmission electron microscopy analysis and whole-genome sequencing. Two phages (vB_PaMB13 and vB_PaMB17) that demonstrated in vitro synergistic and bactericidal interactions with antipseudomonal antibiotics (tobramycin and ceftazidime) were selected for further investigation using the checkerboard method. The study revealed synergy between all phages and either antibiotic, tobramycin or ceftazidime, against P. aeruginosa. Similarly, the percentage survival rates increased in the in vivo model when both phages and antibiotics were used in combination. Overall, our study provides further support for the idea that phage-antibiotic synergy could be an effective strategy for improving treatment outcomes. Full article

Bacteriophages, or phages, are viruses that infect and kill specific bacteria, offering a promising alternative to antibiotics in livestock production. With growing concerns over antibiotic resistance, phages have gained renewed interest due to their ability to target harmful pathogens without disturbing beneficial gut microbiota. This review explores the application of dietary phage supplementation in monogastric animals, particularly pigs and poultry. In pigs, phage use has demonstrated beneficial effects such as improved growth performance, enhanced gut health, and reduced infections from Salmonella and E. coli. Various delivery methods, including feed and water supplementation, have been studied, with microencapsulation showing promising results for stability and effectiveness. Similarly, in poultry, phages have been successfully used to control pathogens like Salmonella, Campylobacter, and avian pathogenic E. coli, improving gut health, immunity, and overall performance. Several commercial phage products are already in use, demonstrating both safety and efficacy. Despite these advantages, challenges such as a narrow host range, bacterial resistance, and regulatory limitations remain. Therefore, further research is necessary to understand phage–host interactions, optimize delivery strategies, and evaluate long-term effects under normal and disease-free conditions. This review highlights the potential of bacteriophages as safe, targeted, and sustainable alternatives to antibiotics in monogastric animal production, contributing to improved animal health and reduced antibiotic use. Full article

CRISPR-Cas systems are best known as adaptive immune defenses in prokaryotes, but they also function as versatile regulators bridging bacterial immunity with host-related processes. Beyond neutralizing invasive phages and plasmids, these systems influence core aspects of bacterial physiology, such as modulating gene expression, stress responses, biofilm formation, quorum sensing, and virulence. Notably, CRISPR-mediated regulation can facilitate immune evasion at the host-pathogen interface, underscoring these systems as central orchestrators of microbial survival and host interactions. In addition, CRISPR-Cas has rapidly become a cornerstone of synthetic biology and microbiome engineering. Recent strategies repurpose native and engineered CRISPR systems to precisely modulate microbiome composition or deliver sequence-specific antimicrobials, underscoring the expanding translational potential of this system. Collectively, emerging insights highlight both the canonical immune function and non-canonical regulatory roles of CRISPR-Cas, as well as their broad biological and biotechnological relevance. This review provides a critical synthesis of these developments, illustrating how CRISPR-Cas bridges adaptive immunity and microbial physiology, and outlines future directions for harnessing this duality to deepen understanding of microbial physiology and inform new translational applications. Full article

Objectives: To explore the genetic basis of phage resistance in sequentially generated capsular mutants of phage-resistant Klebsiella pneumoniae using an established phage library. Methods: Sequential induction strategies were employed to obtain phage-resistant K. pneumoniae capsular mutants by exposing ST11-K64 K. pneumoniae Kp2325 to different single phages. Whole genome sequencing and bioinformatic analysis were used to elucidate the capsular-related genetic changes in phage-resistant mutants. Phenotypic changes were assessed through gene complementation, growth assays, phage cleavage spectrum analysis, TEM for phage morphology, CPS analysis, biofilm formation, and virulence assays. Results: Three sequentially generated phage-resistant K. pneumoniae capsular mutants were obtained, designated R1, R2 and R3. The narrowing of the phage cleavage spectrum and the evolutionary trade-offs of biological phenotypes were observed. Key genetic changes included: (1) ISKpn26 insertion disrupting wcaJ in R1; (2) combined wcaJ insertion and 9-bp deletion in waaH in R2; and (3) CPS gene cluster deletion in R3 were identified as key mechanisms of phage resistance in K. pneumoniae mutants R1, R2 and R3, respectively. Conclusions: Sequential exposure to different single phages led to rapid evolution of phage resistance in K. pneumoniae via genetic mutations that disrupt capsular synthesis. These findings highlight the critical role of bacterial capsule in phage–host interactions and emphasize the need to use phage cocktails targeting different types of receptors to counteract the evolution of bacterial defense mechanisms in phage therapy. Full article

Phage therapy has emerged as a promising alternative for combating infections caused by drug-resistant pathogens. Among these, Enterococcus faecalis remains a significant public health concern due to its persistence in clinical settings and frequent involvement in healthcare-associated infections (HAIs). In this study, we report the characterization of the lytic bacteriophage vB_EfaS_LOK1, isolated from urban sewage using E. faecalis strain IIH-74.4 as the host. Transmission electron microscopy revealed morphological features consistent with the phages formerly classified within the Siphoviridae family. The phage exhibited high thermal and pH stability, remaining viable up to 70 °C and within a pH range of 4–11. It displayed a latent period of 20 min and a burst size of 72 PFU/cell. Notably, vB_EfaS_LOK1 exhibited a narrow host range, lysing only the strain used for their isolation. Genomic analysis revealed a 41.2 kb double-stranded DNA genome devoid of known virulence or antibiotic resistance genes. Phylogenomic analysis classified the phage within the genus Efquatrovirus (Caudoviricetes), suggesting it represents a newly isolated bacteriophage species. Functional annotation identified genes related to DNA replication, host interaction, and bacterial lysis, including endolysins and holins with putative antimicrobial properties. Long-term stability assays demonstrated that tryptic soy broth (TSB) with CaCl₂/MgCl₂ at 4 °C maintained viability for at least 90 days. Collectively, these findings support the potential of vB_EfaS_LOK1 as a potential candidate for the development of phage-based therapies targeting E. faecalis. Full article

Persistent diarrhea of unknown etiology in children under 2 years of age is a common problem and poses a major challenge for the health sector. However, knowledge of the composition and dysbiosis of the intestinal phageome, phage-associated bacteriome in the persistent diarrhea remains limited. In this study, a process for phage enrichment and metagenomic extraction was developed and applied to recover gut phage metagenomes from 30 healthy children and 30 children with persistent diarrhea for high-throughput sequencing. Taxonomic annotation using Kraken2 revealed that, besides Norwalk virus, Primate bocaparvovirus 1 and Human-associated gemykibivirus 2, phage communities in the diarrhea group showed reduced diversity and contained sample-dependent phages targeting Salmonella enterica, Enterobacter, Shigella flexneri, Clostridioides difficile, Pseudomonas aeruginosa, Streptococcus miti, uropathogenic Escherichia coli and functioned balancing bacterial communities. Bacterial fraction in the metagenomic datasets reflected clear patterns of dysbiosis, including a severe deficiency of beneficial bacteria, an increase in Firmicutes, a marked decline in Actinobacteria, Bacteroidetes, Proteobacteria and sample-dependent enrichment of Enterococcus, Escherichia and Acinetobacter in diarrhea cases. This study, for the first time, investigated the dynamics of gut phageome, phage-associated bacteriome in children with persistent diarrhea of unknown causes in Vietnam, providing new insight for complementary treatment. Full article