Understanding and Exploiting Phage-Host Interactions

Whole genome sequencing of the novel polyvalent bacteriophage Malk1: A powerful biocontrol agent for water pollution

In this study, a novel Malk1 phage, was isolated and characterized for its ability to target a broad range of multidrug-resistant (MDR) bacterial strains. Malk1, classified within the Siphoviridae family, showed lytic activity with a capsid diameter of 84 nm and a tail length of 205 nm. It demonstrated a short latent period of 18 min and a burst size of 102 virions per infected cell. The phage exhibited strong thermal stability up to 60 °C and maintained activity across a pH range of 6.0-10.0. However, exposure to hand soap and 70 % ethanol reduced its titers by over 94 % and 97 %, respectively. Malk1 lysed 92 % of the tested bacterial strains and had a genome of 44.3 kb, encoding 75 open reading frames (ORFs), with no genes for toxins, antibiotic resistance, or CRISPR elements, making it a virulent phage. A novel design utilizing immobilized polyvalent Malk1 phage on plastic sheets demonstrated superior efficacy in reducing multi-drug resistant (MDR) bacterial strains. The removal efficiencies for C.freundii (78-91 %), E.coli (74-85 %), S.enterica (60-76 %), and S.flexneri (63-72 %) were significantly higher compared to purified phage, which achieved removal efficiencies of 63-69 %, 58-66 %, 52-63 %, and 55-68 %, respectively, after 6 to 8 h. Furthermore, the immobilized phage treatment led to a 94.1 % improvement in the removal of physicochemical pollutants in wastewater, significantly surpassing the 65.3 % removal achieved with purified phage. The treatment process led to significant improvements in water quality, achieving an average removal efficiency of 71.1 % for electrical conductivity, 67.52 % for turbidity, 73.67 % for total dissolved solids (TDS), 88.02 % for biochemical oxygen demand (BOD), and 81.88 % for ammonia (NH₃). Additionally, the average dissolved oxygen (DO) levels increased by 79.17 % compared to untreated wastewater. These findings highlight the promising potential of Malk1 phage, particularly in its immobilized form, for pathogen control and enhancing water quality. ORIGINALITY-SIGNIFICANCE STATEMENT: We introduce the newly isolated polyvalent Malk1 phage, which has been thoroughly genome characterized and annotated. Immobilized Malk1 phage has proven effective in controlling drainage water pollution and addressing global concerns for irrigation water quality. Our experiments successfully reduced several multi-drug-resistant (MDR) bacterial strains in highly polluted drainage water, leading to significant improvements in water quality in a short time and at an affordable cost, facilitated by our innovative laboratory design.

Bacteriophage-based live bacteria detection for rapid infection diagnosis

Bacterial bloodstream infections cause high morbidity and mortality. Although bacteria can be detected by various methods, culture methods are often used for the detection of live, accurate, reproducible, and selective bacterial identification. However, the culture method is time-consuming, and clinicians often start treatment immediately due to the long determination time. This reduces the bacterial density detectable by culture, and in some cases, makes determination difficult. To overcome this challenge, we propose a method that directly combines bacteriophage-based lysis with quantitative PCR (qPCR). This method enables the simple and rapid detection of bacteria without the need for pre-concentration or DNA extraction steps. Escherichia coli K12 (E. coli K12) was used as the model bacterium, and bacteria lysed by the E. coli K12-specific bacteriophage were detected using qPCR. The total analysis time was less than 3 h, and only live bacterial cells were selectively lysed. The method was also used to detect bacteria spiked into reference plasma samples, and bacterial DNA was detected via qPCR. The results obtained from the calibration graph created with cultured bacteria and the one created by spiking bacteria into reference plasma were consistent. The similarities between the calibration graphs from both methods were found to be in the range of 92-102.7 %. The LOD and LOQ values for bacteria spiked into reference plasma were calculated as 14.80 and 3.5x10³ CFU/mL, respectively.

The Nonbacterial Infant Microbiome and Necrotizing Enterocolitis

Necrotizing enterocolitis (NEC) is among the most devastating neonatal illnesses of premature infants. Although it is a disease of multifactorial etiology associated with bacterial dysbiosis, several reports of viral and some fungal infections associated with NEC have been published. Despite the abundance of viruses-primarily bacteriophages, and "virus-like particles" in the normal infant gut flora, there is limited understanding of the contribution of these elements to newborn gut health and disease. This study aims to review existing evidence on normal newborn virome and mycobiome development and present insights into the complex inter-kingdom interactions between gut bacteria, viruses, and fungi in the intestinal ecosystem, exploring their potential role in predisposing the preterm infant to NEC. · We have reviewed a number of viral and fungal infections reported in association with NEC-like illnesses.. · Bacteriophages play a crucial role in the gut microbiome development, but their role in pathogenesis of NEC and potential for therapeutic use is unknown.. · Development of next-gen metagenomic tools are needed to enhance our understanding of viral diversity, bacteriophages, and the gut virome in the context of neonatal health and disease..

Phage-derived proteins: Advancing food safety through biocontrol and detection of foodborne pathogens

The emergence of antimicrobial-resistant foodborne pathogens poses a continuous health risk and economic burden as they can easily spread through contaminated food. Therefore, the demand for new antimicrobial agents to address this problem is steadily increasing. Similarly, the development of rapid, sensitive, and accurate pathogen detection tools is a prerequisite for ensuring food safety. Phage-derived proteins have become innovative tools for combating these pathogens because of their potent antimicrobial activity and host specificity. Phage proteins are relatively free from regulation compared to phages per se, and there are no concerns about the transduction of harmful genes. With recent progress in next-generation sequencing technology, the analysis of phage genomes has become more accessible, and numerous phage proteins with potential for biocontrol and detection have been identified. This review provides a comprehensive overview of phage protein research on food safety from 2006 to the present, a pivotal period marked by the certification of phages as Generally Recognized As Safe (GRAS). Emphasizing recent advancements, we investigated the diverse applications of various phage proteins for biocontrol and detection purposes. While highlighting the successful implementation of these proteins, we also address the current bottlenecks and propose strategies to overcome these challenges. By summarizing the current state of research on phage-derived proteins, this review contributes to a deeper understanding of their potential as effective antimicrobial agents and tools for detecting foodborne pathogens.

Phage treatment of multidrug-resistant bacterial infections in humans, animals, and plants: The current status and future prospects

Phages, including the viruses that lyse bacterial pathogens, offer unique therapeutic advantages, including their capacity to lyse antibiotic-resistant bacteria and disrupt biofilms without harming the host microbiota. The lack of new effective antibiotics and the growing limitations of existing antibiotics have refocused attention on phage therapy as an option in complex clinical cases such as burn wounds, cystic fibrosis, and pneumonia. This review describes clinical cases and preclinical studies in which phage therapy has been effective in both human and veterinary medicine, and in an agricultural context. In addition, critical challenges, such as the narrow host range of bacteriophages, the possibility of bacterial resistance, and regulatory constraints on the widespread use of phage therapy, are addressed. Future directions include optimizing phage therapy through strategies ranging from phage cocktails to broadening phage host range through genetic modification, and using phages as vaccines or biocontrol agents. In the future, if phage can be efficiently delivered, maintained in a stable state, and phage-antibiotic synergy can be achieved, phage therapy will offer much needed treatment options. However, the successful implementation of phage therapy within the current standards of practice will also require the considerable development of regulatory infrastructure and greater public acceptance. In closing, this review highlights the promise of phage therapy as a critical backup or substitute for antibiotics. It proposes a new role as a significant adjunct to, or even replacement for, antibiotics in treating multidrug-resistant bacterial infections.

Protein-Based Degraders: From Chemical Biology Tools to Neo-Therapeutics

The nascent field of targeted protein degradation (TPD) could revolutionize biomedicine due to the ability of degrader molecules to selectively modulate disease-relevant proteins. A key limitation to the broad application of TPD is its dependence on small-molecule ligands to target proteins of interest. This leaves unstructured proteins or those lacking defined cavities for small-molecule binding out of the scope of many TPD technologies. The use of proteins, peptides, and nucleic acids (otherwise known as "biologics") as the protein-targeting moieties in degraders addresses this limitation. In the following sections, we provide a comprehensive and critical review of studies that have used proteins and peptides to mediate the degradation and hence the functional control of otherwise challenging disease-relevant protein targets. We describe existing platforms for protein/peptide-based ligand identification and the drug delivery systems that might be exploited for the delivery of biologic-based degraders. Throughout the Review, we underscore the successes, challenges, and opportunities of using protein-based degraders as chemical biology tools to spur discoveries, elucidate mechanisms, and act as a new therapeutic modality.

Enhancing phage therapy by coating single bacteriophage-infected bacteria with polymer to preserve phage vitality

The efficacy of bacteriophages in treating bacterial infections largely depends on the phages' vitality, which is impaired when they are naturally released from their hosts, as well as by culture media, manufacturing processes and other insults. Here, by wrapping phage-invaded bacteria individually with a polymeric nanoscale coating to preserve the microenvironment on phage-induced bacterial lysis, we show that, compared with naturally released phages, which have severely degraded proteins in their tail, the vitality of phages isolated from polymer-coated bacteria is maintained. Such latent phages could also be better amplified, and they more efficiently bound and lysed bacteria when clearing bacterial biofilms. In mice with bacterially induced enteritis and associated arthritis, latent phages released from orally administered bacteria coated with a polymer that dissolves at neutral pH had higher bioavailability and led to substantially better therapeutic outcomes than the administration of uncoated phages.

Bacteria- and Phage-Derived Proteins in Phage Infection

Phages have exerted severe evolutionary pressure on prokaryotes over billions of years, resulting in major rearrangements. Without every enzyme involved in the phage-bacterium interaction being examined; bacteriophages cannot be used in practical applications. Numerous studies conducted in the past few years have uncovered a huge variety of bacterial antiphage defense systems; nevertheless, the mechanisms of most of these systems are not fully understood. Understanding the interactions between bacteriophage and bacterial proteins is important for efficient host cell infection. Phage proteins involved in these bacteriophage-host interactions often arise immediately after infection. Here, we review the main groups of phage enzymes involved in the first stage of viral infection and responsible for the degradation of the bacterial membrane. These include polysaccharide depolymerases (endosialidases, endorhamnosidases, alginate lyases, and hyaluronate lyases), and peptidoglycan hydrolases (ectolysins and endolysins). Host target proteins are inhibited, activated, or functionally redirected by the phage protein. These interactions determine the phage infection of bacteria. Proteins of interest are holins, endolysins, and spanins, which are responsible for the release of progeny during the phage lytic cycle. This review describes the main bacterial and phage enzymes involved in phage infection and analyzes the therapeutic potential of bacteriophage-derived proteins.

Discovery, structural characteristics and evolutionary analyses of functional domains in Acinetobacter baumannii phage tail fiber/spike proteins

BACKGROUND

The global rise in multidrug-resistant Acinetobacter baumannii infections poses a significant healthcare challenge. Bacteriophage offer a promising alternative to antibiotics for treating A. baumannii infections. Phage tail fiber and spike proteins are essential for host recognition, with some exhibiting depolymerase activity that aids in degrading the bacterial cell wall, facilitating infection. Detailed studies of the functional domains responsible for depolymerase activity and receptor-binding in phage tail fiber/spike proteins are a crucial step toward developing effective phage treatments.

RESULTS

A total of 32 functional domains were identified across 313 tail fiber and spike proteins from 204 publicly available Acinetobacter baumannii phages using InterPro and AlphaFold3. Domains associated with depolymerase function were Pectin lyase-like domain (PLD), phage_tailspike_middle domain (PTMD), Transglycosidases domain (TGD), and SGNH hydrolase domain (SHD). These domains were primarily found in phages from the Autographiviridae family, specifically within the Friunavirus genus. The predominant PLD domain displayed high variability, with its sequence conserved only in a 25-amino-acid region among two closely related fiber/spike protein lineages. All enzymatic domains exhibit high sequence diversity yet retain structural stability, which is essential for enzymatic function. As for receptor-binding domains, four types of pyocin_knob domains (PKD) were initially identified, characterized by unique β-sheet and α-helix configurations. Each type of PKD exhibited distinct potential receptor-binding sites, primarily located within the α-helix region, and was closely associated with the Obolenskvirus genus, as well as the Autographiviridae and Straboviridae families. The G3DSA:2.60.40.3940 domain, exhibiting minor structural variations, was predominantly found in phages of the Obolenskvirus genus. Additionally, a novel Obo-β-sandwich structure, identified as a potential receptor-binding domain, was discovered within Obolenskvirus genus cluster. The structural diversity of these receptor-binding domains accounts for their interactions with various receptors.

CONCLUSIONS

This research deepens the understanding of the relationship between A. baumannii phage genera and the functional domains within their tail fiber/spike proteins, emphasizing the compatibility between structural characteristics and functional roles. The data obtained could serve as a reference for the targeted modification of phages or their tail fiber/spike proteins, enhancing their therapeutic applications.

Isolation, characterization, and whole-genome analysis of the novel temperate bacteriophage Ph-p5 infecting Glutamicibacter halophytocola

Bacteria of the genus Glutamicibacter, due to their ubiquity, nutritional versatility, and ability to adapt to environmental stresses, play an important role in natural ecosystems and have been extensively studied. Nevertheless, there remains a significant gap in our knowledge regarding Glutamicibacter phages, particularly in comparison to those of the related actinobacteria. To date, only two virulent phages infecting G. arilaitensis have been described. To our knowledge, this is the first report on the isolation, characterization, and genome analysis of a temperate phage targeting G. halophytocola, an endophytic bacterium known for its plant-growth-promoting effect. The phage Ph-p5, with siphovirus structure, was isolated from soil. It exhibited a long latent period (120 min), a moderate burst size (87 ± 3 PFU/infected cell), and stability over a wide range of pH and temperature. The circularly permuted linear double-stranded DNA genome of phage Ph-p5, comprising 43,694 bp with a G + C content of 57.1%, contains 65 putative protein-coding sequences and one sequence encoding tRNA. Of the identified open reading frames, 33 were of unknown function, while the remaining ones were grouped into functional modules, including structural proteins, DNA replication and regulation, lysogeny, and lysis. The presence of intact lysogeny-related genes, together with the capacity for lysogenisation of the host strain G. halophytocola BIM B-1594, provides evidence that Ph-p5 is a temperate phage. Phylogenetic analysis demonstrated that phage Ph-p5 belongs to the class Caudoviricetes but exhibits significant divergence from known phages and may be assigned to a new genus, for which we propose the name "Petuglutavirus".

Novel Anti-Microbial/Anti-Inflammatory Combination Improves Clinical Outcome of Bacillus cereus Endophthalmitis

Purpose

The purpose of this study was to explore the therapeutic potential of the novel combination of Bacillus bacteriophage lysin (PlyB) and a synthetic TLR2/4 inhibitor (oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, OxPAPC) in the treatment of experimental Bacillus cereus endophthalmitis.

Methods

C57BL/6J mice were injected with 100 colony forming units (CFUs) Bacillus cereus to induce endophthalmitis. Two hours postinfection, groups of mice were treated with either PlyB, PlyB with OxPAPC, or the groups were left untreated to serve as a control. A group of uninfected mice was injected with only PlyB to serve as a treatment control. Eight hours post-treatment, infected/treated mice were analyzed for bacterial counts, retinal function, histology, and inflammation.

Results

Groups treated with PlyB alone or PlyB/OxPAPC showed significantly reduced bacterial loads compared with untreated eyes. Compared with untreated eyes, PlyB and PlyB/OxPAPC-treated eyes retained significant A-wave and B-wave function. PlyB/OxPAPC-treated eyes retained greater A- and B-wave function compared with eyes treated with PlyB alone. Histology showed that retinal structures were well preserved, and retinal layers were distinguishable in eyes treated with PlyB and PlyB/OxPAPC. Ninety-five percent of infiltrating CD45+ cells in infected untreated eyes were Ly6G+/Ly6C+ neutrophils. Infected eyes treated with PlyB and PlyB/OxPAPC had significantly reduced numbers of CD45+ immune cells compared with untreated eyes. Eyes treated with PlyB/OxPAPC had a significantly lower number of neutrophils than eyes treated with PlyB alone.

Conclusions

These results demonstrated that the novel combination of bacteriophage lysin and TLR2/4 inhibitor was a successful treatment option for treating experimental Bacillus cereus endophthalmitis.

A Phage-Based Approach to Identify Antivirulence Inhibitors of Bacterial Type IV Pili

The increasing threat of antibiotic resistance underscores the urgent need for innovative strategies to combat infectious diseases, including the development of antivirulants. Microbial pathogens rely on their virulence factors to initiate and sustain infections. Antivirulants are small molecules designed to target virulence factors, thereby attenuating the virulence of infectious microbes. The bacterial type IV pilus (T4P), an extracellular protein filament that depends on the T4P machinery (T4PM) for its biogenesis, dynamics and function, is a key virulence factor in many significant bacterial pathogens. While the T4PM presents a promising antivirulence target, the systematic identification of inhibitors for its multiple protein constituents remains a considerable challenge. Here we report a novel high-throughput screening (HTS) approach for discovering T4P inhibitors. It uses Pseudomonas aeruginosa, a high-priority pathogen, in combination with its T4P-targeting phage, φKMV. Screening of a library of 2168 compounds using an optimised protocol led to the identification of tuspetinib, based on its deterrence of the lysis of P. aeruginosa by φKMV. Our findings show that tuspetinib also inhibits two additional T4P-targeting phages, while having no effect on a phage that recognises lipopolysaccharides as its receptor. Additionally, tuspetinib impedes T4P-mediated motility in P. aeruginosa and Acinetobacter species without impacting growth or flagellar motility. This bacterium-phage pairing approach is applicable to a broad range of virulence factors that are required for phage infection, paving ways for the development of advanced chemotherapeutics against antibiotic-resistant infections.

Insights from Shigella bacteriophage genomes analysis

Shigella species, a major cause of shigellosis, remain a substantial global health issue and the emergence of antibiotic-resistant Shigella strains has aggravated the situation. Hence, four Shigella phages were investigated to provide insights into the evolutionary trajectories and genomic properties of Shigella-infecting bacteriophages using comparative genome analysis. Analysis shows that these four phages belong to the Tequatrovirus genus and include a considerable number of proteins for 'Tail' and "DNA, RNA and Nucleotide Metabolism," indicating their aptitude for specialized host interaction and replication efficiency. The identification of 10 tRNAs further support that, these phages have high replication efficiency. Thus, this study improves our understanding of phage evolution by exposing the genetic mechanisms that drive phage adaptability and host specificity. This also highlights the significance of phage genomic research in developing viable therapies for antibiotic-resistant Shigella infections.

PHIStruct: improving phage-host interaction prediction at low sequence similarity settings using structure-aware protein embeddings

MOTIVATION

Recent computational approaches for predicting phage-host interaction have explored the use of sequence-only protein language models to produce embeddings of phage proteins without manual feature engineering. However, these embeddings do not directly capture protein structure information and structure-informed signals related to host specificity.

RESULTS

We present PHIStruct, a multilayer perceptron that takes in structure-aware embeddings of receptor-binding proteins, generated via the structure-aware protein language model SaProt, and then predicts the host from among the ESKAPEE genera. Compared against recent tools, PHIStruct exhibits the best balance of precision and recall, with the highest and most stable F1 score across a wide range of confidence thresholds and sequence similarity settings. The margin in performance is most pronounced when the sequence similarity between the training and test sets drops below 40%, wherein, at a relatively high-confidence threshold of above 50%, PHIStruct presents a 7%-9% increase in class-averaged F1 over machine learning tools that do not directly incorporate structure information, as well as a 5%-6% increase over BLASTp.

AVAILABILITY AND IMPLEMENTATION

The data and source code for our experiments and analyses are available at https://github.com/bioinfodlsu/PHIStruct.

Microscopic phage adsorption assay: High-throughput quantification of virus particle attachment to host bacterial cells

Phages, viruses of bacteria, play a pivotal role in Earth's biosphere and hold great promise as therapeutic and diagnostic tools in combating infectious diseases. Attachment of phages to bacterial cells is a crucial initial step of the interaction. The classic assay to quantify the dynamics of phage attachment involves coculturing and enumeration of bacteria and phages, which is laborious, lengthy, hence low-throughput, and only provides ensemble estimates of model-based adsorption rate constants. Here, we utilized fluorescence microscopy and particle tracking to obtain trajectories of individual virus particles interacting with cells. The trajectory durations quantified the heterogeneity in dwell time, the time that each phage spends interacting with a bacterium. The average dwell time strongly correlated with the classically measured adsorption rate constant. We successfully applied this technique to quantify host-attachment dynamics of several phages including those targeting key bacterial pathogens. This approach should benefit the field of phage biology by providing highly quantitative, model-free readouts at single-virus resolution, helping to uncover single-virus phenomena missed by traditional measurements. Owing to significant reduction in manual effort, our method should enable rapid, high-throughput screening of a phage library against a target bacterial strain for applications such as therapy or diagnosis.

Investigating potential auxiliary anaerobic digestion activity of phage under polyvinyl chloride microplastic stress

Polyvinyl chloride (PVC) microplastics present in sewage were trapped in sludge, thereby hindering anaerobic digestion performance of waste active sludge (WAS). Phages regulate virocell metabolism by encoding auxiliary metabolic genes (AMGs) related to energy acquisition and material degradation, supporting hosts survive in harsh environments and play a crucial role in biogeochemical cycles. This study investigated the potential effects of phages on the recovery of WAS anaerobic digestion under PVC stress. We observed a significant alteration in the phage community induced by PVC microplastics. Phages encoded AMGs related to anaerobic digestion and cell growth probably alleviate PVC microplastics inhibition on WAS anaerobic digestion, and 54.2 % of hydrolysis-related GHs and 40.8 % of acidification-related AMGs were actively transcribed in the PVC-exposed group. Additionally, the degradation of chitin and peptidoglycan during hydrolysis and the conversion of glucose to pyruvate during acidification were more susceptible to phages. Prediction of phage-host relationship indicated that the phyla Pseudomonadota were predominantly targeted hosts by hydrolysis-related and acidification-related phages, and PVC toxicity had minimal impact on phage-host interaction. Our findings highlight the importance of phages in anaerobic digestion and provide a novel strategy for using phages in the functional recovery of microplastic-exposed sludge.

From forgotten cure to modern medicine: The resurgence of bacteriophage therapy

OBJECTIVES

The unregulated use of antibiotics has led to the rise of antibiotic-resistant bacterial strains. This study explores bacteriophage therapy as an alternative treatment, highlighting its history, significance, and advancements in Europe, the United States, and the Middle East.

METHODS

A comprehensive literature review on bacteriophage therapy was conducted, focusing on its development, clinical trials, and patient treatment applications. The study also examined challenges, limitations, criteria for ideal phage selection, and manipulation techniques.

RESULTS

The United States and several European countries have advanced in phage therapy, progressing from clinical trials to patient treatment, whereas Middle Eastern countries are still in the early stages. Bacteriophages offer specificity, abundance, and minimal side effects, but challenges like safety concerns and potential resistance limit their widespread use.

CONCLUSION

Bacteriophage therapy shows promise as an antibiotic alternative but faces safety and resistance challenges. Continued research and better regulatory frameworks, especially in the Middle East, are needed to realize its potential.

Repurposing an Endogenous CRISPR-Cas System to Generate and Study Subtle Mutations in Bacteriophages

While bacteriophage applications benefit from effective phage engineering, selecting the desired genotype after subtle modifications remains challenging. Here, we describe a two-phase endogenous CRISPR-Cas-based phage engineering approach that enables selection of small defined edits in Pectobacterium carotovorum phage ZF40. We designed plasmids containing sequences homologous to ZF40 and a mini-CRISPR array. The plasmids allowed genome editing through homologous recombination and counter-selection against non-recombinant phage genomes using an endogenous type I-E CRISPR-Cas system. With this technique, we first deleted target genes and subsequently restored loci with modifications. This two-phase approach circumvented major challenges in subtle phage modifications, including inadequate sequence distinction for CRISPR-Cas counter-selection and the requirement of a protospacer-adjacent motif, limiting sequences that can be modified. Distinct 20-bp barcodes were incorporated through engineering as differential target sites for programmed CRISPR-Cas activity, which allowed quantification of phage variants in mixed populations. This method aids studies and applications that require mixtures of similar phages.

Strain-Specific Infection of Phage AP1 to Rice Bacterial Brown Stripe Pathogen Acidovorax oryzae

Bacteriophage (phage) AP1 has been reported to effectively lyse Acidovorax oryzae, the causative agent of bacterial brown stripe in rice. However, phage AP1 exhibits strain-specific lysis patterns. In order to enhance the potential of phages for biological control of rice bacterial brown stripe, this study investigated the possible mechanism of strain-specific infection by characterizing phage AP1 and its susceptible (RS-2) and resistant (RS-1) strains. Based on the current classification standards and available database information, phage AP1 was classified into the class Caudoviricetes, and it is a kind of podophage. Comparative analysis of the susceptible and resistant strains showed no significant differences in growth kinetics, motility, biofilm formation, or effector Hcp production. Interestingly, the resistant strain demonstrated enhanced virulence compared to the susceptible strain. Prokaryotic expression studies indicated that six putative structural proteins of phage AP1 exhibited varying degrees of binding affinity (1.90-9.15%) to lipopolysaccharide (LPS). However, pull-down assays and bacterial two-hybrid analyses revealed that only gp66 can interact with four host proteins, which were identified as glycosyltransferase, RcnB, ClpB, and ImpB through immunoprecipitation and mass spectrometry analyses. The role of LPS in the specific infection mechanism of phage AP1 was further elucidated through the construction of knockout mutant strains and complementary strains targeting a unique gene cluster (wbzB, wbzC, wbzE, and wbzF) involved in LPS precursor biosynthesis. These findings provide novel insights into the mechanisms of phage-host specificity, which are crucial for the effective application of phage AP1 in controlling rice bacterial brown stripe.

Revolutionising infection control: building the next generation of phage banks

The escalating global burden of antimicrobial resistance (AMR) represents a critical public health challenge. This rise in antibiotic resistance is concomitant with heightened antibiotic consumption, with an estimated annual usage of 100,000 to 200,000 tons. A recent systematic review, which analysed data from 204 countries, reported that AMR was responsible for 4.95 million deaths in 2019 (Murray et al., 2022). The growing threat of AMR is imposing a significant financial burden on the global economy, with the CDC reporting an additional annual cost of $20 billion in the U.S. and €9 billion in Europe. The emerging field of bacteriophage therapy offers promising potential as a game-changer in the era of AMR. However, existing literature reveals numerous research gaps and technological challenges, including insufficient information on phage pharmacology, genomics, and a lack of preclinical and clinical data. In addition to conducting further research to address existing knowledge gaps, establishing phage banks in clinical facilities could be a transformative advancement in the fight against AMR.

Development of phage-containing hydrogel for treating Enterococcus faecalis-infected wounds

BACKGROUND

Chronic wound infections caused by Enterococcus faecalis pose formidable challenges in clinical management, exacerbated by the emergence of vancomycin-resistant strains. Phage therapy offers a targeted approach but encounters delivery hurdles. Due to their biocompatibility and controlled release properties, hydrogels hold promise as carriers.

OBJECTIVE

This study aimed to fabricate phage-containing hydrogels using sodium alginate (SA), carboxymethyl cellulose (CMC), and hyaluronic acid (HA) to treat E. faecalis-infected wounds. We assessed the efficacy of these hydrogels both in vitro and in vivo.

METHODS

The hydrogel was prepared using SA-CMC-HA polymers. Phage SAM-E.f 12 was incorporated into the SA-CMC-HA hydrogel. The hydrogel's swelling index was measured after 24 h, and degradation was assessed over seven days. Surface morphology and composition were analyzed using Scanning Electron Microscopy (SEM) and Fourier-transform infrared spectroscopy (FTIR). Antibacterial activity was tested via optical density (OD) and disk diffusion assays. Phage release and stability were evaluated over a month. In vivo efficacy was tested in mice through wound healing and bacterial count assays, with histopathological analysis.

RESULTS

Hydrogels exhibited a swelling index of 0.43, a water absorption rate of %30, and 23% degradation over seven days. FTIR confirmed successful polymer incorporation. In vitro studies demonstrated that phage-containing hydrogels significantly inhibited bacterial growth, with an OD of 0.3 compared to 1.1 for the controls. Hydrogels remained stable for four weeks. In vivo, phage-containing hydrogels reduced bacterial load and enhanced wound healing, as shown by improved epithelialization and tissue restoration.

CONCLUSION

Phage-containing hydrogels effectively treat wounds infected with E. faecalis-infected wounds, promoting wound healing through controlled phage release. These hydrogels can improve clinical outcomes in the treatment of infected wounds.

In vitro and in vivo assessment of the competence of a novel lytic phage vB_EcoS_UTEC10 targeting multidrug resistant Escherichia coli with a robust biofilm eradication activity

Escherichia coli (E. coli) is a leading cause of human infections worldwide and is considered a major cause of nosocomial infections, sepsis, meningitis and diarrhea. Lately, there has been an alarming increase in the incidence of antimicrobial resistance among clinical E. coli isolates. In the current study, a novel bacteriophage (phage) vB_EcoS_UTEC10 was isolated and characterized. The isolated phage showed high stability over wide temperature and pH ranges beside its promising bacteriolytic activity against multidrug resistant (MDR) E. coli isolates. In addition, vB_EcoS_UTEC10 showed a marked antibiofilm capability against mature E. coli biofilms. Genomic investigation revealed that vB_EcoS_UTEC10 has a double stranded DNA genome that consists of 44,772 bp comprising a total of 73 open reading frames (ORFs), out of which 35 ORFs were annotated as structural or functional proteins, and none were related to antimicrobial resistance or lysogeny. In vivo investigations revealed a promising bacteriolytic activity of vB_EcoS_UTEC10 against MDR E. coli which was further supported by a significant reduction in bacterial load in specimens collected from the phage-treated mice. Histopathology examination demonstrated minimal signs of inflammation and necrosis in the tissues of phage-treated mice compared to the degenerative tissue damage observed in untreated mice. In summary, the present findings suggest that vB_EcoS_UTEC10 has a remarkable ability to eradicate MDR E. coli infections and biofilms. These findings could be further invested for the development of targeted phage therapies that offer a viable alternative to traditional antibiotics against resistant E. coli.

Microscopic Phage Adsorption Assay: High-throughput quantification of virus particle attachment to host bacterial cells

Phages, viruses of bacteria, play a pivotal role in Earth's biosphere and hold great promise as therapeutic and diagnostic tools in combating infectious diseases. Attachment of phages to bacterial cells is a crucial initial step of the interaction. The classic assay to quantify the dynamics of phage attachment involves co-culturing and enumeration of bacteria and phages, which is laborious, lengthy, hence low-throughput, and only provides ensemble estimates of model-based adsorption rate constants. Here, we utilized fluorescence microscopy and particle tracking to obtain trajectories of individual virus particles interacting with cells. The trajectory durations quantified the heterogeneity in dwell time, the time that each phage spends interacting with a bacterium. The average dwell time strongly correlated with the classically-measured adsorption rate constant. We successfully applied this technique to quantify host-attachment dynamics of several phages including those targeting key bacterial pathogens. This approach should benefit the field of phage biology by providing highly quantitative, model-free readouts at single-virus resolution, helping to uncover single-virus phenomena missed by traditional measurements. Owing to significant reduction in manual effort, our method should enable rapid, high-throughput screening of a phage library against a target bacterial strain for applications such as therapy or diagnosis.

Rationalisation of the purification process for a phage active pharmaceutical ingredient

The resurgence of phage therapy, once abandoned in the early 20th century in part due to issues related to the purification process and stability, is spurred by the global threat of antibiotic resistance. Engineering advances have enabled more precise separation unit operations, improving overall purification efficiency. The present review discusses the physicochemical properties of impurities commonly found in a phage lysate, e.g., contaminants, phage-related impurities, and propagation-related impurities. Differences in phages and bacterial impurities properties are leveraged to elaborate a four-step phage purification process: clarification, capture and concentration, subsequent purification and polishing. Ultimately, a framework for rationalising the development of a purification process is proposed, considering three operational characteristics, i.e., scalability, transferability to various phages and duration. This guide facilitates the preselection of a sequence of unit operations, which can then be confronted with the expected impurities to validate the theoretical capacity of the process to purify the phage lysate.

Alginate binding enhances the structural stability and potentiates the lytic activity of bacteriophage endolysin's partially folded conformation

Polysaccharide polymers are increasingly being used as chaperon-like macromolecules in assisting protein folding of unfolded protein molecules. They interact with unfolded or partially folded proteins in a charge and conformation specific manner that results in the formation of stable protein-polysaccharide complexes. In most of the cases, the complex formation of protein-polysaccharide is driven via non-covalent interactions that have found to endorse the activity of proteins. T4L (18.7 kDa) and T7L (17 kDa) endolysins belong to the hydrolase and amidase class of peptidoglycan degrading enzymes. Both T4L and T7L exist in partially folded forms and are devoid of lytic activity at low pH conditions. In the current study, we assessed the binding of alginate with T4L and T7L at pH 7 and 3 using variety of biophysical and biochemical techniques. Spectroscopic studies revealed differential structural modulations of partially folded T4L and T7L upon their interaction with alginate. Further, the complex formation of alginate with partially folded T4L/T7L was confirmed by ITC and STEM. Additionally, the formed complexes of alginate with both T4L/T7L PF endolysins were found to be chemically and enzymatically stable. Moreover, such complexes were also marked with differential enhancement in their lytic activities at acidic pH conditions. This implied the potency of alginate as an excellent choice of matrix to preserve the structural and functional integrity of partially folded forms of T4L and T7L at highly acidic conditions.

Phage therapy: A novel approach against multidrug-resistant pathogens

The rapid rise of multidrug-resistant (MDR) organisms has created a critical need for alternative treatment options. Phage therapy is gaining attention as an effective way to fight bacterial infections by using lytic bacteriophages to specifically target and kill harmful bacteria. This review discusses several phage therapeutic options and emphasizes new developments in phage biology. Phage treatment has proven to be successful against MDR bacteria, as evidenced by multiple human clinical trials that indicate favorable results in treating a range of diseases caused by these pathogens. Despite these promising results, challenges such as phage resistance, regulatory hurdles, and the need for standardized treatment protocols remain. To effectively combat MDR bacterial infections, future research must focus on enhancing phage effectiveness, guaranteeing safety for human usage and incorporating phage therapy into clinical practice.

Bacteriophage as a potential biotherapeutics to combat present-day crisis of multi-drug resistant pathogens

The rise of Multi-Drug Resistant (MDR) bacterial pathogens to most, if not all, currently available antibacterial agents has become a global threat. As a consequence of the antibiotic resistance epidemic, phage therapy has emerged as a potential alternative to conventional antibiotics. Despite the high therapeutic advantages of phage therapy, they have not yet been successfully used in the clinic due to various limitations of narrow host specificity compared to antibiotics, poor adhesion on biofilm surface, and susceptibility to both human and bacterial defences. This review focuses on the antibacterial effect of bacteriophage and their recent clinical trials with a special emphasis on the underlying mechanism of lytic phage action with the help of endolysin and holin. Furthermore, recent clinical trials of natural and modified endolysins and some marketed products have also been emphasized with future prospective.

Advances in Bioreceptor Layer Engineering in Nanomaterial-based Sensing of Pseudomonas Aeruginosa and its Metabolites

Pseudomonas aeruginosa is a pathogen that infects wounds and burns and causes severe infections in immunocompromised humans. The high virulence, the rise of antibiotic-resistant strains, and the easy transmissibility of P. aeruginosa necessitate its fast detection and control. The gold standard for detecting P. aeruginosa, the plate culture method, though reliable, takes several days to complete. Therefore, developing accurate, rapid, and easy-to-use diagnostic tools for P. aeruginosa is highly desirable. Nanomaterial-based biosensors are at the forefront of detecting P. aeruginosa and its secondary metabolites. This review summarises the biorecognition elements, biomarkers, immobilisation strategies, and current state-of-the-art biosensors for P. aeruginosa. The review highlights the underlying principles of bioreceptor layer engineering and the design of optical, electrochemical, mass-based, and thermal biosensors based on nanomaterials. The advantages and disadvantages of these biosensors and their future point-of-care applications are also discussed. This review outlines significant advancements in biosensors and sensors for detecting P. aeruginosa and its metabolites. Research efforts have identified biorecognition elements specific and selective towards P. aeruginosa. The stability, ease of preparation, cost-effectiveness, and integration of these biorecognition elements onto transducers are pivotal for their application in biosensors and sensors. At the same time, when developing sensors for clinically significant analytes such as P. aeruginosa, virulence factors need to be addressed, such as the sensor's sensitivity, reliability, and response time in samples obtained from patients. The point-of-care applicability of the developed sensor may be an added advantage since it enables onsite determination. In this context, optical methods developed for P. aeruginosa offer promising potential.

Chemical inhibition of cell surface modification sensitizes bacteria to phage infection

Many bacteriophages that infect Gram-positive bacteria rely on the bacterial cell surface polymer wall teichoic acid (WTA) as a receptor. However, some bacteria modulate their cell wall with d-alanine residues, which can disrupt phage adsorption. The prevalence and significance of WTA alanylation as an anti-phage defense is unknown. A chemical inhibitor of WTA d-alanylation could be employed to efficiently screen phage-host combinations for those that exhibit alanylation-dependent infections. Since the incorporation of d-alanine residues into the cell wall requires the activity of d-alanine:alanyl carrier protein ligase (DltA), a DltA inhibitor was employed as this tool. Herein, we found that a chemical probe inhibiting DltA activity impeded bacterial cell wall alanylation and enhanced infectivity of many phages against Bacillus subtilis, including phages Phi29, SPP1, SPO1, SP50, and Goe2. This finding reveals the breadth of immunity conferred by WTA alanylation in B. subtilis, which was previously known to impact only phages Phi29 and SPP1, but not SPO1, SP50, or Goe2. DltA inhibition selectively promoted infection by several phages that bind WTA, having no impact on the flagellotropic phage PBS1. Unexpectedly, DltA inhibition also had no effect on phage SP10, which binds to WTA. This selective chemical tool has the potential to unravel bacteriophage interactions with bacteria, leading to improved phage therapies in the future.

Characterization and Genome Analyses of the Novel Phages P2 and vB_AhydM-H1 Targeting Aeromonas hydrophila

Background

The emergence of antibiotic-resistant Aeromonas hydrophila strains presents a global health and aquaculture challenge. Bacteriophages offer promise as an alternative to antibiotics for treating drug-resistant Aeromonas infections.

Methods

Two new phages, P2 and vB_AhydM-H1, targeting pathogenic A. hydrophila were isolated from sewage water. Their morphology, growth characteristics, lytic activity, stability, and genomes were analyzed.

Results

Phage P2, a member of genus Ahphunavirus, and vB_AhydM-H1, a novel member of genus Pahsextavirus, exhibited narrow host ranges, extended latent periods, and typical burst sizes. Both phages remained stable at 40°C for 1 h and within a pH range of 4 to 10 for 3 h. The genomes of P2 and vB_AhydM-H1 spanned 42,660 bp with 49 open reading frames (ORFs) and 52,614 bp with 72 ORFs, respectively. Proteomic (ViPTree) and phylogenetic (VICTOR) analyses confirmed that both phages aligned with their respective families. DeepTMHMM predictions suggested that P2 and vB_AhydM-H1 encode three and four ORFs with transmembrane domains, respectively.

Conclusions

Safe for environmental and clinical use because of their lytic nature, and lack of virulence and resistance genes, these newly isolated phages expand the arsenal against antibiotic-resistant Aeromonas infections.

The Potential of Phage Treatment to Inactivate Planktonic and Biofilm-Forming Pseudomonas aeruginosa

Pseudomonas aeruginosa is a common cause of hospital-acquired infections and exhibits a strong resistance to antibiotics. An alternative treatment option for bacterial infections is the use of bacteriophages (or phages). In this study, two distinct phages, VB_PaD_phPA-G (phPA-G) and VB_PaN_phPA-Intesti (phPA-Intesti), were used as single suspensions or in a phage cocktail to inactivate the planktonic cells and biofilms of P. aeruginosa. Preliminary experiments in culture medium showed that phage phPA-Intesti (reductions of 4.5-4.9 log CFU/mL) outperformed phPA-G (reductions of 0.6-2.6 log CFU/mL) and the phage cocktail (reduction of 4.2 log CFU/mL). Phage phPA-Intesti caused a maximum reduction of 5.5 log CFU/cm2 in the P. aeruginosa biofilm in urine after 4 h of incubation. The combination of phage phPA-Intesti and ciprofloxacin did not improve the efficacy of bacterial inactivation nor reduce the development of resistant mutants. However, the development of resistant bacteria was lower in the combined treatment with the phage and the antibiotic compared to treatment with the antibiotic alone. This phage lacks known toxins, virulence, antibiotic resistance, and integrase genes. Overall, the results suggest that the use of phage phPA-Intesti could be a potential approach to control urinary tract infections (UTIs), namely those caused by biofilm-producing and multidrug-resistant strains of P. aeruginosa.

A Novel Truncated CHAP Modular Endolysin, CHAPSAP26-161, That Lyses Staphylococcus aureus, Acinetobacter baumannii, and Clostridioides difficile, and Exhibits Therapeutic Effects in a Mouse Model of A. baumannii Infection

Development of novel antibacterial agents is imperative due to the increasing threat of antibiotic-resistant pathogens. This study aimed to develop the enhanced antibacterial activity and in-vivo efficacy of a novel truncated endolysin, CHAPSAP26-161, derived from the endolysin LysSAP26, against multidrug-resistant bacteria. CHAPSAP26-161 exhibited higher protein purification efficiency in E. coli and antibacterial activity than LysSAP26. Moreover, CHAPSAP26-161 showed the higher lytic activity against A. baumannii with minimal bactericidal concentrations (MBCs) of 5-10 μg/ml, followed by Staphylococcus aureus with MBCs of 10-25 μg/ml. Interestingly, CHAPSAP26-161 could lyse anaerobic bacteria, such as Clostridioides difficile, with MBCs of 25-50 μg/ml. At pH 4-8 and temperatures of 4°C-45°C, CHAPSAP26-161 maintained antibacterial activity without remarkable difference. The lytic activity of CHAPSAP26-161 was increased with Zn2+. In vivo tests demonstrated the therapeutic effects of CHAPSAP26-161 in murine systemic A. baumannii infection model. In conclusion, CHAPSAP26-161, a truncated endolysin that retains only the CHAP domain from LysSAP26, demonstrated enhanced protein purification efficiency and antibacterial activity compared to LysSAP26. It further displayed broad-spectrum antibacterial effects against S. aureus, A. baumannii, and C. difficile. Our in vitro and in-vivo results of CHAPSAP26-161 highlights its promise as an innovative therapeutic option against those bacteria with multiple antibiotic resistance.

The Novel Concept of Synergically Combining: High Hydrostatic Pressure and Lytic Bacteriophages to Eliminate Vegetative and Spore-Forming Bacteria in Food Products

The article focuses on the ongoing challenge of eliminating vegetative and spore-forming bacteria from food products that exhibit resistance to the traditional preservation methods. In response to this need, the authors highlight an innovative approach based on the synergistic utilization of high-hydrostatic-pressure (HHP) and lytic bacteriophages. The article reviews the current research on the use of HHP and lytic bacteriophages to combat bacteria in food products. The scope includes a comprehensive review of the existing literature on bacterial cell damage following HHP application, aiming to elucidate the synergistic effects of these technologies. Through this in-depth analysis, the article aims to contribute to a deeper understanding of how these innovative techniques can improve food safety and quality. There is no available research on the use of HHP and bacteriophages in the elimination of spore-forming bacteria; however, an important role of the synergistic effect of HHP and lytic bacteriophages with the appropriate adjustment of the parameters has been demonstrated in the more effective elimination of non-spore-forming bacteria from food products. This suggests that, when using this approach in the case of spore-forming bacteria, there is a high chance of the effective inactivation of this biological threat.

Synergistic Antimicrobial Effects of Phage vB_AbaSi_W9 and Antibiotics against Acinetobacter baumannii Infection

Acinetobacter baumannii is a challenging multidrug-resistant pathogen in healthcare. Phage vB_AbaSi_W9 (GenBank: PP146379.1), identified in our previous study, shows lytic activity against 26 (89.66%) of 29 carbapenem-resistant Acinetobacter baumannii (CRAB) strains with various sequence types (STs). It is a promising candidate for CRAB treatment; however, its lytic efficiency is insufficient for complete bacterial lysis. Therefore, this study aimed to investigate the clinical utility of the phage vB_AbaSi_W9 by identifying antimicrobial agents that show synergistic effects when combined with it. The A. baumannii ATCC17978 strain was used as the host for the phage vB_AbaSi_W9. Adsorption and one-step growth assays of the phage vB_AbaSi_W9 were performed at MOIs of 0.001 and 0.01, respectively. Four clinical strains of CRAB belonging to different sequence types, KBN10P04948 (ST191), LIS2013230 (ST208), KBN10P05982 (ST369), and KBN10P05231 (ST451), were used to investigate phage-antibiotic synergy. Five antibiotics were tested at the following concentration: meropenem (0.25-512 µg/mL); colistin, tigecycline, and rifampicin (0.25-256 µg/mL); and ampicillin/sulbactam (0.25/0.125-512/256 µg/mL). The in vitro synergistic effect of the phage and rifampicin was verified through an in vivo mouse infection model. Phage vB_AbaSi_W9 demonstrated 90% adsorption to host cells in 1 min, a 20 min latent period, and a burst size of 114 PFU/cell. Experiments combining phage vB_AbaSi_W9 with antibiotics demonstrated a pronounced synergistic effect against clinical strains when used with tigecycline and rifampicin. In a mouse model infected with CRAB KBN10P04948 (ST191), the group treated with rifampicin (100 μg/mL) and phage vB_AbaSi_W9 (MOI 1) achieved a 100% survival rate-a significant improvement over the phage-only treatment (8.3% survival rate) or antibiotic-only treatment (25% survival rate) groups. The bacteriophage vB_AbaSi_W9 demonstrated excellent synergy against CRAB strains when combined with tigecycline and rifampicin, suggesting potential candidates for phage-antibiotic combination therapy in treating CRAB infections.

Plastisphere-hosted viruses: A review of interactions, behavior, and effects

Microbial communities, including bacteria, diatoms, and fungi, colonize plastic surfaces, forming biofilms known as the "plastisphere." Recent research has revealed that plastispheres also host a wide range of viruses, sparking interest in microbial ecology and virology. This shared habitat allows viruses to replicate, interact, infect, and spread, potentially impacting the environment and human health. Consequently, viruses attached to microplastics are now recognized to have broad effects on cellular and immune responses. However, the ecology and implications of viruses hosted in plastisphere habitats remain poorly understood, highlighting their fundamental importance as a subject of study. This review explores various pathways for virus attachment to plastispheres, factors influencing these interactions, their impacts within plastisphere and host-associated environments, and associated issues. It also summarizes current research and identifies knowledge gaps. We anticipate that this paper will help improve our predictive understanding of plastisphere viruses in natural settings and emphasizes the need for more research in real-world environments to advance the field.

Determinants in the phage life cycle: The dynamic nature of ssDNA phage FLiP and host interactions under varying environmental conditions and growth phases

The influence of environmental factors on the interactions between phages and bacteria, particularly single-stranded DNA (ssDNA) phages, has been largely unexplored. In this study, we used Finnlakevirus FLiP, the first known ssDNA phage species with a lipid membrane, as our model phage. We examined the infectivity of FLiP with three Flavobacterium host strains, B330, B167 and B114. We discovered that FLiP infection is contingent on the host strain and conditions such as temperature and bacterial growth phase. FLiP can infect its hosts across a wide temperature range, but optimal phage replication varies with each host. We uncovered some unique aspects of phage infectivity: FLiP has limited infectivity in liquid-suspended cells, but it improves when cells are surface-attached. Moreover, FLiP infects stationary phase B167 and B114 cells more rapidly and efficiently than exponentially growing cells, a pattern not observed with the B330 host. We also present the first experimental evidence of endolysin function in ssDNA phages. The activity of FLiP's lytic enzymes was found to be condition-dependent. Our findings underscore the importance of studying phage ecology in contexts that are relevant to the environment, as both the host and the surrounding conditions can significantly alter the outcome of phage-host interactions.

Mycobacteriophages: therapeutic approach for mycobacterial infections

Tuberculosis (TB) is a significant global health threat, and cases of infection with non-tuberculous mycobacteria (NTM) causing lung disease (NTM-LD) are rising. Bacteriophages and their gene products have garnered interest as potential therapeutic options for bacterial infections. Here, we have compiled information on bacteriophages and their products that can kill Mycobacterium tuberculosis or NTM. We summarize the mechanisms whereby viable phages can access macrophage-resident bacteria and not elicit immune responses, review methodologies of pharmaceutical product development containing mycobacteriophages and their gene products, mainly lysins, in the context of drug regulatory requirements and we discuss industrially relevant methods for producing pharmaceutical products comprising mycobacteriophages, emphasizing delivery of mycobacteriophages to the lungs. We conclude with an outline of some recent case studies on mycobacteriophage therapy.

Isolation and Characterization of Novel Bacteriophages to Target Carbapenem-Resistant Acinetobacter baumannii

The spread of multidrug-resistant Acinetobacter baumannii in hospitals and nursing homes poses serious healthcare challenges. Therefore, we aimed to isolate and characterize lytic bacteriophages targeting carbapenem-resistant Acinetobacter baumannii (CRAB). Of the 21 isolated A. baumannii phages, 11 exhibited potent lytic activities against clinical isolates of CRAB. Based on host spectrum and RAPD-PCR results, 11 phages were categorized into four groups. Three phages (vB_AbaP_W8, vB_AbaSi_W9, and vB_AbaSt_W16) were further characterized owing to their antibacterial efficacy, morphology, and whole-genome sequence and were found to lyse 37.93%, 89.66%, and 37.93%, respectively, of the 29 tested CRAB isolates. The lytic spectrum of phages varied depending on the multilocus sequence type (MLST) of the CRAB isolates. The three phages contained linear double-stranded DNA genomes, with sizes of 41,326-166,741 bp and GC contents of 34.4-35.6%. Genome-wide phylogenetic analysis and single gene-based tree construction revealed no correlation among the three phages. Moreover, no genes were associated with lysogeny, antibiotic resistance, or bacterial toxins. Therefore, the three novel phages represent potential candidates for phage therapy against CRAB infections.

What's on a prophage: analysis of Salmonella spp. prophages identifies a diverse range of cargo with multiple virulence- and metabolism-associated functions

The gain of mobile elements, such as prophages, can introduce cargo to the recipient bacterium that could facilitate its persistence in or expansion to a new environment, such as a host. While previous studies have focused on identifying and characterizing the genetic diversity of prophages, analyses characterizing the cargo that prophages carry have not been extensively explored. We characterized prophage regions from 303 Salmonella spp. genomes (representing 254 unique serovars) to assess the distribution of prophages in diverse Salmonella. On average, prophages accounted for 3.7% (0.1%-8.8%) of the total genomic content of each isolate. Prophage regions annotated as Gifsy 1 and Salmon Fels 1 were the most commonly identified intact prophages, suggesting that they are common throughout the Salmonella genus. Among 21,687 total coding sequences (CDSs) from intact prophage regions in subsp. enterica genomes, 7.5% (median; range: 1.1%-47.6%) were categorized as having a function not related to prophage integration or phage structure, some of which could potentially provide a functional attribute to the host Salmonella cell. These predicted functions could be broadly categorized into CDSs involved in: (i) modification of cell surface structures (i.e., glycosyltransferases); (ii) modulation of host responses (e.g., SodC/SodA, SopE, ArtAB, and typhoid toxin); (iii) conferring resistance to heavy metals and antimicrobials; (iv) metabolism of carbohydrates, amino acids, and nucleotides; and (v) DNA replication, repair, and regulation. Overall, our systematic analysis of prophage cargo highlights a broader role for prophage cargo in influencing the metabolic, virulence, and resistance characteristics of Salmonella.

IMPORTANCE

Lysogenic bacteriophages (phages) can integrate their genome into a bacterial host's genome, potentially introducing genetic elements that can affect the fitness of the host bacterium. The functions of prophage-encoded genes are important to understand as these genes could be mobilized and transferred to a new host. Using a large genomic dataset representing >300 isolates from all known subspecies and species of Salmonella, our study contributes important new findings on the distribution of prophages and the types of cargo that diverse Salmonella prophages carry. We identified a number of coding sequences (CDSs) annotated as having cell surface-modifying attributes, suggesting that prophages may have played an important role in shaping Salmonella's diverse surface antigen repertoire. Furthermore, our characterization of prophages suggests that they play a broader role in facilitating the acquisition and transfer of CDSs associated with metabolism, DNA replication and repair, virulence factors, and to a lesser extent, antimicrobial resistance.

Therapeutic efficacy of a K5-specific phage and depolymerase against Klebsiella pneumoniae in a mouse model of infection

Klebsiella pneumoniae has become one of the most intractable gram-negative pathogens infecting humans and animals due to its severe antibiotic resistance. Bacteriophages and protein products derived from them are receiving increasing amounts of attention as potential alternatives to antibiotics. In this study, we isolated and investigated the characteristics of a new lytic phage, P1011, which lyses K5 K. pneumoniae specifically among 26 serotypes. The K5-specific capsular polysaccharide-degrading depolymerase dep1011 was identified and expressed. By establishing murine infection models using bovine strain B16 (capable of supporting phage proliferation) and human strain KP181 (incapable of sustaining phage expansion), we explored the safety and efficacy of phage and dep1011 treatments against K5 K. pneumoniae. Phage P1011 resulted in a 60% survival rate of the mice challenged with K. pneumoniae supporting phage multiplication, concurrently lowering the bacterial burden in their blood, liver, and lungs. Unexpectedly, even when confronted with bacteria impervious to phage multiplication, phage therapy markedly decreased the number of viable organisms. The protective efficacy of the depolymerase was significantly better than that of the phage. The depolymerase achieved 100% survival in both treatment groups regardless of phage propagation compatibility. These findings indicated that P1011 and dep1011 might be used as potential antibacterial agents to control K5 K. pneumoniae infection.

Partial Characterization of Three Bacteriophages Isolated from Aquaculture Hatchery Water and Their Potential in the Biocontrol of Vibrio spp

Bacteriophages are currently considered one of the most promising alternatives to antibiotics under the 'One Health' approach due to their ability to effectively combat bacterial infections. This study aimed to characterize Vibrio species in hatchery water samples collected from an aquaculture farm and investigate the biocontrol potential of their bacteriophages. Vibrio spp. (n = 32) isolates confirmed by LNA probe-based qPCR were used as hosts. Three Vibrio phages were isolated. IKEM_vK exhibited a broad host range, infecting V. harveyi (n = 8), V. alginolyticus (n = 2), V. azureus (n = 1), and V. ordalii (n = 1). IKEM_v5 showed lytic activity against V. anguillarum (n = 4) and V. ordalii (n = 1), while IKEM_v14 was specific to V. scophtalmi (n = 4). The morphological appearance of phages and their lytic effects on the host were visualized using scanning electron microscopy (SEM). All three phages remained relatively stable within the pH range of 6-11 and up to 60 °C. The lytic activities and biofilm inhibition capabilities of these phages against planktonic Vibrio cells support their potential applications in controlling vibriosis in aquaculture systems.

Phage therapy as a glimmer of hope in the fight against the recurrence or emergence of surgical site bacterial infections

PURPOSE

Over the last decade, surgery rates have risen alarmingly, and surgical-site infections are expanding these concerns. In spite of advances in infection control practices, surgical infections continue to be a significant cause of death, prolonged hospitalization, and morbidity. As well as the presence of bacterial infections and their antibiotic resistance, biofilm formation is one of the challenges in the treatment of surgical wounds.

METHODS

This review article was based on published studies on inpatients and laboratory animals receiving phage therapy for surgical wounds, phage therapy for tissue and bone infections treated with surgery to prevent recurrence, antibiotic-resistant wound infections treated with phage therapy, and biofilm-involved surgical wounds treated with phage therapy which were searched without date restrictions.

RESULTS

It has been shown in this review article that phage therapy can be used to treat surgical-site infections in patients and animals, eliminate biofilms at the surgical site, prevent infection recurrence in wounds that have been operated on, and eradicate antibiotic-resistant infections in surgical wounds, including multi-drug resistance (MDR), extensively drug resistance (XDR), and pan-drug resistance (PDR). A cocktail of phages and antibiotics can also reduce surgical-site infections more effectively than phages alone.

CONCLUSION

In light of these encouraging results, clinical trials and research with phages will continue in the near future to treat surgical-site infections, biofilm removal, and antibiotic-resistant wounds, all of which could be used to prescribe phages as an alternative to antibiotics.

Marine bacteriophages disturb the associated microbiota of Aurelia aurita with a recoverable effect on host morphology

The concept of the metaorganism describes a multicellular host and its diverse microbial community, which form one biological unit with a combined genetic repertoire that significantly influences health and survival of the host. The present study delved into the emerging field of bacteriophage research within metaorganisms, focusing on the moon jellyfish Aurelia aurita as a model organism. The previously isolated Pseudomonas phage BSwM KMM1 and Citrobacter phages BSwM KMM2 - KMM4 demonstrated potent infectivity on bacteria present in the A. aurita-associated microbiota. In a host-fitness experiment, Baltic Sea subpopulation polyps were exposed to individual phages and a phage cocktail, monitoring polyp survival and morphology, as well as microbiome changes. The following effects were obtained. First, phage exposure in general led to recoverable malformations in polyps without affecting their survival. Second, analyses of the community structure, using 16S rRNA amplicon sequencing, revealed alterations in the associated microbial community in response to phage exposure. Third, the native microbiota is dominated by an uncultured likely novel Mycoplasma species, potentially specific to A. aurita. Notably, this main colonizer showed resilience through the recovery after initial declines, which aligned with abundance changes in Bacteroidota and Proteobacteria, suggesting a dynamic and adaptable microbial community. Overall, this study demonstrates the resilience of the A. aurita metaorganism facing phage-induced perturbations, emphasizing the importance of understanding host-phage interactions in metaorganism biology. These findings have implications for ecological adaptation and conservation in the rapidly changing marine environment, particularly regarding the regulation of blooming species and the health of marine ecosystems during ongoing environmental changes.

Pharmacokinetics and Biodistribution of Phages and their Current Applications in Antimicrobial Therapy

Antimicrobial resistance remains a critical global health concern, necessitating the investigation of alternative therapeutic approaches. With the diminished efficacy of conventional small molecule drugs due to the emergence of highly resilient bacterial strains, there is growing interest in the potential for alternative therapeutic modalities. As naturally occurring viruses of bacteria, bacteriophage (or phage) are being re-envisioned as a platform to engineer properties that can be tailored to target specific bacterial strains and employ diverse antibacterial mechanisms. However, limited understanding of key pharmacological properties of phage is a major challenge to translating its use from preclinical to clinical settings. Here, we review modern advancements in phage-based antimicrobial therapy and discuss the in vivo pharmacokinetics and biodistribution of phage, addressing critical challenges in their application that must be overcome for successful clinical implementation.

Gut microbiota-gonadal axis: the impact of gut microbiota on reproductive functions

The influence of gut microbiota on physiological processes is rapidly gaining attention globally. Despite being under-studied, there are available data demonstrating a gut microbiota-gonadal cross-talk, and the importance of this axis in reproduction. This study reviews the impacts of gut microbiota on reproduction. In addition, the possible mechanisms by which gut microbiota modulates male and female reproduction are presented. Databases, including Embase, Google scholar, Pubmed/Medline, Scopus, and Web of Science, were explored using relevant key words. Findings showed that gut microbiota promotes gonadal functions by modulating the circulating levels of steroid sex hormones, insulin sensitivity, immune system, and gonadal microbiota. Gut microbiota also alters ROS generation and the activation of cytokine accumulation. In conclusion, available data demonstrate the existence of a gut microbiota-gonadal axis, and role of this axis on gonadal functions. However, majority of the data were compelling evidences from animal studies with a great dearth of human data. Therefore, human studies validating the reports of experimental studies using animal models are important.

Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection

Circularity confers protection to viral genomes where linearity falls short, thereby fulfilling the form follows function aphorism. However, a shift away from morphology-based classification toward the molecular and ecological classification of viruses is currently underway within the field of virology. Recent years have seen drastic changes in the International Committee on Taxonomy of Viruses' operational definitions of viruses, particularly for the tailed phages that inhabit the human gut. After the abolition of the order Caudovirales, these tailed phages are best defined as members of the class Caudoviricetes. To determine the epistemological value of genome topology in the context of the human gut virome, we designed a set of seven experiments to assay the impact of genome topology and representative viral selection on biological interpretation. Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short-read polishing, we showed that circular and linear virus genomes differ remarkably in terms of genome quality, GC skew, transfer RNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage-host interaction. Furthermore, the disparity profile changes during dereplication. In particular, our phage-host interaction results demonstrated that proportional abundances cannot be meaningfully compared without due regard for genome topology and dereplication threshold, which necessitates the need for standardized reporting. As a best practice guideline, we recommend that comparative studies of the human gut virome always report the ratio of circular to linear viral genomes along with the dereplication threshold so that structural and functional metrics can be placed into context when assessing biologically relevant metagenomic properties such as proportional abundance.

Isolation and characterization of Bacillus cereus bacteriophage DZ1 and its application in foods

Bacillus cereus is a pathogenic bacterium that causes food contamination, resulting in food poisoning such as diarrhea and emesis. Therefore, it is crucial to develop effective strategies to control this bacterium. In this study, we isolated and characterized a novel B. cereus phage, named DZ1. Morphological and genomic analyses revealed that phage DZ1 is a new species belonging to the Andromedavirus genus. Phage DZ1 was tolerant to a wide range of pH values (5-9), temperatures (4-55 ℃), and high concentrations of NaCl solution (1000 mM). B. cereus with 21 different sequence types (STs) can be lysed by phage DZ1. Importantly, phage DZ1 inhibited B. cereus growth in spiked rice substrates or milk up to 36 and 72 h, respectively, with suppression of 3 log. Therefore, phage DZ1 is a useful biocontrol agent for the control of B. cereus in the food industry.

Tradeoffs between phage resistance and nitrogen fixation drive the evolution of genes essential for cyanobacterial heterocyst functionality

Harmful blooms caused by diazotrophic (nitrogen-fixing) Cyanobacteria are becoming increasingly frequent and negatively impact aquatic environments worldwide. Cyanophages (viruses infecting Cyanobacteria) can potentially regulate cyanobacterial blooms, yet Cyanobacteria can rapidly acquire mutations that provide protection against phage infection. Here, we provide novel insights into cyanophage:Cyanobacteria interactions by characterizing the resistance to phages in two species of diazotrophic Cyanobacteria: Nostoc sp. and Cylindrospermopsis raciborskii. Our results demonstrate that phage resistance is associated with a fitness tradeoff by which resistant Cyanobacteria have reduced ability to fix nitrogen and/or to survive nitrogen starvation. Furthermore, we use whole-genome sequence analysis of 58 Nostoc-resistant strains to identify several mutations associated with phage resistance, including in cell surface-related genes and regulatory genes involved in the development and function of heterocysts (cells specialized in nitrogen fixation). Finally, we employ phylogenetic analyses to show that most of these resistance genes are accessory genes whose evolution is impacted by lateral gene transfer events. Together, these results further our understanding of the interplay between diazotrophic Cyanobacteria and their phages and suggest that a tradeoff between phage resistance and nitrogen fixation affects the evolution of cell surface-related genes and of genes involved in heterocyst differentiation and nitrogen fixation.

Unraveling Physical Interactions of Clostridioides difficile with Phage and Phage-Derived Proteins Using In Vitro and Whole-Cell Assays

Physical interactions between bacteria and phages provide valuable insights into the mechanisms of phage infection and may provide information on the use of phages as a therapeutic approach. In this study, we employed a combination of in vitro and whole-cell assays to examine the interactions between Clostridioides difficile and phages and phage-derived proteins. These techniques can also be adapted for studying the physical interactions between other bacterial species and their associated phages.