Pharokka: a fast scalable bacteriophage annotation tool

Exploration of the feasibility of clinical application of phage treatment for multidrug-resistant Serratia marcescens-induced pulmonary infection

Serratia marcescens (S. marcescens) commonly induces refractory infection due to its multidrug-resistant nature. To date, there have been no reports on the application of phage treatment for S. marcescens infection. This study was conducted to explore the feasibility of phage application in treating refractory S. marcescens infection by collaborating with a 59-year-old male patient with a pulmonary infection of multidrug-resistant S. marcescens. Our experiments included three domains: i) selection of the appropriate phage, ii) verification of the efficacy and safety of the selected phage, iii) confirmation of phage-bacteria interactions. Our results showed that phage Spe5P4 is appropriate for S. marcescens infection. Treatment with phage Spe5P4 showed good efficacy, manifested as amelioration of symptoms, hydrothorax examinations, and chest computed tomography findings. Phage treatment did not worsen hepatic and renal function, immunity-related indices, or indices of routine blood examination. It did not induce or deteriorate drug resistance of the involved antibiotics. Importantly, no adverse events were reported during the treatment or follow-up periods. Thus, phage treatment showed satisfactory safety. Finally, we found that phage treatment did not increase the bacterial load, cytotoxicity, virulence, or phage resistance of S. marcescens, indicating satisfactory phage-bacteria interactions between Spe5P4 and S. marcescens, which are useful for the future application of phage Spe5P4 against S. marcescens. This work provides evidence and a working basis for further application of phage Spe5P4 in treating refractory S. marcescens infections. We also provided a methodological basis for investigating clinical application of phage treatment against multidrug-resistant bacterial infections in the future.

Isolation of phages infecting the zoonotic pathogen Streptococcus suis reveals novel structural and genomic characteristics

Bacteriophage research has experienced a renaissance in recent years, owing to their therapeutic potential and versatility in biotechnology, particularly in combating antibiotic resistant-bacteria along the farm-to-fork continuum. However, certain pathogens remain underexplored as targets for phage therapy, including the zoonotic pathogen Streptococcus suis which causes infections in pigs and humans. Despite global efforts, the genome of only one infective S. suis phage has been described. Here, we report the isolation of two phages that infect S. suis: Bonnie and Clyde. The phages infect 58 of 100 S. suis strains tested, including representatives of seven different serotypes and thirteen known sequence types from diverse geographical origins. Clyde suppressed bacterial growth in vitro within two multi-strain mixes designed to simulate a polyclonal S. suis infection. Both phages demonstrated stability across various temperatures and pH levels, highlighting their potential to withstand storage conditions and maintain viability in delivery formulations. Genome comparisons revealed that neither phage shares significant nucleotide identity with any cultivated phages in the NCBI database and thereby represent novel species belonging to two distinct novel genera. This study is the first to investigate the adhesion devices of S. suis infecting phages. Structure prediction and analysis of adhesion devices with AlphaFold2 revealed two distinct lineages of S. suis phages: Streptococcus thermophilus-like (Bonnie) and S. suis-like (Clyde). The structural similarities between the adhesion devices of Bonnie and S. thermophilus phages, despite the lack of nucleotide similarity and differing ecological niches, suggest a common ancestor or convergent evolution, highlighting evolutionary links between pathogenic and non-pathogenic streptococcal species. These findings provide valuable insights into the genetic and phenotypic characteristics of phages that can infect S. suis, providing new data for the therapeutic application of phages in a One Health context.

Exploring viral diversity in fermented vegetables through viral metagenomics

Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.

Isolation, characterization, and application of a novel Vibrio parahaemolyticus bacteriophage from retail shrimp in Sarawak, Malaysia

Shrimp farming, a highly profitable sector in global aquaculture, has seen remarkable growth in recent years. This increasing demand and the expansion of farming operations, including in Sarawak, Malaysia, highlight the sector's potential. However, the industry faces significant challenges, particularly the prevalence of vibriosis, a bacterial infection caused by Vibrio species. Contamination of food products has also increased the risk of vibriosis in humans. The widespread use of antibiotics to combat this disease has led to the rapid emergence of antimicrobial resistance (AMR) bacteria. This study specifically focuses on the isolation and characterization of phage EniLVP02, a novel bacteriophage with the potential to combat V. parahaemolyticus infections. EniLVP02 was successfully isolated from shrimp purchased at a retail market and exhibited strong lytic activity against V. parahaemolyticus strains. Structural analysis categorized EniLVP02 within the Straboviridae family, belonging to the class Caudoviricetes. The phage displayed a narrow host range and lytic nature only towards V. parahaemolyticus strains isolated from the Telaga Air shrimp farm. Phage EniLVP02 exhibited long latent period of 120 min and large burst size of 144 phages per infected cells. Stability studies revealed EniLVP02's resilience across various pH (pH 4.0-9.0) and temperature (28 °C-65 °C) conditions, particularly at physiological temperatures. Comparative genome analyses indicated its distinct evolutionary relationship and low homology with other Vibriophages, suggesting its novelty. EniLVP02 demonstrated significant potential in biofilm prevention and destruction, with absorbance (OD600 nm) reduction from 0.592 ± 0.055 to 0.204± 0.016 and from 0.843± 0.003 to 0.174± 0.026 respectively. Moreover, in the treatment of V. parahaemolyticus-contaminated shrimp meat, EniLVP02 effectively inhibit bacterial concentrations by 75.2 % at room temperature and 16.2 % at 4 °C after 24 h. Genomic sequencing revealed low similarity between EniLVP02 with other phages, suggesting its novelty. Importantly, the absence of lysogeny-related, antibiotic resistance, and virulence genes in its genome supports EniLVP02's safety for therapeutic use. This study underscores the importance of exploring phages from retail food products for therapeutic applications and highlights the promising attributes of phage EniLVP02 in combating V. parahaemolyticus infections in aquaculture. Further investigations on its compatibility with other phages and application in diverse food matrices are warranted to assess its full potential.

AcrDB update: Predicted 3D structures of anti-CRISPRs in human gut viromes

Anti-CRISPR (Acr) proteins play a key role in phage-host interactions and hold great promise for advancing genome-editing technologies. However, finding new Acrs has been challenging due to their low sequence similarity. Recent advances in protein structure prediction have opened new pathways for Acr discovery by using 3D structure similarity. This study presents an updated AcrDB, with the following new features not available in other databases: (1) predicted Acrs from human gut virome databases, (2) Acr structures predicted by AlphaFold2, (3) a structural similarity search function to allow users to submit new sequences and structures to search against 3D structures of experimentally known Acrs. The updated AcrDB contains predicted 3D structures of 795 candidate Acrs with structural similarity (TM-score ≥0.7) to known Acrs supported by at least two of the three non-sequence similarity-based tools (TM-Vec, Foldseek, AcrPred). Among these candidate Acrs, 121 are supported by all three tools. AcrDB also includes 3D structures of 122 experimentally characterized Acr proteins. The 121 most confident candidate Acrs were combined with the 122 known Acrs and clustered into 163 sequence similarity-based Acr families. The 163 families were further subject to a structure similarity-based hierarchical clustering, revealing structural similarity between 44 candidate Acr (cAcr) families and 119 known Acr families. The bacterial hosts of these 163 Acr families are mainly from Bacillota, Pseudomonadota, and Bacteroidota, which are all dominant gut bacterial phyla. Many of these 163 Acr families are also co-localized in Acr operons. All the data and visualization are provided on our website: https://pro.unl.edu/AcrDB.

Comprehensive genomic and evolutionary analysis of biofilm matrix clusters and proteins in the Vibrio genus

Vibrio cholerae pathogens cause cholera, an acute diarrheal disease resulting in significant morbidity and mortality worldwide. Biofilms in vibrios enhance their survival in natural ecosystems and facilitate transmission during cholera outbreaks. Critical components of the biofilm matrix include the Vibrio polysaccharides produced by the vps-1 and vps-2 gene clusters and the biofilm matrix proteins encoded in the rbm gene cluster, together comprising the biofilm matrix cluster. However, the biofilm matrix clusters and their evolutionary patterns in other Vibrio species remain underexplored. In this study, we systematically investigated the distribution, diversity, and evolution of biofilm matrix clusters and proteins across the Vibrio genus. Our findings reveal that these gene clusters are sporadically distributed throughout the genus, even appearing in species phylogenetically distant from Vibrio cholerae. Evolutionary analysis of the major biofilm matrix proteins RbmC and Bap1 shows that they are structurally and sequentially related, having undergone structural domain and modular alterations. Additionally, a novel loop-less Bap1 variant was identified, predominantly represented in two phylogenetically distant V. cholerae subspecies clades that share specific gene groups associated with the presence or absence of the protein. Furthermore, our analysis revealed that rbmB, a gene involved in biofilm dispersal, shares a recent common ancestor with Vibriophage tail proteins, suggesting that phages may mimic host functions to evade biofilm-associated defenses. Our study offers a foundational understanding of the diversity and evolution of biofilm matrix clusters in vibrios, laying the groundwork for future biofilm engineering through genetic modification.

IMPORTANCE

Biofilms help vibrios survive in nature and spread cholera. However, the genes that control biofilm formation in vibrios other than Vibrio cholerae are not well understood. In this study, we analyzed the biofilm matrix gene clusters and proteins across diverse Vibrio species to explore their patterns and evolution. We discovered that these genes are spread across different Vibrio species, including those not closely related to V. cholerae. We also found various forms of key biofilm proteins with different structures. Additionally, we identified genes involved in biofilm dispersal that are related to vibriophage genes, highlighting the role of phages in biofilm development. This study not only provides a foundational understanding of biofilm diversity and evolution in vibrios but also leads to new strategies for engineering biofilms through genetic modification, which is crucial for managing cholera outbreaks and improving the environmental resilience of these bacteria.

Phage-antibiotic synergy to combat multidrug resistant strains of Gram-negative ESKAPE pathogens

Bacteriophage-antibiotic-synergy (PAS) was investigated to target Pseudomonas aeruginosa, Klebsiella pneumoniae, Acinetobacter baumannii and Enterobacter cloacae. Whole genome sequencing indicated that bacteriophage KPW17 targeting K. pneumoniae, clustered with genus Webervirus, ECSR5 targeting E. cloacae clustered with Eclunavirus, PAW33 targeting P. aeruginosa clustered with Bruynoghevirus, while ABTW1 targeting A. baumannii clustered with Vieuvirus. PAS analysis showed that the combination of ciprofloxacin (CIP) and levofloxacin (LEV) with PAW33 resulted in the synergistic eradication of all tested P. aeruginosa strains. Similarly, the combined use of doripenem (DOR) and LEV with KPW17 resulted in the synergistic eradication of the environmental and clinical K. pneumoniae strains, while the combined use of DOR and gentamicin (CN) with ECSR5 was synergistic against the clinical E. cloacae NCTC 13406. Gentamicin with ECSR5, however, only exhibited an additive effect for E. cloacae 4L, while ABTW1 with piperacillin-tazobactam (TZP) and imipenem (IPM) resulted in an indifferent interaction between the bacteriophage and tested antibiotics against the clinical A. baumannii AB3, i.e., the activity of the combination is equal to the activity of most active agent. Thus, while the observed PAS may offer an opportunity for the re-introduction or more efficient application of certain antibiotics to combat antibiotic resistance, extensive research is required to determine the optimal phage-antibiotic combinations, dosages and treatment regiments.

Characterization of a virulent phage, P12L (genus Drulisvirus), targeting Klebsiella pneumoniae capsule type K2

A virulent bacteriophage, P12L, infecting hypermucoviscous Klebsiella pneumoniae of capsule-type K2 was characterized. The phage was found to have podovirus-like morphology, with an icosahedral head and a short tail. It exhibited efficient adsorption with a burst size of 183 PFU/cell. The viral genome is a linear dsDNA molecule that is 42,343 bp in length and contains 62 putative open reading frames (ORFs). It lacks genes associated with drug resistance or virulence factors and encodes two predicted domains associated with depolymerase activity. Because depolymerase can degrade polysaccharide capsules and promote efficient phage-host interactions, phage P12L shows potential as a biocontrol agent.

Genome sequence of a lytic phage phi1_092060 targeting ST2 KL104-type Acinetobacter baumannii

We describe the genome of a lytic phage isolated from sewage, which is capable of lysing ST2 KL104-type carbapenem-resistant Acinetobacter baumannii strains. The genome is 167,208 bp in length, has a guanine-cytosine (GC) content of 37%, and includes 266 protein-coding sequences and five tRNAs.

Genomic variation in Pseudomonas aeruginosa clinical respiratory isolates with de novo resistance to a bacteriophage cocktail

Pseudomonas aeruginosa is an opportunistic pathogen that can cause sinus infections and pneumonia in cystic fibrosis (CF) patients. Bacteriophage therapy is being investigated as a treatment for antibiotic-resistant P. aeruginosa infections. Although virulent bacteriophages have shown promise in treating P. aeruginosa infections, the development of bacteriophage-insensitive mutants (BIMs) in the presence of bacteriophages has been described. The aim of this study was to examine the genetic changes associated with the BIM phenotype. Biofilms of three genetically distinct P. aeruginosa strains, including PAO1 (ATCC 15692), and two clinical respiratory isolates (one CF and one non-CF) were grown for 7 days and treated with either a cocktail of four bacteriophages or a vehicle control for 7 consecutive days. BIMs isolated from the biofilms were detected by streak assays, and resistance to the phage cocktail was confirmed using spot test assays. Comparison of whole genome sequencing between the recovered BIMs and their respective vehicle control-treated phage-sensitive isolates revealed structural variants in two strains, and several small variants in all three strains. These variations involved a TonB-dependent outer membrane receptor in one strain, and mutations in lipopolysaccharide synthesis genes in two strains. Prophage deletion and induction were also noted in two strains, as well as mutations in several genes associated with virulence factors. Mutations in genes involved in susceptibility to conventional antibiotics were also identified in BIMs, with both decreased and increased antibiotic sensitivity to various antibiotics being observed. These findings may have implications for future applications of lytic phage therapy.IMPORTANCELytic bacteriophages are viruses that infect and kill bacteria and can be used to treat difficult-to-treat bacterial infections, including biofilm-associated infections and multidrug-resistant bacteria. Pseudomonas aeruginosa is a bacterium that can cause life-threatening infections. Lytic bacteriophage therapy has been trialed in the treatment of P. aeruginosa infections; however, sometimes bacteria develop resistance to the bacteriophages. This study sheds light on the genetic mechanisms of such resistance, and how this might be harnessed to restore the sensitivity of multidrug-resistant P. aeruginosa to conventional antibiotics.

Isolation and characterization of a novel lytic bacteriophage Pv27 with biocontrol potential against Vibrio parahaemolyticus infections in shrimp

Background

Vibrio parahaemolyticus is a major disease-causing species of Vibrio that is pathogenic to both farmed shrimp and humans. With the increasing spread of antibiotic-resistant V. parahaemolyticus strains, bacteriophages (or phages) are considered potential agents for biocontrol as an alternative to antibiotics. In this study, a bacteriophage capable of lysing V. parahaemolyticus, named Pv27, was isolated, characterized, and evaluated for its potential to control Vibrio infections as a natural therapy.

Methods

Phage Pv27 was isolated using the double-layer agar technique and its morphology was characterized by transmission electron microscopy (TEM). We further assessed the host range specificity, optimal multiplicity of infection (MOI), one-step growth kinetics, and environmental stability of Pv27 under various pH and temperature conditions. The inhibitory activity of Pv27 against V. parahaemolyticus was evaluated in vitro. Finally, genomic analysis of Pv27 was conducted through whole-genome sequencing, followed by functional annotation of open reading frames (ORFs) and phylogenetic analysis.

Results

Phage Pv27 exhibited a Myovirus-like morphology, characterized by an icosahedral head (92.7 ± 2 nm) and a contractile tail (103 ± 11 nm), and belongs to the class Caudoviricetes. Pv27 demonstrated high lytic activity against its host cells, with a short latent period of approximately 25 minutes and a large burst size of 112 plaque-forming units (PFU) per infected cell. The phage displayed significant tolerance to a wide pH range (from 3 to 11) and remained heat-stable at temperatures up to 60 °C for 90 min. Genetically, Pv27 possesses a circular double-stranded DNA genome spanning 191,395 base pairs, with a G + C content of 35% and comprising 355 open reading frames (ORFs). Remarkably, up to 23 tRNA genes were identified in its genome, while no genes associated with antibiotic resistance, virulence, or lysogeny were detected, suggesting its potential as a valuable biocontrol agent. Results from the VIRIDIC, Basic Local Alignment Search Tool (BLAST) and phylogenetic analyses revealed that Pv27 is closely related to the two known Vibrio phages, phiKT1024 and phiTY18. Several genes associated with enhanced environmental competitiveness were also identified in the Pv27 genome, including those encoding a PhoH-like phosphate starvation-inducible protein and endolysin. Phage Pv27 effectively lyses V. parahaemolyticus highlighting its potential as a biocontrol agent.

Isolation and identification of Klebsiella pneumoniae phage ΦK2046: optimizing its antibacterial potential in combination with chlorhexidine

BACKGROUND

Hospital-acquired infections (HAIs) significantly increase morbidity and mortality worldwide, with Klebsiella pneumoniae (K. pneumoniae) being a leading HAI pathogen requiring targeted eradication in healthcare settings. The growing bacterial tolerance to chemical disinfectants, like chlorhexidine, highlights an urgent need for novel disinfection strategies. Bacteriophages, which employ unique mechanisms to lyse bacteria, offer a potential solution. Combining phages with disinfectants could reduce the use of chemical agents and delay the development of bacterial resistance. However, the use of phages for contamination control in clinical environments remains underexplored.

METHODS

ΦK2046 was isolated from hospital wastewater and characterized by transmission electron microscopy, one-step growth curve, optimal multiplicity of infection, and stability analysis. Whole-genome sequencing was performed to identify the genomic characteristics of ΦK2046. The antibacterial and antibiofilm effects of ΦK2046 combined with chlorhexidine were assessed through growth curves, time-kill assays, crystal violet staining, and scanning electron microscopy. A contaminated medical device model was established to assess the ΦK2046-chlorhexidine combination's biofilm reduction efficacy, and different dosing sequences and timing intervals were evaluated for their impact on biofilms formed on urinary catheters.

RESULTS

ΦK2046, characterized by a short latency period, strong environmental stability, safety, and tolerance to chlorhexidine, significantly enhanced the antibacterial and antibiofilm effects of chlorhexidine against FK2046, and reduce the emergence of resistant strains. In contaminated medical device models, the combination of ΦK2046 and chlorhexidine diminished bacterial load and biofilm formation on surfaces. A "phage-first" dosing sequence, particularly with a 90-min interval before chlorhexidine treatment, showed superior efficacy in biofilm reduction.

CONCLUSIONS

This study, using ΦK2046 as an example, demonstrates the potential of phages to enhance the antibacterial and antibiofilm effects of chlorhexidine and their feasibility in medical device disinfection. This innovative approach not only improves chlorhexidine's disinfecting power but also effectively tackles the issue of reduced susceptibility of K. pneumoniae to chlorhexidine. The research advances the development and application of phage-based disinfectants and lays a foundation for establishing a phage library with adjuvant properties for disinfectants.

Phollow reveals in situ phage transmission dynamics in the zebrafish gut microbiome at single-virion resolution

Bacteriophages show promise for microbiome engineering, but studying their transmission dynamics in multimember communities and animal hosts is technically challenging. We therefore created 'Phollow', a live imaging-based approach for tracking phage replication and spread in situ with single-virion resolution. Following interbacterial phage transmission is achieved by marking virions with distinct fluorescent proteins during assembly in newly infected cells. In vitro cell virology studies revealed clouds of phage virions dispersing upon bacterial lysis, leading to rampant transmission. Combining Phollow with optically transparent zebrafish, we visualized phage outbreaks within the vertebrate gut. We observed that virions from a zebrafish-derived Plesiomonas strain, but not a human-derived E. coli, rapidly disseminate systemically to the liver and brain. Moreover, antibiotics triggered waves of interbacterial transmission and sudden shifts in gut community ecology. Phollow ultimately empowers multiscale investigations of phage transmission and transkingdom interactions that have the potential to open new avenues for phage-based microbiome therapies.

Genome sequences of two phages active against cystic fibrosis isolates of Pseudomonas aeruginosa

We describe the genomes of two Pseudomonas aeruginosa phages of the genus Bruynoghevirus, WRAIR_EPa83 and WRAIR_EPa87. They consist of 45,622 and 45,077 bp, with 52.52% and 52.11% guanine-cytosine content, contain 81 and 80 coding sequences, two and three tRNA genes, and direct terminal repeats of 183 and 184 bp, respectively.

Isolation and genomic characterization of Psychrobacillus isolate L3 and bacteriophage Spoks: a new phage-host pair from Antarctic soil

BACKGROUND

Most habitats on Earth house unfathomable microbial diversity, yet much of it remains uncultured. The same applies to temperate phages, most of which documented to date are predicted purely in silico from the prophage-like genomic regions of the bacteria, lacking any experimental evidence of their functional integrity (e.g., the ability to undergo lytic replication). Hard-to-access parts of our planet with unique environments serve as especially promising places to collect samples for the isolation of novel microbes highly divergent from those isolated thus far. Antarctica, a continent mostly covered by a thick ice sheet, is one such area of our planet rife with novel microbiological entities. In this study, we aimed to isolate and characterize a novel culturable phage-host pair from Antarctic soils.

RESULTS

Psychrobacillus phage Spoks was retrieved alongside its host bacterial strain designated as "L3" from an ice-free soil sample collected at Waddington Bay, Graham Coast, Antarctica. Whole-genome sequencing of both the phage and the host revealed that they are divergent from, respectively, viruses and bacteria cultured and characterized thus far, and the intergenomic differences suggest that both might represent novel taxa. The genome of siphophage Spoks is a 36,472 bp long linear double-stranded DNA molecule with 11 base long 3' cohesive overhangs. Spoks can integrate into the chromosome of its isolation host strain in a site-specific fashion. Integration takes place in the genomic region of the host chromosome between the ORFs predicted to encode a DNA topoisomerase III and a BlaI/MecI/CopY family transcriptional regulator via recombination between attP and attB, which share a 19 bp "core" overlap sequence. L3 lysogens containing Spoks are not stable, with regular spontaneous induction occurring. Although the attachment site overlap sequence was found in the publicly available genomic sequences of several other Psychrobacillus spp. strains isolated from different habitats, none were found to contain a Spoks-like prophage.

CONCLUSIONS

The isolation and characterization of Psychrobacillus temperate phage Spoks and its host strain L3 from Antarctica highlight the potential for discovering novel biological entities divergent from their closest cultured relatives with relative ease, given access to such difficult-to-access undersampled environments, and are expected to encourage similar studies.

Characterization and genome analysis of the novel virulent Burkholderia phage Bm1, which is active against pan-drug-resistant Burkholderia multivorans

The escalating challenges of antibiotic resistance in bacterial pathogens have necessitated the exploration of alternative therapeutic strategies. Among these, bacteriophage therapy has regained attention as a promising approach to combat multidrug-resistant bacteria. Bacteriophages are viruses that infect and lyse specific bacterial strains, making them attractive candidates for targeted antimicrobial treatment. Burkholderia multivorans, a Gram-negative bacterium, is known to cause opportunistic infections, particularly in individuals with a compromised immune system or with cystic fibrosis. The prevalence of antibiotic-resistant Burkholderia strains has raised concerns about treatment options. In this study, we characterized the Burkholderia phage Bm1, a virulent bacteriophage isolated from an environmental source. Electron microscopy revealed that Bm1 phage particles have myovirus morphology, with an icosahedral head of 72 nm in diameter and a contractile tail of 100 nm in length and 18 nm in width. The genome of phage Bm1 consists of a double-stranded DNA of 67,539 bp with a terminal repeat region at each end. Comparative analysis indicated that the closest relative of phage Bm1 is Burkholderia phage BCSR129, with a calculated VIRIDIC identity of 57.7%. The apparent absence of an integrase gene suggests that the Burkholderia phage Bm1 has a strictly lytic life cycle.

Weberviruses are gut-associated phages that infect Klebsiella spp

Weberviruses are bacteriophages (phages) that can infect and lyse clinically relevant, multidrug-resistant (MDR) strains of Klebsiella. They are an attractive therapeutic option to tackle Klebsiella infections due to their high burst sizes, long shelf life, and associated depolymerases. In this study, we isolated and characterized seven new lytic phages and compared their genomes with those of their closest relatives. Gene-sharing network, ViPTree proteome, and terL gene-sequence-based analyses incorporating all publicly available webervirus genomes [n = 258 from isolates, n = 65 from metagenome-assembled genome (MAG) datasets] confirmed the seven phages as members of the genus Webervirus and identified a novel genus (Defiantjazzvirus) within the family Drexlerviridae. Using our curated database of 265 isolated phage genomes and 65 MAGs (n = 330 total), we found that weberviruses are distributed globally and primarily associated with samples originating from the gut: sewage (154/330, 47%), wastewater (83/330, 25%), and human faeces (66/330, 20%). We identified three distinct clusters of potential depolymerases encoded within the 330 genomes. Due to their global distribution, frequency of isolation and lytic activity against the MDR clinical Klebsiella strains used in this study, we conclude that weberviruses and their depolymerases show promise for development as therapeutic agents against Klebsiella spp.

Phage Endolysins as Promising and Effective Candidates for Use Against Uropathogenic Escherichia coli

The presented in silico and phylogenetic analysis of putative endolysins potentially produced by phages infecting uropathogenic Escherichia coli (UPEC) demonstrates their remarkable diversity. These proteins exhibit significant variations in sequence length, molecular weight, isoelectric point, and stability, as well as diverse functional domains determining their enzymatic activity, including lysin, lysozyme, hydrolase, amidase, and peptidase functions. Due to their predicted lytic properties, endolysins hold great promise in combating UPEC bacteria, including those within biofilms, which are often highly resistant to conventional treatments. Despite their potential, several challenges hinder the full utilization of endolysins. These include the relatively small number of identified proteins, challenges in the annotation process, and the scarcity of studies evaluating their efficacy in vitro and in vivo against Gram-negative bacteria. In this work, we emphasize these challenges while also underlining the potential of endolysins as an effective tool against UPEC infections. Their effectiveness could be significantly enhanced when combined with agents that disrupt the outer membrane of these bacteria, making them a promising alternative or complement to existing antimicrobial strategies. Further research is necessary to fully explore their therapeutic potential.

Complete genome sequence of Escherichia coli phage Eryne

Bacteriophage Eryne is a new virus infecting clinical and laboratory strains of Escherichia coli that targets surface glycans. We report the 145,026 bp genome of phage Eryne and show that it belongs to the genus Justusliebigvirus of the Stephanstirmvirinae, known for their multivalent host recognition.

Genome sequence of the broad-host-range phage phi1_092033 against Acinetobacter baumannii

We report the genome of a phage phi1_092033, isolated from sewage, which effectively lyses carbapenem-resistant Acinetobacter baumannii strains of various capsule types. phi1_092033 represents a species of genus Saclayvirus. Its genome consists of 104,070 bp, with a GC content of 38%, containing 188 protein-coding sequences and 13 tRNAs.

Complete genome sequences of 14 lytic bacteriophages against Acinetobacter baumannii from Kenya belonging to the genera Obolenskvirus and Friunavirus

We report the genome sequences of 14 Acinetobacter phages isolated in Kenya, belonging to the genera Friunavirus and Obolenskvirus. They have double-stranded DNA with genome sizes between 39 and 45 kb and G + C content from 38% to 39%. The genomes contain 56 to 93 predicted coding sequences.

Proteomic Analysis of Marine Bacteriophages: Structural Conservation, Post-Translational Modifications, and Phage-Host Interactions

Marine bacteriophages, the most abundant biological entities in marine ecosystems, are essential in biogeochemical cycling. Despite extensive genomic data, many phage genes remain uncharacterised, creating a gap between genomic diversity and gene function knowledge. This gap limits our understanding of phage life cycles, assembly, and host interactions. In this study, we used mass spectrometry to profile the proteomes of 13 marine phages from diverse lifestyles and hosts. The analysis accurately annotated hypothetical genes, mapped virion protein arrangements, and revealed structural similarities among phages infecting the same host, particularly in tail fibre proteins. Protein structure comparisons showed conservation and variability in head and tail proteins, particularly in key domains involved in virion stabilisation and host recognition. For the first time, we identified post-translational modifications (PTMs) in marine phage proteins, which may enhance phage adaptability and help evade host immune systems. These findings suggest that phages optimise their infection strategies through structural variations and PTM modifications, improving their adaptability and host interactions.

Targeting Chronic Biofilm Infections With Patient-derived Phages: An In Vitro and Ex Vivo Proof-of-concept Study in Patients With Left Ventricular Assist Devices

Background

Phage therapy is being reconsidered as a valuable approach to combat antimicrobial resistance. We recently established a personalized phage therapy pipeline in healthy volunteers, where therapeutic phages were isolated from individuals' skin microbiota. In this study, we aim to validate this pipeline in end-stage heart failure patients supported by left ventricular assist devices (LVADs), focusing on phages targeting Staphylococcus epidermidis, a common pathogen responsible for LVAD infections.

Methods

Over a 2.5-year period, 45 LVAD patients were consistently sampled at their driveline exit sites and foreheads. S epidermidis strains from patients' foreheads were used to amplify patient-specific phages. Newly isolated phages were characterized and tested against S epidermidis isolates (n = 42) from the patient cohort. The virulent phage vB_SepS_BE22, isolated from a patient with a driveline infection, was further tested for its bactericidal activity against S epidermidis biofilms ex vivo with rifampicin on driveline biofilms.

Results

S epidermidis was detected in 32 patients, 3 of whom had driveline infections. Phages were isolated from 8 patients, 6 of which were unique and exhibited narrow host ranges, infecting 19%-52% of S epidermidis strains. vB_SepS_BE22, isolated from patient ID25's microbiota, was the only phage that specifically killed S epidermidis clones linked to a patient's infection. vB_SepS_BE22 also reduced bacterial loads in exponential and stationary phase cultures, as well as in biofilms on drivelines when combined with rifampicin.

Conclusions

This study validated a personalized phage therapy approach, where phages from a patient's own microbiota can be used in chronic infection settings as therapeutic agents.

Completing the BASEL phage collection to unlock hidden diversity for systematic exploration of phage-host interactions

Research on bacteriophages, the viruses infecting bacteria, has fueled the development of modern molecular biology and inspired their therapeutic application to combat bacterial multidrug resistance. However, most work has so far focused on a few model phages which impedes direct applications of these findings in clinics and suggests that a vast potential of powerful molecular biology has remained untapped. We have therefore recently composed the BASEL collection of Escherichia coli phages (BActeriophage SElection for your Laboratory), which made a relevant diversity of phages infecting the E. coli K-12 laboratory strain accessible to the community. These phages are widely used, but their assorted diversity has remained limited by the E. coli K-12 host. We have therefore now genetically overcome the two major limitations of E. coli K-12, its lack of O-antigen glycans and the presence of resident bacterial immunity. Restoring O-antigen expression resulted in the isolation of diverse additional viral groups like Kagunavirus, Nonanavirus, Gordonclarkvirinae, and Gamaleyavirus, while eliminating all known antiviral defenses of E. coli K-12 additionally enabled us to isolate phages of Wifcevirus genus. Even though some of these viral groups appear to be common in nature, no phages from any of them had previously been isolated using E. coli laboratory strains, and they had thus remained largely understudied. Overall, 37 new phage isolates have been added to complete the BASEL collection. These phages were deeply characterized genomically and phenotypically with regard to host receptors, sensitivity to antiviral defense systems, and host range. Our results highlighted dominant roles of the O-antigen barrier for viral host recognition and of restriction-modification systems in bacterial immunity. We anticipate that the completed BASEL collection will propel research on phage-host interactions and their molecular mechanisms, deepening our understanding of viral ecology and fostering innovations in biotechnology and antimicrobial therapy.

Population structure and gene flux of Listeria monocytogenes ST121 reveal prophages as a candidate driver of adaptation and persistence in food production environments

Listeria monocytogenes is a bacterial pathogen found in an increasing number of food categories, potentially reflecting an expanding niche and food safety risk profile. In the UK, Listeria monocytogenes sequence type (ST) 121 is more frequently isolated from foods and food environments than from cases of clinical listeriosis, consistent with a relatively low pathogenicity. In this study, we determined the evolution associated with the environmental persistence of a Listeria monocytogenes clone by investigating clone-specific genome features in the context of the ST121 population structure from international sources. To enable unambiguous comparative genomic analysis of ST121 strains, we constructed 16 new high-quality genome assemblies from Listeria monocytogenes isolated from foods, food environments and human clinical sources in the UK from 1987 to 2019. Our dataset was supplemented with additional UK and international genomes from databases held by the Institut Pasteur and the UK Health Security Agency. Time-scaled phylogenetic reconstruction revealed that clade-specific microevolution correlated with key characteristics that may confer adaptations important for success in the environmental niche. For example, a prophage designated LP-13-6 unique to a clade is associated with multi-year persistence in a food production setting. This prophage, observed in a strain that persisted for over a decade, may encode mechanisms facilitating environmental persistence, including the exclusion of other bacteriophages. Pangenome analysis provided insights into other candidate genetic elements associated with persistence and biocide tolerance. The comparative genomic dataset compiled in this study includes an international collection of 482 genome sequences that serve as a valuable resource for future studies to explore conserved genes, regulatory regions, mutations and variations associated with particular traits, such as environmental persistence, pathogenicity or biocide tolerance.

Characterization and therapeutic potential of newly isolated bacteriophages targeting the most common Salmonella serovars in Europe

Despite meticulous monitoring of Salmonella spp. throughout the food chain to ensure safer animal food products for consumers, the number of salmonellosis cases in humans continues to rise annually in Europe. Phage therapy emerges as a promising tool for controlling and eradicating Salmonella in primary production. This study aimed to fully characterize new phage therapy candidates isolated from animal sources. To achieve this, a phenotypic and genetic characterization of five phage isolates was conducted. The five phages demonstrated physical stability across a wide range of temperatures and pH levels, effectively lysing 12 different Salmonella serovars, including the most prevalent ones in the European Union in recent years, as well as multidrug-resistant strains isolated from the field. Additionally, four of the phages exhibited depolymerase production in the host range, with genomic analysis confirming that all five possessed sequences encoding for this activity, suggesting their potential as surface-disinfecting agents. Genetic analysis further revealed that the phages belong to distinct genera: Felixounavirus, Cornellvirus, Skatevirus, Agtevirus and Berlinvirus. Notably, none of the phages contained harmful sequences that could compromise their future application, such as virulence factors, antibiotic resistance genes or temperate markers. Overall, these five phages show promise as suitable candidates for phage therapy applications or phage-based Salmonella eradication strategies, where their integration in the existing biocontrol measures may enhance both food safety and public health.

Genomic and proteomic characterization of four novel Schitoviridae family phages targeting uropathogenic Escherichia coli strain

BACKGROUND

Escherichia coli-associated urinary tract infections (UTIs) are among the most prevalent bacterial infections in humans. Typically, antibiotic medication is used to treat UTIs, but over the time, growth of multidrug resistance among these bacteria has created a global public health issue that necessitates other treatment modalities, such as phage therapy.

METHODS

The UPEC strain PSU-5266 (UE-17) was isolated from human urine samples, while phages were obtained from wastewater. These phages were characterized through host range analysis, stability studies, adsorption assays, and electron microscopy. Additionally, genomic, phylogenetic, and proteomic analyses were conducted to provide further insights.

RESULTS

The current study describes the isolation and characterization of four Escherichia coli phages designated as UE-S5a, UE-S5b, UE-M3 and UE-M6. Bactericidal assays depicted that all bacteriophages exhibited a strong lytic ability against uropathogenic E. coli (UPEC) strain PSU-5266 (UE-17). The phages displayed a broad host range (31-41%) among 104 tested isolates and adsorption rate of 15-20 min. They were stable within pH range of 5-11 and temperature range of 4 to 55 °C. Electron microscopy showed that all phages have icosahedral heads (70-74 nm) and short non-contractile tails, thus exhibiting a podovirus morphology. Sequencing results showed that they have linear double stranded DNA, genome of 73 to 76 kb in length, with GC content of 42% and short direct terminal repeats. Their genomes contain 84-88 predicted genes with putative functions predicted to 42-48% of gene products. The phylogenetic and comparative genomic analysis results depicted that these phages, sharing > 98% sequence similarity, are new members of genus Gamaleyavirus of subfamily Enquatrovirinae, in the Schitoviridae family. Mass spectrometric analysis of purified phage particles identified 44-56 phage particle-associated proteins (PPAPs) belonging to various functional groups such as lysis proteins, structural proteins, DNA packaging related proteins, and proteins involved in replication, metabolism and regulation. In addition, no genes encoding virulence factors, antibiotic resistance or lysogeny factors were identified.

CONCLUSION

The overall findings suggest that these bacteriophages are potential candidates for phage therapy in treating UTIs caused by UPEC strains.

Characterising phages for the control of pathogenic bacteria associated with bivalve consumption

In the present study, five new bacteriophages (or phages) were characterized, and their efficacy in controlling pathogenic bacteria-Escherichia coli, Salmonella enterica serovar Typhimurium, Salmonella enterica serovar Enteritidis, Aeromonas hydrophila, and Vibrio parahaemolyticus-associated with bivalve consumption was evaluated. The isolated phages include both siphovirus [vB_EcoS_UALMA_PCEc3 (PCEc3), vB_SeTS_UALMA_PCST1 (PCST1), and vB_VpaS_UALMA_PCVp3 (PCVp3)] and myovirus [vB_SeEM_UALMA_PCSE1 (PCSE1) and vB_AhyM_UALMA_PCAh2 (PCAh2)] morphotypes. Four phages are safe for bacterial control, with only one (PCAh2) showing potential lysogenic characteristics. All phages exhibited a narrow host range, capable of infecting up to six additional bacterial strains besides their original host, and four could infect the host bacteria of other phages. Adsorption rates ranged from 24% and 98% within 1 h. One-step growth assays revealed different latent periods, ranging from 10 to 120 min, and low to average burst sizes, ranging from 7.60 to 83.97 PFU/mL. Generally, increasing the multiplicity of infection (MOI) enhanced phage efficiency significantly. All phages effectively reduced the bacterial load of their respective hosts, achieving maximum reductions between 3.73 and 5.57 log CFU/mL within 10 h of treatment. These results suggest that phage biocontrol can be an effective alternative to combat pathogenic bacteria associated with bivalve consumption.

Complete genome sequences of three Pseudomonas aeruginosa phages of the genus Phikmvvirus

We describe the genomes of three lytic Pseudomonas aeruginosa phages of the genus Phikmvvirus. The genomes of phages vB_Pae4841-AFR43, vB_Pae10145-KEN1, and vB_Pae9718-KEN10 consist of 43,426, 43,406, and 43,118 bp, with 62.4%, 62.3%, and 62.2% GC content, contain 63, 66, and 64 coding sequences, respectively, and no tRNA genes.

Genome sequences of Klebsiella pneumoniae bacteriophages SF_KL2 and SF_KL25

This report describes the genomes of Klebsiella pneumoniae phages SF_KL2 and SF_KL25, which infect the encapsulated multidrug-resistant K. pneumoniae known to cause nosocomial infections. SF_KL2 and SF_KL25 belong to the genus Webervirus (siphovirus morphotype) and have genomes of 48,737 and 49,170 bp, respectively. The phages were isolated from wastewater in northern Portugal.

VIRGO2: Unveiling the Functional and Ecological Complexity of the Vaginal Microbiome with an Enhanced Non-Redundant Gene Catalog

Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. This study expands our understanding of the function and ecology of the vaginal microbiome using VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 revealed novel insights, including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2,500 metagenomes and 4,000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.

Infection and Genomic Properties of Single- and Double-Stranded DNA Cellulophaga Phages

Bacterial viruses (phages) are abundant and ecologically impactful, but laboratory-based experimental model systems vastly under-represent known phage diversity, particularly for ssDNA phages. Here, we characterize the genomes and infection properties of two unrelated marine flavophages-ssDNA generalist phage phi18:4 (6.5 Kbp) and dsDNA specialist phage phi18:1 (39.2 Kbp)-when infecting the same Cellulophaga baltica strain #18 (Cba18), of the class Flavobacteriia. Phage phi18:4 belongs to a new family of ssDNA phages, has an internal lipid membrane, and its genome encodes primarily structural proteins, as well as a DNA replication protein common to ssDNA phages and a unique lysis protein. Phage phi18:1 is a siphovirus that encodes several virulence genes, despite not having a known temperate lifestyle, a CAZy enzyme likely for regulatory purposes, and four DNA methyltransferases dispersed throughout the genome that suggest both host modulation and phage DNA protection against host restriction. Physiologically, ssDNA phage phi18:4 has a shorter latent period and smaller burst size than dsDNA phage phi18:1, and both phages efficiently infect this host. These results help augment the diversity of characterized environmental phage-host model systems by studying infections of genomically diverse phages (ssDNA vs. dsDNA) on the same host.

Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multidrug-resistant lineages

Staphylococcus pseudintermedius is the foremost cause of opportunistic canine skin and mucosal infections worldwide. Multidrug-resistant (MDR) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) lineages have disseminated globally in the last decade and present significant treatment challenges. However, little is known regarding the factors that contribute to the success of MDR lineages. In this study, we compared the genome sequence of 110 UK isolates of S. pseudintermedius with 2166 genomes of S. pseudintermedius populations from different continents. A novel core genome multi-locus typing scheme was generated to allow large-scale, rapid and detailed analysis of S. pseudintermedius phylogenies and was used to show that the S. pseudintermedius population structure is broadly segregated into an MDR population and a non-MDR population. MRSP lineages are predicted to encode certain resistance genes either chromosomally or on plasmids, and this is associated with their MLST sequence type. A comparison of lineages most frequently implicated in disease, ST-45 and ST-71, with the phylogenetically related ST-496 lineage that has a comparatively low disease rate, revealed that ST-45 and ST-71 genomes encode distinct combinations of phage-defence systems and concurrently encode a high number of intact prophages. In contrast, ST-496 genomes encode a wider array of phage defence systems and lack intact and complete prophages. These findings indicate that MRSP lineages have significant structural genomic differences and that prophage integration and differential antiviral systems correlate with the emergence of successful genotypes.

Isolation, characterization and genomic analysis of bacteriophages for biocontrol of vibriosis caused by Vibrio alginolyticus

Vibrio alginolyticus is a significant opportunistic pathogen in marine environments, affecting both marine organisms and humans. The rise of antibiotic-resistant strains has prompted the exploration of bacteriophages as alternative biological control agents. In this study, 414 lytic bacteriophages specific to V. alginolyticus were isolated from various seafood and environmental samples. Phages P122, P125, and P160 demonstrated the broadest host range, effectively lysing 79.01 % of fish pathogenic V. alginolyticus strains and 44.69 % of environmental strains. However, no activity was observed against clinical V. alginolyticus strains or other tested species, including V. harveyi, Escherichia coli, Staphylococcus aureus, and Aeromonas hydrophila. One-step growth curve analysis revealed latent periods of 40 to 60 min and burst sizes ranging from 140 to 367 PFU/infected cells. Transmission electron microscopy (TEM) classified these phages within the class of Caudoviricetes with an icosahedral head and a long non-contractile tail. Moreover, whole-genome sequencing (WGS) identified genome sizes of approximately 76 kb, with 272-280 open reading frames (ORFs), no tRNA and pathogenic-associated genes. Comparative genomic analysis showed over 97 % similarity with other Vibrio phages. Phylogenetic analysis based on the terminase subunit also confirmed phages P122, P125, and P160 belonging to the class of Caudoviricetes. The phages were non-toxic to Galleria mellonella larvae and showed promise in reducing mortality rates when used as a cocktail treatment. The study highlights the potential of these phages as effective biocontrol agents in aquaculture, offering a promising alternative to antibiotics for managing Vibrio infections.

LoVis4u: a locus visualization tool for comparative genomics and coverage profiles

Comparative genomic analysis often involves visualization of alignments of genomic loci. While several software tools are available for this task, ranging from Python and R libraries to stand-alone graphical user interfaces, a tool is lacking that offers fast, automated usage and the production of publication-ready vector images. Here we present LoVis4u, a command-line tool and Python API designed for highly customizable and fast visualization of multiple genomic loci. LoVis4u generates vector images in PDF format based on annotation data from GenBank or GFF files. It is capable of visualizing entire genomes of bacteriophages as well as plasmids and user-defined regions of longer prokaryotic genomes. Additionally, LoVis4u offers optional data processing steps to identify and highlight accessory and core genes in input sequences. Finally, LoVis4u supports the visualization of genomic signal track profiles from sequencing experiments. LoVis4u is implemented in Python3 and runs on Linux and MacOS. The command-line interface covers most practical use cases, while the provided Python API allows usage within a Python program, integration into external tools, and additional customization. The source code is available at the GitHub page: github.com/art-egorov/lovis4u. Detailed documentation that includes an example-driven guide is available from the software home page: art-egorov.github.io/lovis4u.

Genomic and phenotypic characterization of staphylococci isolated from the skin of non-human primates

The growth of wildlife tourism coupled with continued deforestation has resulted in increased contact between non-human primates (NHPs) and humans. Such events may promote the transmission of potentially pathogenic bacteria such as Staphylococcus spp. However, the presence and associated virulence of staphylococci associated with NHPs remain poorly characterized. To help address this, we isolated staphylococci from the skin of four NHP species housed at a UK zoo and characterized their antimicrobial resistance, virulence factors and prophage. We recovered 82 isolates from mannitol salt agar, of which 28 were tentatively confirmed as staphylococci by 16S rRNA gene sequencing. Fourteen isolates were determined to be unique, based on differences in their 16S rRNA gene sequences and origins of isolation. Whole-genome sequencing of the 14 isolates and subsequent genomic analysis identified 5 species, belonging to the genus Staphylococcus (Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus pasteuri, Staphylococcus saprophyticus and Staphylococcus warneri). Bioinformatic prediction of antimicrobial resistance genes identified a total of 85 resistance determinants across all 14 isolates, potentially rendering them resistant to a range of antibiotic classes. However, phenotypic testing revealed only a single case of clinical resistance. Isolates belonging to the species S. pasteuri were identified as the most proficient biofilm formers. Potentially complete prophages were identified in 11 of the sequenced isolates. Prophage JCT0104_p1, identified within the genome of S. aureus JCT0104, was found to encode the virulence factor staphylokinase, which is associated with pathogenesis in humans. Our findings contribute to the limited knowledge of the diversity and characteristics of staphylococci residing on the skin of captive NHPs.

Potential of a newly isolated lytic bacteriophage to control Pseudomonas coronafaciens pv. garcae in coffee plants: Molecular characterization with in vitro and ex vivo experiments

Traditionally, control of coffee plant bacterial halo blight (BHB) caused by the phytopathogen Pseudomonas coronafaciens pv. garcae (Pcg) involves frequent spraying of coffee plantations with non-environmentally friendly and potentially bacterial resistance-promoting copper products or with kasugamycin hydrochloride. In this study we report a leap forward in the quest for a new ecofriendly approach, characterizing (both physicochemically and biologically) and testing both in vitro and ex vivo a new lytic phage for Pcg. An in-depth molecular (genomic and DNA structural features) characterization of the phage was also undertaken. Phage PcgS01F belongs to the class Caudoviricetes, Drexlerviridae family and genus Guelphvirus, and presents a siphovirus-like morphotype. Phage PcgS01F showed a latency period of 40 min and a burst size of 46 PFU/host cell, allowing to conclude that it replicates well in Pcg IBSBF-158. At Multiplicity Of Infection (MOI, or the ratio of phage to bacteria) 1000, the performance of phage PcgS01F was much better than at MOI 10, promoting increasing bacterial reductions until the end of the in vitro inactivation assays, stabilizing at a significant 82 % bacterial load reduction. Phage PcgS01F infected and killed Pcg cells ex vivo in coffee plant leaves artificially contaminated, with a maximum of Pcg inactivation of 7.66 log CFU/mL at MOI 1000 after 36 h of incubation. This study provides evidence that the isolated phage is a promising candidate against the causative agent of BHB in coffee plants.

Phage cocktail against Vibrio parahaemolyticus causing acute hepatopancreatic necrosis disease (AHPND) in Penaeus vannamei: Genomic, biological, and pathological characterization

Phages vB_Pd_PDCC-1, vB_Vc_SrVc9, and vB_Vp_PvVp11 were found to be lytic against Vibrio parahaemolyticus acute hepatopancreatic necrosis disease (AHPND) and other pathogenic vibrios. The complete genomic and biological characterization of phage vB_Vp_PvVp1 was conducted, and a cocktail of these three phages was applied to juvenile Penaeus vannamei infected with V. parahaemolyticus AHPND. Water samples collected during the challenges were analyzed using metagenomics. At the end of the experimental infection, the phage cocktail did not improve shrimp survival compared to the positive control group (infected only with bacteria). This suggests the emergence of phage-resistant V. parahaemolyticus strains. However, a significantly lower mortality rate was observed 12 h post-infection, along with a shortening of the disease course in the phage therapy treatment. A phage-resistant strain of V. parahaemolyticus AHPND was in vitro isolated. For the first time, we report the identification of nucleotide variants in the glycosyltransferase gene of this mutant strain through genome sequencing. Although the phage cocktail was ineffective in controlling AHPND, some protective benefits of phage therapy were noted in P. vannamei during the acute phase-the most critical stage-compared to the positive control. Phage therapy decreased alpha diversity and altered the microbiota composition during the challenge, increasing V. parahaemolyticus. The Vibrio AHPND pathogen produces a potent PirAB toxin, making this disease difficult to manage. Further studies are needed to explore synergistic approaches as effective therapeutic tools.

Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles

Advances in metagenomics have led to the identification of new intestinal temperate bacteriophages. However, their experimental characterization remains challenging due to a limited understanding of their lysogenic-lytic cycle and the common lack of plaque formation in vitro. In this study, we investigated the hankyphage, a widespread transposable phage of prominent Bacteroides symbionts. Hankyphages spontaneously produced virions in laboratory conditions even in the absence of inducer, but virions did not show any evidence of infectivity. To increase virion production and raise the chances of observing infection events, we identified a master repressor of the hankyphage lytic cycle, RepCHP, whose silencing amplified hankyphage gene expression, and enhanced replicative transposition and virion production. However, attempts to infect or lysogenize new host cells with different capsular types remained unsuccessful. Transmission electron microscopy and capsid DNA sequencing revealed an abnormal virion morphology and incomplete DNA packaging of the hankyphage, suggesting that it cannot complete its assembly in laboratory conditions for reasons that are yet to be identified. Still, metavirome and phylogenetic analyses were suggestive of hankyphage horizontal transmission. We could also detect the activity of diversity-generating retroelements (DGRs) that mutagenize the hankyphage tail fiber, and likely contribute to its broad host range. This study sheds light on the life cycle of this abundant intestinal bacteriophage and highlights important gaps in our understanding of the factors required for the completion of its life cycle. Elucidating this puzzle will be critical to gain a better understanding of the hankyphage biology and ecological role.

High-Performance Genome Annotation for a Safer and Faster-Developing Phage Therapy

Phage therapy, which uses phages to decrease bacterial load in an ecosystem, introduces a multitude of gene copies (bacterial and phage) into said ecosystem. While it is widely accepted that phages have a significant impact on ecology, the mechanisms underlying their impact are not well understood. It is therefore paramount to understand what is released in the said ecosystem, to avoid alterations with difficult-to-predict-but potentially huge-consequences. An in-depth annotation of therapeutic phage genomes is therefore essential. Currently, the average published phage genome has only 20-30% functionally annotated genes, which represents a hurdle to overcome to deliver safe phage therapy, for both patients and the environment. This study aims to compare the effectiveness of manual versus automated phage genome annotation methods. Twenty-seven phage genomes were annotated using SEA-PHAGE and Rime Bioinformatics protocols. The structural (gene calling) and functional annotation results were compared. The results suggest that during the structural annotation step, the SEA-PHAGE method was able to identify an average of 1.5 more genes per phage (typically a frameshift gene) and 5.3 gene start sites per phage. Despite this difference, the impact on functional annotation appeared to be limited: on average, 1.2 genes per phage had erroneous functions, caused by the structural annotation. Rime Bioinformatics' tool (rTOOLS, v2) performed better at assigning functions, especially where the SEA-PHAGE methods assigned hypothetical proteins: 7.0 genes per phage had a better functional annotation on average, compared to SEA PHAGE's 1.7. The method comparison detailed in this article indicate that (1) manual structural annotation is marginally superior to rTOOLS automated structural annotation; (2) rTOOLS automated functional annotation is superior to manual functional annotation. Previously, the only way to obtain a high-quality annotation was by using manual protocols, such as SEA-PHAGES. In the relatively new field of phage therapy, which requires support to advance, manual work can be problematic due to its high cost. Rime Bioinformatics' rTOOLS software allows for time and money to be saved by providing high-quality genome annotations that are comparable to manual results, enabling a safer and faster-developing phage therapy.

Structural conservation and functional role of TfpY-like proteins in type IV pilus assembly

Type IV pili (T4P) are important virulence factors that allow bacteria to adhere to and rapidly colonize their hosts. T4P are primarily composed of major pilins that undergo cycles of extension and retraction and minor pilins that initiate pilus assembly. Bacteriophages use T4P as receptors and exploit pilus dynamics to infect their hosts. Some bacteria encode pilin accessory proteins that post-translationally glycosylate major pilins to evade phage binding. TfpY is an accessory protein of unknown function that is widespread and structurally conserved among T4P-expressing bacteria. Here, we use Pseudomonas aeruginosa as a model to characterize the functional role of TfpY and its homologues in pilus assembly. TfpY expression is required for optimal pilus assembly and function; however, it does not provide phage defence, unlike previously characterized accessory proteins. TfpY can cross-complement twitching in strains expressing heterologous P. aeruginosa pilins, suggesting TfpY and its homologues play a common role in pilus assembly. We showed that TfpY likely interacts with the major pilin and specific minor pilins but is not incorporated into the pilus itself. We propose that TfpY, along with the minor pilins at the pilus tip, primes pilus assembly. We identified two unique gain-of-function mutations in T4P regulatory genes that non-specifically restore twitching in tfpY mutants by increasing levels of cAMP and expression of T4P components. This study enhances our understanding of the complex functional and regulatory relationships between pilin and accessory proteins.

IMPORTANCE

Type IV pili are surface filaments that enable versatile pathogens, like Pseudomonas aeruginosa, to adhere to and colonize surfaces. Pili are composed of diverse proteins called pilins, which serve as host receptors for phages. P. aeruginosa uses specific accessory proteins to glycosylate pilins to evade phage infection. Here, we show that TfpY is a conserved accessory protein that does not mediate phage defence. Instead, we propose a mechanism where TfpY facilitates efficient pilus assembly and function. A better understanding of TfpY function will provide insight into how its associated pilins have evolved to resist phage infection in the absence of post-translational modification, how some phages overcome this barrier to infection, and how this can guide the design of phage-based therapeutics.

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.

Complete genome sequence of Salmonella enterica bacteriophage SeKF_80, isolated from wastewater in British Columbia

Salmonella enterica is a Gram-negative inhabitant of the gastrointestinal tract of warm-blooded animals and commonly implicated in foodborne illness. Here, we describe the isolation of Salmonella enterica phage SeKF_80. The 89,965 bp genome contains 174 predicted coding sequences with 44 predicted functions. Phage SeKF_80 shares species-level similarity with Salmonella phages 7-11.

Complete genome sequence of lytic bacteriophage BAU.Micro_SLP-22 infecting avian Salmonella spp

A lytic bacteriophage, BAU.Micro_SLP-22, was isolated from drain water in search of bio-controlling agents against avian salmonellosis. The phage genome is comprised of 59,738 bp with 56.96% guanine-cytosine content, encoding 81 protein-coding genes containing no transfer RNAs, antibiotic resistance, virulence, temperate marker, and clustered regularly interspaced short palindromic repeat coding sequences.

Virome assembly reveals draft genomes of native Pseudomonas phages isolated from a paediatric bronchoalveolar lavage sample

We present lung virome data recovered through shotgun metagenomics in bronchoalveolar lavage fluid from an infant with cystic fibrosis, who tested positive for Stenotrophomonas maltophilia infection. Using a bioinformatic pipeline for virus characterization in shotgun metagenomic data, we identified five viral contigs representing Pseudomonas phages classified as Caudoviricetes.

The rapid detection of a neonatal unit outbreak of a wild-type Klebsiella variicola using decentralized Oxford Nanopore sequencing

BACKGROUND

Klebsiella variicola has been implicated in neonatal intensive care unit (NICU) outbreaks previously and can be misidentified as Klebsiella pneumoniae. An increased incidence of K. pneumoniae bacteremia on the NICU of our institution was notified to the infection prevention and control (IPC) team in May 2024. The four isolates involved displayed wild-type susceptibility, so had not been detected via multidrug-resistant organism surveillance. This triggered investigation with a nanopore-based decentralized whole-genome sequencing (dWGS) system in operation at our laboratory.

METHODS

Since early 2022, the hospital laboratory at Wellington Regional Hospital has been performing dWGS using the Oxford Nanopore MinION device. This allows for prospective genomic surveillance of certain hospital-associated organisms, but also rapid reactive investigation of possible outbreaks. Isolates are sequenced in the hospital laboratory and undergo multilocus sequence typing (MLST). If transmission events are suspected, sequence data are transferred to the reference laboratory, the Institute for Environmental Science and Research (ESR) for high-resolution bioinformatic analysis.

RESULTS

Within 48 h of notification isolates had been subcultured and sequenced. This showed that three of four isolates were in fact K. variicola, and two of these were sequence type (ST)6385. This sequence type had not been seen previously at our institution, so transmission was suspected. Environmental sampling revealed K. variicola ST6385 in two sink traps on the unit, and prospective sequencing of all K. pneumoniae isolates from NICU samples revealed two further infants with K. variicola ST6385. Subsequent phylogenetic analysis at ESR using original sequence data showed tight clustering of these isolates, confirming an outbreak. Sink traps were disinfected, environmental cleaning procedures were updated, and a strict focus on hand hygiene was reinforced on the ward. No further isolates were detected, and the outbreak was closed after two months.

CONCLUSIONS

Access to dWGS at the level of the local hospital laboratory permitted rapid identification of an outbreak of an organism displaying no unusual antimicrobial resistance features at a point where there were only two known cases. This in turn facilitated a rapid IPC response.

Isolation, Characterization, and Anti-Biofilm Activity of a Novel Kaypoctavirus Against K24 Capsular Type, Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates

Background/Objectives: The significant outbreak of multidrug-resistant Klebsiella pneumoniae has emerged as a primary global concern associated with high morbidity and mortality rates. Certain strains of K. pneumoniae are highly resistant to most antibiotics available in clinical practice, exacerbating the challenge of bacterial infections. Methods: Phage vB_KpnP_PW7 (vKPPW7) was isolated and characterized. Its morphology, stability, adsorption rate, one-step growth curve, lytic activity, whole-genome sequence analysis, and antibacterial and antibiofilm activities were evaluated. Results: The virulent phage has a 73,658 bp linear dsDNA genome and was classified as a new species of the genus Kaypoctavirus, subfamily Enquatrovirinae, and family Schitoviridae. Phage vKPPW7 has a high adsorption rate, a short latent period, and a large burst size. The phage showed activity against 18 K. pneumoniae isolates with the K24 capsular type but was unable to lyse K. pneumoniae isolates whose capsular type was not classified as K24. Additionally, phage vKPPW7 demonstrated strong stability across various temperatures and pH values. The phage exhibited antibacterial activity, and scanning electron microscopy (SEM) confirmed its ability to lyse MDR K. pneumoniae with the K24 capsular type. Furthermore, phage vKPPW7 effectively removed preformed biofilm and prevented biofilm formation, resulting in reduced biofilm biomass and biofilm viability compared to controls. The architecture of phage-treated biofilms was confirmed under SEM. Conclusions: These findings suggest that phage vKPPW7 holds promise for development as a therapeutic or biocontrol agent.

Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks

The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.

Identification of Diverse Bacteriophages Associated with Bees and Hoverflies

Bacteriophages are the most numerous, ubiquitous, and diverse biological entities on the planet. Prior studies have identified bacteriophages associated with pathogenic and commensal microbiota of honeybees. In this study we expand on what is known about bacteriophages from the lineages Caudoviricetes, Inoviridae, and Microviridae, which are associated with honeybees (Apidae, Apis mellifera), solitary bees of the genus Nomia (Halictidae, Nomia), and hoverflies (Syrphidae). The complete genomes of seven caudoviruses, seven inoviruses, and 288 microviruses were assembled from honeybees (n = 286) and hoverflies in Arizona (n = 2). We used bacterial host predictive software and sequence read mapping programs to infer the commensal and transient bacterial hosts of pollinating insects. Lastly, this study explores the phylogenetic relationships of microviruses sampled from bees, opportunistically sampled pollinating insects such as hoverflies, and blackflies.

Geographic variation in abundance and diversity of Acinetobacter baumannii Vieuvirus bacteriophages

Introduction

Prophages play a crucial role in the genomic diversity of Acinetobacter baumannii, contributing to its pathogenicity and adaptation.

Methods

In this study, we induced and sequenced seven prophages from five isolates of A. baumannii. These were analyzed with 967 prophages identified from various isolates worldwide, plus 21 genomes of other phages infecting A. baumannii previously reported in NCBI. To have an overview of the populations of the prophages infecting A. baumannii.

Results

Our analysis revealed 13 major prophage clusters within the analyzed A. baumannii isolates. Notably, prophages belonging to the Vieuvirus genus were the most prevalent. Specifically, Vieuvirus-related phages were frequently identified in isolates from Thailand, Mexico, China, and South Korea, which show the geographic prevalence of A. baumannii prophages.

Discussion

This study highlights the importance of considering geographic factors to fully understand prophage diversity and their significant role in the evolutionary dynamics of A. baumannii.