Search Results (433)

Antibiotic-resistant Pseudomonas aeruginosa presents a critical global health challenge, particularly in hospital-acquired infections. Bacteriophages offer a promising therapeutic avenue due to their ability to target and lyse resistant strains. This study characterizes Pseudomonas phage Banzai, a newly isolated Pbunavirus (family Lindbergviridae) with lytic activity against multiple P. aeruginosa isolates, including multidrug-resistant strains. Genomic analysis revealed a 66,189 bp genome, lacking antibiotic resistance or virulence factors, and suggested a headful packaging mechanism and the presence of a bidirectional component in the replication. In vivo experiments using Galleria mellonella showed therapeutic potential, significantly improving larval survival (87% at 24 h). Host range analysis revealed activity against 13 of 30 P. aeruginosa isolates, including members of O1, O3, O5 and O6 in silico predicted serogroups. Phylogenomic analyses place phage Banzai within the genus Pbunavirus, sharing 94.8% intergenomic similarity with its closest relatives, supporting its classification as a novel species. These findings highlight phage Banzai as a potential candidate for phage therapy, demonstrating genomic stability, a strictly lytic lifestyle, and in vivo efficacy. Full article

Background/Objectives: Mycobacterium abscessus is an opportunistic pathogen causing infections mainly in patients with immunosuppression and chronic pulmonary pathologies. Extended treatment periods are needed to tackle this pathogen, bacterial eradication is rare, and recurrence can take place with time. New alternative treatments are being investigated, such as bacteriophage therapy. This work describes the characterization of the mycobacteriophage P3MA, showing its ability to infect clinical and standard M. abscessus strains. Methods: Phylogenetic analysis, electron microscopy, growth curves, biofilm assays, checkerboard, and granuloma-like medium studies were performed. Results: P3MA inhibited the growth of clinical samples in both planktonic and biofilm states as well as in a granuloma-like model. The study of the interaction with antibiotics revealed that P3MA exhibited an antagonistic effect combined with clarithromycin, indifference with amikacin, and synergy with imipenem. Conclusions: All these results suggest that, after genetic engineering, P3MA could be a promising candidate for phage therapy in combination with imipenem, including lung infections. Full article

The scarab species Protaetia brevitarsis, an edible insect, has been used in traditional medicine, as animal feed, and for converting agricultural organic wastes into biofertilizer. The intestinal tract, which contains a diverse array of microbiota, including viruses, plays a critical role in animal health and homeostasis. We previously conducted a comparative analysis of the gut microbiota of third-instar larvae of P. brevitarsis obtained from five different farms and found significant differences in the composition of the gut bacterial microbiota between farms. To better understand the gut microbiota, the composition of DNA viruses in the hindgut contents of P. brevitarsis larvae obtained from five farms was investigated using metagenomic sequencing in this study. The β-diversity was significantly different between metagenomic data obtained from the five farms (PERMANOVA, pseudo-F = 46.95, p = 0.002). Family-based taxonomic analysis indicated that the relative abundance of viruses in the gut overall metagenome varied significantly between farms, with viral reads comprising approximately 41.2%, 15.0%, 4.3%, 4.0%, and 1.6% of metagenomic sequences from the farms Tohamsan gumbengi farm (TO), Secomnalagum gumbengi (IS), Gumbengi brothers (BR), Kyungpook farm (KB), and Jhbio (JH), respectively. More than 98% of the DNA viruses in the hindgut were bacteriophages, mainly belonging to the Siphoviridae family. At the species level, Phage Min1, infecting the genus Microbacterium, was detected in all farms, and it was the most abundant bacteriophage in intestinal microbiota, with a prevalence of 0.9% to 29.09%. The detected eukaryotic DNA viruses accounted for 0.01% to 0.06% of the intestinal microbiota and showed little or no relationship with insect viruses. Therefore, they most likely originated from contaminated feed or soil. These results suggest that the condition of substrates used as feed is more important than genetic factors in shaping the intestinal viral microbiota of P. brevitarsis larvae. These results can be used as reference data for understanding the hindgut microbiota of P. brevitarsis larvae and, more generally, the gut virome of insects. Full article

Vibrio parahaemolyticus (V. parahaemolyticus) is a preeminent seafood-borne pathogen, imposing significant economic burdens on global aquaculture. The escalating prevalence of multidrug-resistant strains has accentuated the critical urgency for developing sustainable biocontrol strategies. In this study, a bacteriophage designated vB_VPAP_XY75 (XY75) was isolated and biologically characterized to establish an effective control against V. parahaemolyticus. XY75 exhibited remarkable specificity toward V. parahaemolyticus, effectively lysing 46.2% of the target strains while showing no lytic activity against non-target bacterial species. Morphological characterization confirmed its taxonomic assignment to the Myoviridae family, featuring an icosahedral head (40 ± 2 nm) and contractile tail (60 ± 2 nm). XY75 demonstrated strong environmental tolerance, remaining stable at pH 4–11 and temperatures as high as 50 °C. At an optimal multiplicity of infection (MOI = 0.01), XY75 achieved a peak titer of 8.1 × 10¹⁰ PFU/mL, a 5 min latent period, and burst size of 118 PFU/cell. Critically, XY75 reduced V. parahaemolyticus in salmon by more than 5.98 log CFU/g (99.9%) within 6 h at 4 °C, demonstrating exceptional cold tolerance and lytic activity. Genomic analysis confirmed that no virulence or antibiotic resistance genes were present. These results establish XY75 as a safe and efficacious biocontrol candidate for seafood preservation, with particular utility under refrigerated storage conditions. Full article

Background/Objectives: The rapid emergence of antibiotic-resistant Escherichia coli in food and clinical environments necessitates new, clean-label antimicrobials. This study assessed eight Greek native essential oils—oregano, thyme, dittany, rosemary, peppermint, lavender, cistus and helichrysum—for activity against six genetically and phenotypically diverse E. coli strains (reference, pNorm, mecA, mcr-1, blaOXA and O157:H7). We aimed to identify oils with broad-spectrum efficacy and clarify the chemical constituents responsible. Methods: Disk-diffusion assays measured inhibition zones at dilutions from 50% to 1.56% (v/v). MIC and MBC values were determined by broth microdilution. GC–MS profiling identified dominant components, and Spearman rank-order correlations (ρ) linked composition to activity. Shapiro–Wilk tests (W = 0.706–0.913, p ≤ 0.002) indicated non-normal data, so strain comparisons used Kruskal–Wallis one-way ANOVA with Dunn’s post hoc and Bonferroni correction. Results: Oregano, thyme and dittany oils—rich in carvacrol and thymol—exhibited the strongest activity, with MIC/MBC ≤ 0.0625% (v/v) against all strains and inhibition zones > 25 mm at 50%. No strain-specific differences were detected (H = 0.30–3.85; p = 0.998–0.571; p_adj = 1.000). Spearman correlations confirmed that carvacrol and thymol content strongly predicted efficacy (ρ = 0.527–0.881, p < 0.001). Oils dominated by non-phenolic terpenes (rosemary, peppermint, lavender, cistus, helichrysum) showed minimal or no activity. Conclusions: Phenolic-rich EOs maintain potent, strain-independent antimicrobial effects—including against multidrug-resistant and O157:H7 strains—via a multi-target mode that overcomes classical resistance. Their low-dose efficacy and GRAS status support their use as clean-label food preservatives or adjuncts to antibiotics or bacteriophages to combat antimicrobial resistance. Full article

CrAssphage, a bacteriophage that infects human gut-associated Bacteroides spp., has emerged as a potential anthropogenic fecal pollution indicator in environmental matrices. This study investigated the presence and concentration of crAssphages in bivalve mollusks (oysters and mussels) marketed in three cities in the state of Rio de Janeiro, Brazil, sampled from January to December 2022. CrAssphages were detected during the study period in 66.7% (48/72) of sampled oysters and 54.8% (34/62) of sampled mussels, at median concentrations of 1.9 × 10⁴ and 4.2 × 10⁴ genome copies (GC)/g, respectively. These levels were 1–2 log₁₀ higher than those observed for major human enteric viruses, including norovirus genogroups GI and GII, sapovirus, human mastadenovirus (HAdV), rotavirus A, human astrovirus (HAstV), and hepatitis A virus. CrAssphage specificity and sensitivity were calculated for all viruses. Moderate correlations between crAssphage (log₁₀ GC/g) and norovirus GI and GII, HAdV, SaV, and HAstV (Spearman’s rho = 0.581–0.464, p < 0.001) were observed in mussels. Altogether, the data support the use of crAssphage as a molecular indicator of human viral contamination in shellfish, with potential application in routine environmental and food safety monitoring in production areas. Full article

Hybrid modeling techniques are increasingly important for improving predictive accuracy and control in biomanufacturing, particularly in data-limited conditions. This study develops and experimentally validates a hybrid deep learning model predictive control (MPC) framework for recombinant P. pastoris fed-batch fermentations. Bayesian optimization and grid search techniques were employed to identify the best-performing hybrid model architecture: an LSTM layer with 2 hidden units followed by a fully connected layer with 8 nodes and ReLU activation. This design balanced accuracy (NRMSE 4.93%) and computational efficiency (AICc 998). This architecture was adapted to a new, smaller dataset of bacteriophage Qβ coat protein production using transfer learning, yielding strong predictive performance with low validation (3.53%) and test (5.61%) losses. Finally, the hybrid model was integrated into a novel MPC system and experimentally validated, demonstrating robust real-time substrate feed control in a way that allows it to maintain specific target growth rates. The system achieved predictive accuracies of 6.51% for biomass and 14.65% for product estimation, with an average tracking error of 10.64%. In summary, this work establishes a robust, adaptable, and efficient hybrid modeling framework for MPC in P. pastoris bioprocesses. By integrating automated architecture searching, transfer learning, and MPC, the approach offers a practical and generalizable solution for real-time control and supports scalable digital twin deployment in industrial biotechnology. Full article

Canine otitis externa caused by Pseudomonas aeruginosa is a relevant disease in veterinary medicine. Given P. aeruginosa’s high priority status for the development of new antimicrobials, innovative strategies like bacteriophage therapy are essential. Lytic bacteriophages are viruses with high specificity for their bacterial hosts, making them a promising therapeutic choice in both human and veterinary medicine. This study aimed to evaluate the antimicrobial potential of bacteriophages JG005 and JG024, first characterized in terms of their biofilm-forming ability and antimicrobial susceptibility profile, against P. aeruginosa isolates obtained from dogs with otitis externa,. Bacteriophages titer, host range, and activity were assessed against P. aeruginosa biofilms via microtiter assays using crystal violet and Alamar Blue. JG024 showed lytic activity against 61.2% (n = 30/49) of the isolates, while JG005 showed lytic activity against 38.8% (n = 19/49) of the isolates. Crystal violet quantification showed that JG005 can promote strong microbial suppression of 60% (n = 6/10) and 50% (n = 5/10) of the isolates at a multiplicity of infection (MOI) of 10 and 100, respectively. JG024 presented strong microbial suppression of 20% (n = 2/10) of the isolates regardless of the MOI level tested. These phages show promising potential as an innovative treatment for canine otitis externa caused by P. aeruginosa, but further studies are needed before future clinical use. Full article

Most large-scale crude oil spills occur in marine environments. We screened easily propagable/maintainable halophiles to develop agents for the bioremediation of marine spills. A bacterial strain isolated from a polluted region of the Great Salt Lake was characterized and tested for its ability to degrade crude oil. The strain (Salinivibrio costicola) is motile, catalase- and lipase-positive, a facultative anaerobe, and an obligate halophile. Its growth optimum and tolerance ranges are: NaCl (5%, 1.25–10%), pH (8, 6–10), and temperature (22 °C, 4–45 °C). Its genome (3,166,267 bp) consists of two circular chromosomes and a plasmid, containing 3197 genes, including some genes potentially relevant to hydrocarbon metabolism. The strain forms a biofilm but is considered nonpathogenic and is sensitive to some common antibiotics. Lytic bacteriophages infecting the strain are rare in the water samples we tested. The strain survived on desiccated agar media at room temperature for a year, grew optimally in complex media containing 0.1–1% crude oil, but failed to reduce total recoverable petroleum hydrocarbons from crude oil. Thus, a recalcitrant halophile may endure crude oil without mineralizing. Due to some of their advantageous attributes, such strains can be considered for genetic manipulation to develop improved agents for bioremediation. Full article

Background: Iminosugars are natural or synthetic sugar analogues with a very broad spectrum of activities, including those against the most prominent bacterial pathogens, like P. aeruginosa or S. aureus. In a series of studies, we have demonstrated that one of the synthetic iminosugars, PDIA (beta-1-C-propyl-1,4-dideoxy-1,4-imino-L-arabinitol), possesses the ability to suppress biofilm production by different pathogenic bacteria without inhibiting their growth. Thereby, PDIA is able to influence experimental skin infection caused by S. aureus. Methods: To elucidate molecular mechanisms by which PDIA impedes biofilm formation by S. aureus, a transcriptomic study was performed in which a biofilm-producing S. aureus strain was grown in the presence of PDIA for 24 and 48 h in comparison to a control without the iminosugar. The RNA was then isolated, converted into cDNA, sequenced, and data analysis was performed. Results: It appeared that PDIA caused the down-regulation of many bacteriophage genes responsible for the processes of bacterial cell lysis, and some genes responsible for cell wall degradation were also down-regulated. Among the 25 most upregulated genes were those representing the phosphotransferase system (PTS), which is required for carbohydrate uptake and control of carbon metabolism. The ranking of the most significant down-regulated genes after 24 h exposure to PDIA shows that they predominantly coded for both the synthesis and lysis of the peptidoglycan. Conclusions: We have shown here that the influence of PDIA on the expression of S. aureus genes is broad and affects many genes encoding metabolism and ribosomes. Full article

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp), a pathogen causing severe nosocomial infections and high mortality rates, is increasingly becoming a serious global public health threat. Capsular polysaccharide (CPS), a major virulence factor of hvKp, can be enzymatically degraded by bacteriophage-derived depolymerases. However, to our knowledge, depolymerases targeting K. pneumoniae K54-type strains have rarely been identified. Here, we identified and characterized three novel capsule depolymerases, Dep_C, Dep_Y, and Dep_Z, derived from three different K. pneumoniae phages, which retained robust activity across a broad pH range (pH 3.0–12.0) and demonstrated thermal stability up to 50 °C. These depolymerases could efficiently digest the CPS of K. pneumoniae K54-serotype strains, significantly inhibit biofilm formation, and remove their mature biofilms. Although no bactericidal activity was detected, these depolymerases rendered host bacteria susceptible to serum complement-mediated killing. We further demonstrate that Dep_C, Dep_Y, and Dep_Z can effectively and significantly prolong the survival time of mice in a pneumonia model infected with K54-type K. pneumoniae and reduce the colonization and virulence of the bacteria in the mice. These findings indicate that depolymerases Dep_C, Dep_Y, and Dep_Z could increase bacterial susceptibility to host immune responses of hvKp to the host through their degradation effect on the CPS. In conclusion, our study demonstrates that the three capsule depolymerases are promising antivirulent agents to combat CR-hvKp infections. Full article

Background: Multidrug-resistant (MDR) Escherichia coli (E. coli) strains pose a significant public health challenge, which has led to the exploration of alternative therapeutic strategies. Due to their antibacterial and immunomodulatory properties, bacteriophages have emerged as promising therapeutic agents. Methods: This study investigates the effects of GADS24, a novel lytic bacteriophage of E. coli, on human-monocyte-derived dendritic cells (DCs). DCs are exposed to purified GADS24 phage, bacterial lysate, or a combination of both. Flow cytometry was used to assess the expression of surface markers (HLA-DR, CD80, CD83, and CD86), and ELISA was used to measure cytokine production (IL-10 and IL-12p70). Results: Following treatment with bacterial lysate, a significant increase in DC maturation markers was observed. The GADS24 phage alone induced a moderate upregulation of these markers, decreased IL-10 secretion, and increased IL-12p70. Combining bacterial lysate and phage tempered the maturation response compared to the lysate treatment alone. Conclusion: These findings suggest that GADS24 exerts antibacterial activity and modulates host immunity by influencing DC maturation and cytokine production. Due to its dual antimicrobial and immunomodulatory functions, GADS24 is likely to be a valuable adjunctive therapy for multidrug-resistant (MDR) bacterial infections. Furthermore, in vivo studies are necessary to confirm these promising in vitro results. Full article

Pseudomonas aeruginosa (P. aeruginosa) is a common antibiotic-resistant pathogen, posing significant public health threats worldwide. It is a major cause of ocular infections, mostly linked to contact lens wear. P. aeruginosa often produces biofilm during infections, and these are also associated with antibiotic resistance. Bacteriophage (phage) therapy is emerging as a promising approach for treating multidrug-resistant P. aeruginosa. Objective: This study aimed to assess the antibiofilm effects of six phages against P. aeruginosa biofilms isolated from patients with corneal infections. Method: This study examined P. aeruginosa strains for their ability to form biofilms using crystal violet assay. Six P. aeruginosa bacteriophages (DiSu1 to DiSu6) were used, which were isolated from sewage water in Melbourne, Australia. Spot tests were used to assess phage sensitivity. The effect of phages against P. aeruginosa strains was determined using time–kill assay and efficiency of plating. The ability of phage to inhibit biofilm formation over 24 h or reduce preformed biofilms was also studied and confirmed using confocal laser scanning microscopy with Live/Dead staining. Result: After 24 h of incubation, all tested P. aeruginosa strains formed moderate to strong biofilms. All P. aeruginosa strains were sensitive to at least four of the six phages. The highest level of bacterial growth inhibition in the liquid infection model was observed when phages were applied at a multiplicity of infection (MOI) of 100. Certain bacteria/phage combinations were able to inhibit biofilm formation over 24 h, with the combination of strain PA235 and phage DiSu3 producing the highest inhibition (83%) at a MOI of 100. This was followed by the combinations of PA223/DiSu3 (56%), and PA225/DiSu5 (52%). For the reduction in preformed biofilms, the best combinations were PA235 (90%), PA221 (61%), and PA213 and PA225 (57% each), all with DiSu3 after 3 h. However, exposing the biofilm with phages for over 24 h appeared to promote phage resistance as there was evidence of biofilm growth, with the only combination still showing a significant reduction being PA221/DiSu3 (58%) at MOI of 100. Conclusions: This study showed that the effect of phages against P. aeruginosa is concentration (MOI) dependent. Phages at higher MOI have the ability to disrupt, inhibit, and reduce P. aeruginosa biofilms. However, prolonged exposure of the biofilm with phages appeared to promote phage resistance. To enhance phage efficacy and address this form of resistance, further studies utilizing phage cocktails or a combination of phages and antibiotics is warranted. Full article

Enterococcus faecalis (E. faecalis) is a major pathogen responsible for refractory apical periodontitis (RAP). It can penetrate deep into dentinal tubules, form persistent biofilms, and exhibit antibiotic resistance, thereby limiting the efficacy of conventional antimicrobial treatments. Bacteriophages (phages), due to their strong lytic activity and host specificity, have emerged as promising alternatives. In this study, a novel strictly lytic phage, ZXL-01, was isolated from lake water in Jilin, China. ZXL-01 demonstrated remarkable stability under extreme conditions, including thermal tolerance at 60 °C for 1 h and a wide pH range (4–11). Whole-genome sequencing (GenBank accession number: ON113334) revealed a genome of 40,804 bp with no virulence or tRNA genes, confirming its identity as an E. faecalis phage. Importantly, ZXL-01 exhibited potent antibiofilm activity, reducing biofilm biomass by approximately 69.4% in the inhibition group and 68.4% in the lysis group (both p < 0.001). In an in vitro root canal infection model induced by E. faecalis, scanning electron microscope (SEM) observations confirmed that ZXL-01 effectively inhibited biofilm formation and disrupted mature biofilms. These findings highlight the potential of ZXL-01 as a novel antimicrobial agent for the treatment of E. faecalis-associated apical periodontitis. Full article

Fertilization has an important effect on soil antibiotic resistance. Most recent studies have focused on antibiotic resistance genes (ARGs) harbored by bacteria (bARGs); however, little is known about ARGs carried by soil bacteriophages (pARGs) under different fertilization treatments. Here, 24 pARG subtypes were quantified in soils with long-term application of different fertilizers using droplet digital PCR (ddPCR). The results showed that the detection rates of the target ARGs in bacteriophages were 66.67%, 70.83%, and 75.00% in unfertilized, chemically fertilized, and organically fertilized soils, respectively. The total abundance of pARGs in soils amended with organic fertilizer was significantly higher than that in unfertilized and chemically fertilized soils. The multidrug resistance gene (mexF) exhibited the highest abundance in soils amended with organic fertilizer. A significant positive correlation was observed between bARGs and pARGs, and the detected pARG subtype abundances were one to two orders of magnitude lower than those of the corresponding bARGs. The results of variation partitioning analysis revealed that the interaction between the bacterial community and soil properties drove the variation in soil pARGs. Our findings indicate that bacteriophages are important vectors of ARGs, in addition to bacteria, in agricultural soils, and their contribution to antibiotic resistance should not be overlooked. Full article