Interactions between Bacteriophages and Eukaryotic Cells

Optimizing bacteriophage treatment of resistant Pseudomonas

Phage therapy is increasing in relevance as an alternative treatment to combat antibiotic resistant bacteria. Phage cocktails are the state-of-the-art method of administering phages in clinical settings, preferred over monophage treatment because of their ability to eliminate multiple bacterial strains and reduce resistance formation. In our study, we compare monophage applications and phage cocktails to our chosen method of phage sequential treatments. To do so, we isolated four novel bacteriophages capable of infecting Pseudomonas alcaligenes T3, a close relative of P. aeruginosa, and characterized them using sequencing and transmission electron microscopy. While investigating monophage treatments, we observed that different phage concentrations had a strong impact on the timing and amount of resistance formation. When using phage cocktails, we observed that P. alcaligenes were capable of forming resistance in the same timespan it took them to become resistant to single phages. We isolated mutants resistant to each single phage as well as mutants exposed to phage cocktails, resulting in bacteria resistant to all four phages at once. Sequencing these mutants showed that different treatments yielded unique single nucleotide polymorphism mutation patterns. In order to combat resistance formation, we added phages one by one in intervals of 24 h, thus managing to delay resistance development and keeping bacterial growth significantly lower compared to phage cocktails.IMPORTANCEWHO declared antimicrobial resistance a top threat to global health; while antibiotics have stood at the forefront in the fight against bacterial infection, the increasing number of multidrug-resistant bacteria highlights a need to branch out in order to address the threat of antimicrobial resistance. Bacteriophages, viruses solely infecting bacteria, could present a solution due to their abundance, versatility, and adaptability. For this study, we isolated new phages infecting a fast-mutating Pseudomonas alcaligenes strain capable of forming resistance within 30 h. By using a sequential treatment approach of adding one phage after another, we were able to curb bacterial growth significantly more compared to state-of-the-art phage cocktails.

Phage Therapy, a Salvage Treatment for Multidrug-Resistant Bacteria Causing Infective Endocarditis

Infective endocarditis (IE) is defined as an infection of the endocardium, or inner surface of the heart, most frequently affecting the heart valves or implanted cardiac devices. Despite its rarity, it has a high rate of morbidity and mortality. IE generally occurs when bacteria, fungi, or other germs from another part of the body, such as the mouth, spread through the bloodstream and attach to damaged areas in the heart. The epidemiology of IE has changed as a consequence of aging and the usage of implantable cardiac devices and heart valves. The right therapeutic routes must be assessed to lower complication and fatality rates, so this requires early clinical suspicion and a fast diagnosis. It is urgently necessary to create new and efficient medicines to combat multidrug-resistant bacterial (MDR) infections because of the increasing threat of antibiotic resistance on a worldwide scale. MDR bacteria that cause IE can be treated using phages rather than antibiotics to combat MDR bacterial strains. This review will illustrate how phage therapy began and how it is considered a powerful potential candidate for the treatment of MDR bacteria that cause IE. Furthermore, it gives a brief about all reported clinical trials that demonstrated the promising effect of phage therapy in combating resistant bacterial strains that cause IE and how it will become a hope in future medicine.

An Overview of the Public Health Challenges in Diagnosing and Controlling Human Foodborne Pathogens

Pathogens found in food are believed to be the leading cause of foodborne illnesses; and they are considered a serious problem with global ramifications. During the last few decades, a lot of attention has been paid to determining the microorganisms that cause foodborne illnesses and developing new methods to identify them. Foodborne pathogen identification technologies have evolved rapidly over the last few decades, with the newer technologies focusing on immunoassays, genome-wide approaches, biosensors, and mass spectrometry as the primary methods of identification. Bacteriophages (phages), probiotics and prebiotics were known to have the ability to combat bacterial diseases since the turn of the 20th century. A primary focus of phage use was the development of medical therapies; however, its use quickly expanded to other applications in biotechnology and industry. A similar argument can be made with regards to the food safety industry, as diseases directly endanger the health of customers. Recently, a lot of attention has been paid to bacteriophages, probiotics and prebiotics most likely due to the exhaustion of traditional antibiotics. Reviewing a variety of current quick identification techniques is the purpose of this study. Using these techniques, we are able to quickly identify foodborne pathogenic bacteria, which forms the basis for future research advances. A review of recent studies on the use of phages, probiotics and prebiotics as a means of combating significant foodborne diseases is also presented. Furthermore, we discussed the advantages of using phages as well as the challenges they face, especially given their prevalent application in food safety.

The Influence of Bacteriophages on the Metabolic Condition of Human Fibroblasts in Light of the Safety of Phage Therapy in Staphylococcal Skin Infections

Phage therapy has been successfully used as an experimental therapy in the treatment of multidrug-resistant strains of Staphylococcus aureus (MDRSA)-caused skin infections and is seen as the most promising alternative to antibiotics. However, in recent years a number of reports indicating that phages can interact with eukaryotic cells emerged. Therefore, there is a need to re-evaluate phage therapy in light of safety. It is important to analyze not only the cytotoxicity of phages alone but also the impact their lytic activity against bacteria may have on human cells. As progeny virions rupture the cell wall, lipoteichoic acids are released in high quantities. It has been shown that they act as inflammatory agents and their presence could lead to the worsening of the patient's condition and influence their recovery. In our work, we have tested if the treatment of normal human fibroblasts with staphylococcal phages will influence the metabolic state of the cell and the integrity of cell membranes. We have also analyzed the effectiveness of bacteriophages in reducing the number of MDRSA attached to human fibroblasts and the influence of the lytic activity of phages on cell viability. We observed that, out of three tested anti-Staphylococcal phages-vB_SauM-A, vB_SauM-C and vB_SauM-D-high concentrations (10⁹ PFU/mL) of two, vB_SauM-A and vB_SauM-D, showed a negative impact on the viability of human fibroblasts. However, a dose of 10⁷ PFU/mL had no effect on the metabolic activity or membrane integrity of the cells. We also observed that the addition of phages alleviated the negative effect of the MDRSA infection on fibroblasts' viability, as phages were able to effectively reduce the number of bacteria in the co-culture. We believe that these results will contribute to a better understanding of the influence of phage therapy on human cells and encourage even more studies on this topic.

Activity of a Bacteriophage Cocktail to Control Salmonella Growth Ex Vivo in Avian, Porcine, and Human Epithelial Cell Cultures

We examined the activity of phages to control the growth of chicken and swine Salmonella strains in avian (CHIC-8E11), porcine (IPEC-1), and human (HT-29) cell cultures. We optimized a six-phage cocktail by selecting the five most effective myoviruses and a siphovirus that have optimal lysis on prevalent serovars. We observed ∼20% of 7 log10 PFU/well phage and 3-6 log10 CFU bacterial adhesions, and 3-5 log10 CFU bacterial invasion per 2 cm2 of the cultured cells at 2 h post-treatment. The invasive bacteria when plated had a variable reduced susceptibility to the phages. After phage application at an MOI of 10, the prophylaxis regimen had better efficacy at controlling bacterial growth with an up to 6 log10 CFU/well reduction as compared with the 1-2 log10 CFU/well bacterial reduction observed in the remedial and coinfection regimens. Our data support the development of these phages to control salmonellosis in chickens, pigs, and humans.

pH modulates the role of SP6 RNA polymerase in transcription process: an in silico study

SP6 RNA polymerase (SP6 RNAP) is an essential enzyme for the transcription process in SP6 bacteriophage. SP6 RNAP plays a vital role in mRNA vaccine designing technology and other translational biotechnology research due to the high specificity towards its promoter. The self-replicating performance also put this polymerase to study extensively. Despite of the reports emphasizing the function of this enzyme, a detailed structural and functional understanding of RNA polymerase is not reported so far. Here, we report the first-ever information about SP6RNAP structure and its effect on promoter binding at different pH environments using molecular docking and molecular dynamics simulation (MDS) study. We also report the changes in polymerase conformations in different pH conditions using in-silico approach. The docking study was also performed for SP6 RNAP with SP6 promoter at different pH environments using the in-silico docking tools and conducted the MDS study for complexes. MM/PBSA and per residue energy contribution has been performed at three different pH environments. The structural aspects confirmed that the pH 7.9 state favors the polymerase functional activity in the transcription process which was in the range reported using transcription assay. This polymerase's unique features may play its emerging role as an efficient transcription factor in translational biological research.Communicated by Ramaswamy H. Sarma.

Adaptive lifestyle of bacteria determines phage-bacteria interaction

Bacteriophages and their interactions with microbes are not well understood. As a first step toward achieving a better understanding, we isolated and sequenced the Curvibacter phage PCA1 for the purpose of eliminating Curvibacter sp. AEP1.3, the main colonizer of Hydra vulgaris AEP. Our experiments showed that PCA1 phage caused a strong, virulent infection only in sessile Curvibacter sp. AEP1.3 but was unable to infect planktonic and host-associated bacterial cells of the same strain. In an effort to investigate this phenomenon, we compared sessile, planktonic, and host-associated bacteria via RNA sequencing and found that all three states differed significantly in their expression patterns. This finding led us to propose that the adaptive lifestyle of Curvibacter sp. AEP1.3 results in varying degrees of susceptibility to bacteriophage infection. This concept could be relevant for phage research and phage therapy in particular. Finally, we were able to induce phage infection in planktonic cells and pinpoint the infection process to a membrane protein. We further identified potential phage-binding protein candidates based on expression pattern analysis.

Recent Advances in the Application of Bacteriophages against Common Foodborne Pathogens

Bacteriophage potential in combating bacterial pathogens has been recognized nearly since the moment of discovery of these viruses at the beginning of the 20th century. Interest in phage application, which initially focused on medical treatments, rapidly spread throughout different biotechnological and industrial fields. This includes the food safety sector in which the presence of pathogens poses an explicit threat to consumers. This is also the field in which commercialization of phage-based products shows the greatest progress. Application of bacteriophages has gained special attention particularly in recent years, presumably due to the potential of conventional antibacterial strategies being exhausted. In this review, we present recent findings regarding phage application in fighting major foodborne pathogens, including Salmonella spp., Escherichia coli, Yersinia spp., Campylobacter jejuni and Listeria monocytogenes. We also discuss advantages of bacteriophage use and challenges facing phage-based antibacterial strategies, particularly in the context of their widespread application in food safety.

Coliphages as viral indicators of sanitary significance for drinking water

Coliphages are virus that infect coliform bacteria and are used in aquatic systems for risk assessment for human enteric viruses. This mini-review appraises the types and sources of coliphage and their fate and behavior in source waters and engineered drinking water treatment systems. Somatic (cell wall infection) and F+ (male specific) coliphages are abundant in drinking water sources and are used as indicators of fecal contamination. Coliphage abundances do not consistently correlate to human enteric virus abundance, but they suitably reflect the risks of exposure to human enteric viruses. Coliphages have highly variable surface characteristics with respect to morphology, size, charge, isoelectric point, and hydrophobicity which together interact to govern partitioning and removal characteristics during water treatment. The groups somatic and F+ coliphages are valuable for investigating the virus elimination during water treatment steps and as indicators for viral water quality assessment. Strain level analyses (e.g., Qβ or GA-like) provide more information about specific sources of viral pollution but are impractical for routine monitoring. Consistent links between rapid online monitoring tools (e.g., turbidity, particle counters, and flow cytometry) and phages in drinking water have yet to be established but are recommended as a future area of research activity. This could enable the real-time monitoring of virus and improve the process understanding during transient operational events. Exciting future prospects for the use of coliphages in aquatic microbiology are also discussed based on current scientific evidence and practical needs.

HIV, HSV, SARS-CoV-2 and Ebola Share Long-Term Neuropsychiatric Sequelae

Long COVID, in which disease-related symptoms persist for months after recovery, has led to a revival of the discussion of whether neuropsychiatric long-term symptoms after viral infections indeed result from virulent activity or are purely psychological phenomena. In this review, we demonstrate that, despite showing differences in structure and targeting, many viruses have highly similar neuropsychiatric effects on the host. Herein, we compare severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), human immunodeficiency virus 1 (HIV-1), Ebola virus disease (EVD), and herpes simplex virus 1 (HSV-1). We provide evidence that the mutual symptoms of acute and long-term anxiety, depression and post-traumatic stress among these viral infections are likely to result from primary viral activity, thus suggesting that these viruses share neuroinvasive strategies in common. Moreover, it appears that secondary induced environmental stress can lead to the emergence of psychopathologies and increased susceptibility to viral (re)infection in infected individuals. We hypothesize that a positive feedback loop of virus-environment-reinforced systemic responses exists. It is surmised that this cycle of primary virulent activity and secondary stress-induced reactivation, may be detrimental to infected individuals by maintaining and reinforcing the host's immunocompromised state of chronic inflammation, immunological strain, and maladaptive central-nervous-system activity. We propose that this state can lead to perturbed cognitive processing and promote aversive learning, which may manifest as acute, long-term neuropsychiatric illness.

Bacteriophage-Liposomes Complex, a Bi-therapy System to Target Streptococcus pneumonia and Biofilm: A Research Protocol

Introduction: Streptococcus pneumoniae is a gram-positive bacterium, which is the leading cause of death for young children, elderly population, and immunocompromised patients. Its ability to mutate and become resistant to some of the strongest antibiotics makes them difficult to treat and increases the risk of disease spread. Although the development of stronger antibiotics to treat such microbes may be an option, they potentially pose a dangerous threat to the body. As such, a viable treatment option to fight against antimicrobial resistance has yet been found. Methods: The study focuses on utilizing a bi-therapy system to target S. pneumoniae in biofilm, which is the site of emerging antibiotic resistant mutants, by creating levofloxacin-liposomes carrying phages and testing them both in vitro and in vivo. Anticipated results: Using bacteriophage therapy and applying bacteriophage-antibiotic synergy, it is hoped to augment the potency of the treatment while lowering its side-effects. The Cp-1 bacteriophage-liposomes complexes are expected to be specific to the S. pneumoniae to carry antibiotics to sites of infection. Discussion: The therapy could ensure targeted bacterial lysis and site-directed delivery of low-dose drugs to decrease the toxicity effect of the antibiotics. Once the efficacy is established and is proven to be significant, its potency can be tested in BALB/cByJ mice models before bringing this therapy to animal trials then human clinical trials. Conclusion: Bacteriophages are very attractive therapeutic agents that effectively target pathogenic bacteria, safe for the human body, and highly modifiable to combat newly emerging bacterial threats. In addition to its many benefits, the use of bacteriophages could significantly reduce healthcare costs. The potential use of bacteriophages-liposomes complexes could be translated to treat respiratory infections in humans after confirming its efficacy in vitro and in vivo studies.

A Review of Using Mathematical Modeling to Improve Our Understanding of Bacteriophage, Bacteria, and Eukaryotic Interactions

Phage therapy, the therapeutic usage of viruses to treat bacterial infections, has many theoretical benefits in the ‘post antibiotic era.’ Nevertheless, there are currently no approved mainstream phage therapies. One reason for this is a lack of understanding of the complex interactions between bacteriophage, bacteria and eukaryotic hosts. These three-component interactions are complex, with non-linear or synergistic relationships, anatomical barriers and genetic or phenotypic heterogeneity all leading to disparity between performance and efficacy in in vivo versus in vitro environments. Realistic computer or mathematical models of these complex environments are a potential route to improve the predictive power of in vitro studies for the in vivo environment, and to streamline lab work. Here, we introduce and review the current status of mathematical modeling and highlight that data on genetic heterogeneity and mutational stochasticity, time delays and population densities could be critical in the development of realistic phage therapy models in the future. With this in mind, we aim to inform and encourage the collaboration and sharing of knowledge and expertise between microbiologists and theoretical modelers, synergising skills and smoothing the road to regulatory approval and widespread use of phage therapy.

Bacteriophage manipulation of the microbiome associated with tumour microenvironments-can this improve cancer therapeutic response?

Some cancer treatment failures have been attributed to the tumour microbiota, with implications that microbiota manipulation may improve treatment efficacy. While antibiotics have been used to control bacterial growth, their dysbiotic effects on the microbiome, failure to penetrate biofilms and decreased efficacy due to increasing antimicrobial resistance by bacteria, suggest alternatives are needed. Bacteriophages may provide a precise means for targeting oncobacteria whose relative abundance is increased in tumour tissue microbiomes. Fusobacterium, Streptococcus, Peptostreptococcus, Prevotella, Parvimonas, and Treponema species are prevalent in tumour tissue microbiomes of some cancers. They may promote cancer growth by dampening immunity, stimulating release of proinflammatory cytokines, and directly interacting with cancer cells to stimulate proliferation. Lytic bacteriophages against some of these oncobacteria have been isolated and characterised. The search continues for others. The possibility exists for their testing as adjuncts to complement existing therapies. In this review, we highlight the role of oncobacteria, specifically those whose relative abundance in the intra-tumour microbiome is increased, and discuss the potential for bacteriophages against these micro-organisms to augment existing cancer therapies. The capacity for bacteriophages to modulate immunity and kill specific bacteria makes them suitable candidates to manipulate the tumour microbiome and negate the effects of these oncobacteria.