Bacteriophages are more virulent to bacteria with human cells than they are in bacterial culture; insights from HT-29 cells

Effectiveness of Bacteriophage Therapy in Field Conditions and Possible Future Applications

BACKGROUND

Bacteriophages are viruses, which are obligate parasites of specific bacteria for the completion of their lifecycle. Bacteriophages could be the possible alternative to antibioticresistant bacterial diseases. With this objective, extensive research in different fields is published which are discussed in this article.

METHODS

After a review of bacteriophage therapy, bacteriophages were found to be effective against the multidrug-resistant bacteria individually or synergistically with antibiotics. They were found to be more effective, even better than the bacteria in the development of a vaccine.

RESULTS

Apart from the bacteriophages, their cell contents like Lysin enzymes were found equally very much effective. Only the major challenge faced in phage therapy was the identification and characterization of bacteria-specific phages due to the wide genetic diversity of bacterial populations. Similarly, the threshold level of bacteriophages to act effectively was altered by ultraviolet radiation and heat exposure.

CONCLUSION

Thus, bacteriophage therapy offers promising alternatives in the treatment of antibioticresistant bacteria in different fields. However, their effectiveness is determined by a triad of bacteriophages (type & quantity), host (bacteria) and environmental factors.

Interactions between Bacteriophages and Eukaryotic Cells

As the name implies, bacteriophage is a bacterium-specific virus. It infects and kills the bacterial host. Bacteriophages have gained attention as alternative antimicrobial entities in the science community in the western world since the alarming rise of antibiotic resistance among microbes. Although generally considered as prokaryote-specific viruses, recent studies indicate that bacteriophages can interact with eukaryotic organisms, including humans. In the current review, these interactions are divided into two categories, i.e., indirect and direct interactions, with the involvement of bacteriophages, bacteria, and eukaryotes. We discuss bacteriophage-related diseases, transcytosis of bacteriophages, bacteriophage interactions with cancer cells, collaboration of bacteriophages and eukaryotes against bacterial infections, and horizontal gene transfer between bacteriophages and eukaryotes. Such interactions are crucial for understanding and developing bacteriophages as the therapeutic agents and pharmaceutical delivery systems. With the advancement and combination of in silico, in vitro, and in vivo approaches and clinical trials, bacteriophages definitely serve as useful repertoire for biologic target-based drug development to manage many complex diseases in the future.

Bacteriophage-mediated manipulation of the gut microbiome – promises and presents limitations

Gut microbiome (GM) composition and function are linked to human health and disease, and routes for manipulating the GM have become an area of intense research. Due to its high treatment efficacy, the use of fecal microbiota transplantation (FMT) is generally accepted as a promising experimental treatment for patients suffering from GM imbalances (dysbiosis), e.g. caused by recurrent Clostridioides difficile infections (rCDI). Mounting evidence suggests that bacteriophages (phages) play a key role in successful FMT treatment by restoring the dysbiotic bacterial GM. As a refinement to FMT, removing the bacterial component of donor feces by sterile filtration, also referred to as fecal virome transplantation (FVT), decreases the risk of invasive infections caused by bacteria. However, eukaryotic viruses and prophage-encoded virulence factors remain a safety issue. Recent in vivo studies show how cascading effects are initiated when phage communities are transferred to the gut by e.g. FVT, which leads to changes in the GM composition, host metabolome, and improve host health such as alleviating symptoms of obesity and type-2-diabetes (T2D). In this review, we discuss the promises and limitations of FVT along with the perspectives of using FVT to treat various diseases associated with GM dysbiosis.

Bacteriophage K1F targets Escherichia coli K1 in cerebral endothelial cells and influences the barrier function

Bacterial neonatal meningitis results in high mortality and morbidity rates for those affected. Although improvements in diagnosis and treatment have led to a decline in mortality rates, morbidity rates have remained relatively unchanged. Bacterial resistance to antibiotics in this clinical setting further underlines the need for developing other technologies, such as phage therapy. We exploited an in vitro phage therapy model for studying bacterial neonatal meningitis based on Escherichia coli (E. coli) EV36, bacteriophage (phage) K1F and human cerebral microvascular endothelial cells (hCMECs). We show that phage K1F is phagocytosed and degraded by constitutive- and PAMP-dependent LC3-assisted phagocytosis and does not induce expression of inflammatory cytokines TNFα, IL-6, IL-8 or IFNβ. Additionally, we observed that phage K1F temporarily decreases the barrier resistance of hCMEC cultures, a property that influences the barrier permeability, which could facilitate the transition of immune cells across the endothelial vessel in vivo. Collectively, we demonstrate that phage K1F can infect intracellular E. coli EV36 within hCMECs without themselves eliciting an inflammatory or defensive response. This study illustrates the potential of phage therapy targeting infections such as bacterial neonatal meningitis and is an important step for the continued development of phage therapy targeting antibiotic-resistant bacterial infections generally.

Bacteriophages of the lower urinary tract

The discovery of bacteria in the female urinary bladder has fundamentally changed current dogma regarding the urinary tract and related urinary disorders. Previous research characterized many of the bacterial components of the female urinary tract, but the viral fraction of this community is largely unknown. Viruses within the human microbiota far outnumber bacterial cells, with the most abundant viruses being those that infect bacteria (bacteriophages). Similar to observations within the microbiota of the gut and oral cavity, preliminary surveys of the urinary tract and bladder microbiota indicate a rich diversity of uncharacterized bacteriophage (phage) species. Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using phages has therapeutic potential for lower urinary tract symptoms. Furthermore, as natural predators of bacteria, phages have garnered renewed interest for their use as antimicrobial agents, for instance, in the treatment of urinary tract infections.

Biological challenges of phage therapy and proposed solutions: a literature review

Introduction: In light of the emergence of antibiotic-resistant bacteria, phage (bacteriophage) therapy has been recognized as a potential alternative or addition to antibiotics in Western medicine for use in humans.Areas covered: This review assessed the scientific literature on phage therapy published between 1 January 2007 and 21 October 2019, with a focus on the successes and challenges of this prospective therapeutic.Expert opinion: Efficacy has been shown in animal models and experimental findings suggest promise for the safety of human phagotherapy. Significant challenges remain to be addressed prior to the standardization of phage therapy in the West, including the development of phage-resistant bacteria; the pharmacokinetic complexities of phage; and any potential human immune response incited by phagotherapy.

Bacteriophage and the Innate Immune System: Access and Signaling

Bacteriophage and the bacteria they infect are the dominant members of the gastrointestinal microbiome. While bacteria are known to be central to maintenance of the structure, function, and health of the microbiome, it has only recently been recognized that phage too might serve a critical function. Along these lines, bacteria are not the only cells that are influenced by bacteriophage, and there is growing evidence of bacteriophage effects on epithelial, endothelial, and immune cells. The innate immune system is essential to protecting the Eukaryotic host from invading microorganisms, and bacteriophage have been demonstrated to interact with innate immune cells regularly. Here, we conduct a systematic review of the varying mechanisms allowing bacteriophage to access and interact with cells of the innate immune system and propose the potential importance of these interactions.

Bacteriophage Adherence to Mucus Mediates Preventive Protection against Pathogenic Bacteria

Metazoans were proposed to host bacteriophages on their mucosal surfaces in a symbiotic relationship, where phages provide an external immunity against bacterial infections and the metazoans provide phages a medium for interacting with bacteria. However, scarce empirical evidence and model systems have left the phage-mucus interaction poorly understood. Here, we show that phages bind both to porcine mucus and to rainbow trout (Oncorhynchus mykiss) primary mucus, persist up to 7 days in the mucosa, and provide protection against Flavobacterium columnare Also, exposure to mucus changes the bacterial phenotype by increasing bacterial virulence and susceptibility to phage infections. This trade-off in bacterial virulence reveals ecological benefit of maintaining phages in the metazoan mucosal surfaces. Tests using other phage-bacterium pairs suggest that phage binding to mucus may be widespread in the biosphere, indicating its importance for disease, ecology, and evolution. This phenomenon may have significant potential to be exploited in preventive phage therapy.IMPORTANCE The mucosal surfaces of animals are habitat for microbes, including viruses. Bacteriophages-viruses that infect bacteria-were shown to be able to bind to mucus. This may result in a symbiotic relationship in which phages find bacterial hosts to infect, protecting the mucus-producing animal from bacterial infections in the process. Here, we studied phage binding on mucus and the effect of mucin on phage-bacterium interactions. The significance of our research is in showing that phage adhesion to mucus results in preventive protection against bacterial infections, which will serve as basis for the development of prophylactic phage therapy approaches. Besides, we also reveal that exposure to mucus upregulates bacterial virulence and that this is exploited by phages for infection, adding one additional layer to the metazoan-bacterium-phage biological interactions and ecology. This phenomenon might be widespread in the biosphere and thus crucial for understanding mucosal diseases, their outcome and treatment.

Phage penetration of eukaryotic cells: practical implications

The inability to infect eukaryotic cells has been considered as the most undeniable feature of all bacterial viruses. Such specificity, limited only for bacterial hosts, raises questions about the paths and challenges phages should overcome when circulating through the human body. Recently, it has been shown that phages are able to continually penetrate human organs and tissues. Latest reports revealed that phages can cross eukaryotic cell barriers both para- and transcellularly and even reach the nucleus. Further, phages are capable of internalizing within cells through different endocytic mechanisms. Such phenomenon indicates that phages could shape human microbiome composition and affect all aspects of human health. Thus, herein, we summarize the current state of knowledge and describe this phenomenon with a particular emphasis on endocytic pathways.

Missing a Phage: Unraveling Tripartite Symbioses within the Human Gut

Tripartite symbioses between bacteriophages, the epithelial cell layers of the human gut, and bacterial symbionts may play an important and unrecognized role in the function of the gut microbiome. Traditionally, phages residing within the gut were considered to interact only with their bacterial hosts and thereby to facilitate indirect interactions with the epithelial cell layers, and yet a growing body of literature is demonstrating the surprising and diverse ways in which phages directly interact with the eukaryotic cells, organs, and systems of the body.

Tripartite symbioses between bacteriophages, the epithelial cell layers of the human gut, and bacterial symbionts may play an important and unrecognized role in the function of the gut microbiome. Traditionally, phages residing within the gut were considered to interact only with their bacterial hosts and thereby to facilitate indirect interactions with the epithelial cell layers, and yet a growing body of literature is demonstrating the surprising and diverse ways in which phages directly interact with the eukaryotic cells, organs, and systems of the body. Phages can adhere to mucosal surfaces, bind and transcytose epithelial cells, and deliver proteins and nucleic acids to eukaryotic cells directly. These interactions could establish positive-feedback loops leading to the selection of bacterial hosts and their phage symbionts in the gut. The members of my laboratory are working to expand our knowledge on the phage-eukaryote interactions and to redefine the concept of tripartite symbioses within the human body.

The Third Annual Meeting of the European Virus Bioinformatics Center

The Third Annual Meeting of the European Virus Bioinformatics Center (EVBC) took place in Glasgow, United Kingdom, 28-29 March 2019. Virus bioinformatics has become central to virology research, and advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks, being successfully used to detect, control, and treat infections of humans and animals. This active field of research has attracted approximately 110 experts in virology and bioinformatics/computational biology from Europe and other parts of the world to attend the two-day meeting in Glasgow to increase scientific exchange between laboratory- and computer-based researchers. The meeting was held at the McIntyre Building of the University of Glasgow; a perfect location, as it was originally built to be a place for "rubbing your brains with those of other people", as Rector Stanley Baldwin described it. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The meeting featured eight invited and twelve contributed talks, on the four main topics: (1) systems virology, (2) virus-host interactions and the virome, (3) virus classification and evolution and (4) epidemiology, surveillance and evolution. Further, the meeting featured 34 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.

Biodistribution of Liposome-Encapsulated Bacteriophages and Their Transcytosis During Oral Phage Therapy

This study sheds light on the biodistribution of orally administered, liposome-encapsulated bacteriophages, and their transcytosis through intestinal cell layers. Fluorochrome-labeled bacteriophages were used together with a non-invasive imaging methodology in the in vivo visualization of bacteriophages in the stomach and intestinal tract of mice. In those studies, phage encapsulation resulted in a significant increase of the labeled phages in the mouse stomach, even 6 h after their oral administration, and without a decrease in their concentration. By contrast, the visualization of encapsulated and non-encapsulated phages in the intestine were similar. Our in vivo observations were corroborated by culture methods and ex vivo experiments, which also showed that the percentage of encapsulated phages in the stomach remained constant (50%) compared to the amount of initially administered product. However, the use of conventional microbiological methods, which employ bile salts to break down liposomes, prevented the detection of encapsulated phages in the intestine. The ex vivo data showed a higher concentration of non-encapsulated than encapsulated phages in liver, kidney, and even muscle up to 6 h post-administration. Encapsulated bacteriophages were able to reach the liver, spleen, and muscle, with values of 38% ± 6.3%, 68% ± 8.6%, and 47% ± 7.4%, respectively, which persisted over the course of the experiment. Confocal laser scanning microscopy of an in vitro co-culture of human Caco-2/HT29/Raji-B cells revealed that Vybrant-Dil-stained liposomes containing labeled bacteriophages were preferably embedded in cell membranes. No transcytosis of encapsulated phages was detected in this in vitro model, whereas SYBR-gold-labeled non-encapsulated bacteriophages were able to cross the membrane. Our work demonstrates the prolonged persistence of liposome-encapsulated phages in the stomach and their adherence to the intestinal membrane. These observations could explain the greater long-term efficacy of phage therapy using liposome-encapsulated phages.

Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth

For a bacteriophage to be useful for phage therapy it must be both isolated from the environment and shown to have certain characteristics beyond just killing strains of the target bacterial pathogen. These include desirable characteristics such as a relatively broad host range and a lack of other characteristics such as carrying toxin genes and the ability to form a lysogen. While phages are commonly isolated first and subsequently characterized, it is possible to alter isolation procedures to bias the isolation toward phages with desirable characteristics. Some of these variations are regularly used by some groups while others have only been shown in a few publications. In this review I will describe (1) isolation procedures and variations that are designed to isolate phages with broader host ranges, (2) characterization procedures used to show that a phage may have utility in phage therapy, including some of the limits of such characterization, and (3) results of a survey and discussion with phage researchers in industry and academia on the practice of characterization of phages.

Bacteriophages in Dentistry-State of the Art and Perspectives

Bacteriophages, viruses capable of killing bacteria, were discovered in 1915, but the interest in their study has been limited since the advent of antibiotics. Their use in dentistry is still very limited. The authors reviewed studies about bacteriophage structure, mode of action, uses in oral health, and possible future uses in dentistry associated with their possible action over biofilm, as well as the advantages and limitations of phage therapy.

Phage research in ‘organ-on-chip’ devices

The use of ‘organ-on-chip' devices in microbiology research presents enormous opportunities for fundamental and translational research1–4. Yet these approaches have not been widely embraced by the microbiology field. This is particularly evident with bacteriophage (phage) research applications. Traditionally phage research has been an early adopter of experimental techniques and approaches5, having catalysed research in biotechnology, environmental biology, sequencing, and synthetic biology. Here we discuss some of the opportunities that organ-on-chip devices present to both phage and microbiology research, and provide a ‘how to' guide for researchers interested in utilising this approach.

Clinical Indications and Compassionate Use of Phage Therapy: Personal Experience and Literature Review with a Focus on Osteoarticular Infections

The history of phage therapy started with its first clinical application in 1919 and continues its development to this day. Phages continue to lack any market approval in Western medicine as a recognized drug, but are increasingly used as an experimental therapy for the compassionate treatment of patients experiencing antibiotic failure. The few formal experimental phage clinical trials that have been completed to date have produced inconclusive results on the efficacy of phage therapy, which contradicts the many successful treatment outcomes observed in historical accounts and recent individual case reports. It would therefore be wise to identify why such a discordance exists between trials and compassionate use in order to better develop future phage treatment and clinical applications. The multitude of observations reported over the years in the literature constitutes an invaluable experience, and we add to this by presenting a number of cases of patients treated compassionately with phages throughout the past decade with a focus on osteoarticular infections. Additionally, an abundance of scientific literature into phage-related areas is transforming our knowledge base, creating a greater understanding that should be applied for future clinical applications. Due to the increasing number of treatment failures anticipatedfrom the perspective of a possible post-antibiotic era, we believe that the introduction of bacteriophages into the therapeutic arsenal seems a scientifically sound and eminently practicable consideration today as a substitute or adjuvant to antibiotic therapy.

Engineered K1F bacteriophages kill intracellular Escherichia coli K1 in human epithelial cells

Bacterial infections can be treated with bacteriophages that show great specificity towards their bacterial host and can be genetically modified for different applications. However, whether and how bacteriophages can kill intracellular bacteria in human cells remains elusive. Here, using CRISPR/Cas selection, we have engineered a fluorescent bacteriophage specific for E. coli K1, a nosocomial pathogen responsible for urinary tract infections, neonatal meningitis and sepsis. By confocal and live microscopy, we show that engineered bacteriophages K1F-GFP and E. coli EV36-RFP bacteria displaying the K1 capsule, enter human cells via phagocytosis. Importantly, we show that bacteriophage K1F-GFP efficiently kills intracellular E. coli EV36-RFP in T24 human urinary bladder epithelial cells. Finally, we provide evidence that bacteria and bacteriophages are degraded by LC3-associated phagocytosis and xenophagy.

Unravelling the Links between Phage Adsorption and Successful Infection in Clostridium difficile

Bacteriophage (phage) therapy is a promising alternative to antibiotics for the treatment of bacterial pathogens, including Clostridiumdifficile. However, as for many species, in C. difficile the physical interactions between phages and bacterial cells have not been studied in detail. The initial interaction, known as phage adsorption, is initiated by the reversible attachment of phage tail fibers to bacterial cell surface receptors followed by an irreversible binding step. Therefore binding can dictate which strains are infected by the phage. In this study, we investigated the adsorption rates and irreversible binding of three C. difficile myoviruses: CDHM1, CDHM3 and CDHM6 to ten strains that represent ten prevalent C. difficile ribotypes, regardless of their ability to infect. CDHM1 and CDHM3 phage particles adsorbed by ~75% to some strains that they infected. The infection dynamics for CDHM6 are less clear and ~30% of the phage particles bound to all strains, irrespective of whether a successful infection was established. The data highlighted adsorption is phage-host specific. However, it was consistently observed that irreversible binding had to be above 80% for successful infection, which was also noted for another two C. difficile myoviruses. Furthermore, to understand if there is a relationship between infection, adsorption and phage tail fibers, the putative tail fiber protein sequences of CDHM1, CDHM3 and CDHM6 were compared. The putative tail fiber protein sequence of CDHM1 shares 45% homology at the amino acid level to CDHM3 and CDHM6, which are identical to each other. However, CDHM3 and CDHM6 display differences in adsorption, which highlights that there is no obvious relationship between putative tail fiber sequence and adsorption. The importance of adsorption and binding to successful infection is often overlooked, and this study provides useful insights into host-pathogen interactions within this phage-pathogen system.

Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections

Fecal microbiota transplantation has proven to be an effective treatment for infections with the gram-positive enteropathogen Clostridium difficile. Despite its effectiveness, the exact mechanisms that underlie its success are largely unclear. In this review, we highlight the pleiotropic effectors that are transferred during fecal microbiota transfer and relate this to the C. difficile lifecycle. In doing so, we show that it is likely that multiple factors contribute to the elimination of symptoms of C. difficile infections after fecal microbiota transplantation.