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Risks in bacterial phage therapy

Risks in bacterial phage therapy



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I just finished reading J. Craig Venter's book Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life. The book is a little over a year old now, and Venter has an optimistic outlook that bacteriophage therapy will become an effective alternative to gene therapy and viral immunotherapy. He mentioned that the JCVI (J. Craig Venter Institute) is working on such projects. Are other companies also researching, and has progress been made? What are the expected risks? How can rogue, harmful phage mutations be controlled? Can this type of therapy be applied to cancers?


The Eliava Institute in Tiflis (Georgia (a country)) has been at it since the 1930's. A US company sells a phageproduct for desinfection of meat.

The risk of Phagetherapy is there, if the phage is ill choosen or contaminated with other phage it could introduce pathogenic genes to the target or other bacteria.

If those risks are eliminated there is very little risk in phage therapy aside from the fact that it may not work at all. Phagetherapy is most useful in regions where bacteria are normally found, in other places the immunesystem will make short work of it.

The faster and cheaper sequencing gets the more effective phagetherapy will become. Since a "bad" bacteria can quickly be isolated and a proper "phage cocktail" can be prepared. If we get to the point that we can sequence the whole microbiom of a person then i bet that Phagetherapy will be a very normal thing.

To your cancer question, i think its rather hard to apply it to cancer therapy except if u are looking to combat the cancer with a Intracellular bacteria… but then again. How u get the phage to it.

A excellent read on this topic is the Book "the bacteriophages".


You run the risk of the killed cells suddenly releasing huge quantities of cytokines. If this occurs you may cause spike in capillary permeability and basically create massive sepsis. The bacteria will have to be killed SLOWLY to prevent them spilling their contents into the circulatory system. But, I have always believed phages could be engineered to control certain infections like urosepsis. But, any phage therapy may be single use only. I used to inject them into rabbits to prepare antisera used in phage growth experiments, I guess that is one of the reasons phage therapy is out of the mainstream. http://www.nature.com/news/phage-therapy-gets-revitalized-1.15348


A bacteriophage or phage is a virus whose existence dates back to what some say Earth’s primordial times. The function of every type of bacteriophage is to target a specific type of bacteria. Some even see them as the natural mechanism that has allowed a certain order for species to develop and not be destroyed by bacteria. Although they have worked in the dark since the beginning, it is only quite recently that their existence and importance have been noticed.

The discovery of bacteriophages dates back to 1915 by Frederick W. Twort in Great Britain and 1917 by Félix d’Hérelle in France, independently. In a time when the human mind was at a stage of discovery, or rather, rediscovering the hidden secrets of our planet. Once Félix d’Hérelle saw the potential of bacteriophages, he devised therapies that would give humanity a fighting chance against the infestations of bacterial infections, plaguing people at the time. His phage therapies aimed towards helping patients fight against Vibrio cholera causing cholera and against a specific strain of Salmonella causing typhoid fever.

However, discoveries at that time were not surrounded to just phages. Penicillin, and ultimately the production of antibiotics seemed by many an easier therapeutic option and phage therapy was placed aside to collect the dust off a shelf.

Although the majority of the world had forgotten about nature’s ultimate bacteria eater, a few countries continued to maintain and grow their collection of bacteriophages and even continue phage therapies. Georgia and Russia in particular, to this day, have maintained the use of bacteriophages to address bacterial infections. Bacteriophage cocktails are also used in these countries during ecological disasters such as floods, as a preventative measure to reduce the risk of gastrointestinal infections in people.


5 drawbacks of phage therapy

Bacteriophage therapy is now considered to be the best alternative therapeutics to antibiotic treatment. Although phage therapy was started in 1919, the concept of phage therapy died out in the 1940s due to the production of antibiotics in large amount. Over last few decades, due to the emergence of antibiotic resistance, phage therapy is now thought to be a great solution to the antibiotic crisis. In spite of having a lot of advantages of using phage therapy over antibiotics, phage therapy has also some limitations.

1. Phages can’t kill a wide range of pathogens:

Narrow host range can be a disadvantage as the specific phage might not be able to constantly lyse all the pathogenic strains of that certain infection. There are several options to circumvent this problem: using phage with broad host range, using mutant bacteriophage or using a mixture of different phages.

2. Phages cause adverse biological effects:

An unpurified phage preparation can cause several biological effects during phage therapy. Phage multiplication using host cell is a primary step for phage production. During cell lysis, lipopolysaccharide, a component of the cell wall of gram-negative bacteria are released. Lipopolysaccharide acts as an endotoxin and if they are present in high concentration then they can trigger a coagulation cascade, modify hemodynamics, and invoke fever, toxic shock, and hypotension. Purifying phage preparation using chromatography and ultrafiltration can produce endotoxin-free preparation.

3. Temperate phages aren’t antibacterial:

Not all phages can be used for therapeutic propose. Only obligate lytic phages that lyse the bacterial cell directly instead of integrating its genome in bacterial DNA (temperate) are usable for phage therapy. Temperate phages play a major role in the exchange of genetic material between different bacterial strains and often they contribute to the pathogenicity. Some known examples are Cholera toxin from CTXΦ phage and Shiga toxin from H-19B phage acquired by Vibrio cholerae and E.coli respectively.

4. The emergence of phage resistance:

Development of phage-resistant mutation can make the phage therapy unproductive. However, using phage cocktail (a mixture of phages) that uses different cell receptors can restrain rise of phage resistance.

5. Immune response to inactivate phages:

Phage inactivation by human serum can pose a limitation in phage therapy. Some studies have indicated inactivation of phage by human serum while other experiments have documented little or no inactivation or inactivation after a long period of incubation.


The Risks of Antimicrobial Use in Agriculture

The argument against using antibiotics as standard agricultural practice, both to improve growth rates and prevent disease, is not new (Witte, 1998) and has been extensively reviewed previously (Singer et al., 2003). However, unequivocally demonstrating increased resistance as a consequence of agricultural usage has proved elusive (Perry and Wright, 2013). A wave of new data supporting both direct and indirect routes of antibiotic resistance genes between agricultural and human populations suggests a bidirectional zoonotic exchange (Price et al., 2012). For example, recent studies have found diverse and abundant resistance genes in manure prior to disposal in the environment (Zhu et al., 2013) and a high prevalence of resistance to multiple antibiotics in enterobacteria isolated from tomato farms (Micallef et al., 2013) and in bacteria from manure-amended soils (Popowska et al., 2012). Furthermore, methicillin-resistant Staphylococcus aureus (MRSA) rates in workers on swine farms have been shown to be higher than for the average population in both North America and Europe (Voss et al., 2005Khanna et al., 2008 Smith et al., 2009 van Cleef et al., 2010). Finally, calves treated with antibiotics are also more likely to carry MRSA and there is a direct association between intensity of animal contact and human MRSA carriage (Graveland et al., 2010). A similar trend is seen in aquaculture where bacteria nearer to farms were found to have higher levels of antibiotic resistance than nearby coastal regions in Italy (Labella et al., 2013). The increasing number of studies supporting the hypothesis that environmental use of antibiotics has contributed to selection for antibiotic resistance suggests that non-prudent use of antibiotics in healthcare and agriculture may reduce the effectiveness of antibiotic strategies as an essential treatment for disease.

As an alternative to antibiotic use, the application of phages in agriculture is being trialed as a biopesticide to control plant pathogens of tomato (Jones et al., 2012), citrus (Balogh et al., 2008), and onion (Lang et al., 2007) among others (reviewed in Svircev et al., 2011). For example, Erwinia amylovora (the causative agent of fire blight) infections are affecting a number of crop species in orchards across North America and Europe (see Malnoy et al., 2012 for review). Although antibiotics have traditionally been employed to control this disease, the emergence of streptomycin resistant strains (McManus et al., 2002) and a desire to reduce antibiotic use in the environment has led to the use of phages as an alternative. Phage biocontrol clearly has the potential to control fire blight infections, as lytic phages have been isolated that are highly infective to the pathogen, but definitive field trials are currently lacking. Given the evidenced risks of movement of antibiotic resistance genes between agricultural to human pathogens, we should ask whether the large-scale application of phages is likely to repeat these past mistakes. Until appropriate studies are conducted, the subsequent consequences of applying phages in agriculture for the spread of antibiotic resistance, the evolution of the pathogen, and the community of microbes within the plants and soil remain unknown.


NIH Awards Grants to Support Bacteriophage Therapy Research

A computer-generated rendition of a bacteriophage.

A computer-generated rendition of a bacteriophage.

The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, has awarded $2.5 million in grants to 12 institutes around the world to support research on bacteriophage therapy. These awards represent NIAID’s first series of grants focused exclusively on research on this therapy, an emerging field that could yield new ways to fight antimicrobial-resistant bacteria. A 2019 report from CDC found that antibiotic-resistant pathogens cause more than 2.8 million infections in the U.S. each year and more than 35,000 people die.

Bacteriophages (or “phages”) are viruses that can kill or incapacitate specific kinds of bacteria while leaving other bacteria and human cells unharmed. By gathering naturally-occurring phages, or by modifying or engineering phages to display certain properties, researchers hope to create novel anti-bacterial therapeutics. Because phages eliminate bacteria by infecting them, rather by generating compounds like antibiotics which kill bacteria, phages can be used to treat antibiotic-resistant infections. In addition, some evidence suggests that combination therapy containing both phages and antibiotics could prevent bacteria from becoming drug resistant.

Although scientists have been aware of phages and their ability to kill bacteria since 1917, the first U.S.-based clinical trials of phage therapy have only recently begun. Individual U.S. patients have received phage therapy, but only under emergency investigational new drug protocols. In eastern Europe, where the use of phage therapy is more prevalent, its efficacy has not been rigorously demonstrated.

“In recent decades, multidrug-resistant bacteria, particularly those that cause potentially deadly diseases like tuberculosis, have become a serious and growing global public health concern,” said NIAID Director Anthony S. Fauci, M.D. “With these awards, NIAID is supporting research needed to determine if phage therapy might be used in combination with antibiotics—or replace them altogether—in treating evolving antibiotic-resistant bacterial diseases.”

The new NIAID grants support research to address key knowledge gaps in the development of phages as preventative and therapeutic tools for bacterial infections. Basic research supported by these grants will include a study characterizing different types of phages a project studying how phages combat sticky, sheet-like colonies of microorganisms called biofilms, which can be difficult to treat with antibiotics and research to determine how to identify new, potentially useful phages. Some translational research supported by these grants will study how to exploit the interaction between phages and bacteria to create lasting, re-usable therapeutics and engineering viruses to combat Staphylococcus bacteria.


Consent

Assuming phage therapy is eventually approved for ordinary use by physicians, surgeons and infectious disease specialists in hospitals, patients will face the choice of whether to consent to be infected with ‘live’ viruses in order to cure or prevent bacterial infections.

Phage can target infections much more precisely than antibiotics. This means that if they are diagnosed correctly and dosed appropriately, patients given phage therapy can recover from infection with essentially no side effects and few risks. By contrast, broad-spectrum antibiotics often alter or compromise a patient’s microbiome in a way that phage do not. For example, an increasing number of patients develop difficulties associated with clostridium difficile after taking antibiotics. Clostridium difficile is an opportunistic pathogen that multiplies rapidly when competing bacteria are eliminated by a patient’s use of antibiotics. The consequences of c. diff can include long-term damage to digestion and gut health ( Brown et al., 2017).

In principle, consenting to phage therapy isn’t much different than consenting to a vaccination. When efficacy is high and risk is low, patient consent is fairly straightforward to obtain, even if patients do not understand the precise scientific mechanisms of the treatment. But phage are different than vaccines, and the risks of phage treatment are mostly a function of physician uncertainty about which infection exists, and which phage is appropriate to select as a treatment. For phage therapy to work well, bacterial infections have to be precisely diagnosed (a costly endeavor), the appropriate cocktail of phage must be selected (or engineered), and the treatment must be delivered in a way that is likely to obviate the patient’s immune system ( Kingwell, 2015).

Informed consent is the bedrock of modern medical ethics ( Flanigan, 2017). But patients are notoriously ignorant about the details of infections, and often conflate bacteria and viruses. Moreover, most practicing physicians currently don’t know much about phage viruses since research is in its early stages. For robust consent to be given for phage therapy, patients and physicians will presumably have to spend more time discussing the known and unknown risks associated with treatment than they do in simple cases in which antibiotics are selected and administered to treat a normal case of pneumonia or staph.

For too long we have taken for granted that when in doubt we can prescribe a powerful, broad-spectrum antibiotic, administered intravenously in cases of urgent need. But as bacteria continue to evolve resistance to standard antibiotics, we will need to explore phage therapy as an alternative in some cases. And until we know quite a bit more about phage, consent will be difficult to obtain because the science is complex, the efficacy is not precisely understood, and the treatment is more difficult for physicians to explain to their patients. For these reasons, in the near future phage will likely be used mainly for topical treatment of skin infections, as a way to sterilize food, to clean hospitals and medical devices, and as a last resort treatment when the best available antibiotics fail to cure a patient.

The purpose of this section is not to develop a novel theory of consent, but to highlight how phage therapy may generate unique challenges that differ from more familiar treatments at the stage of clinical trials and in ordinary clinical settings. The challenge stems mainly from scientific complexity and medical uncertainty.


Biologists turn eavesdropping viruses into bacterial assassins

Professor Bonnie Bassler and graduate student Justin Silpe discovered a bacteria-killing virus that can eavesdrop on bacterial conversations. They re-engineered it to attack diseases including salmonella, E. coli and cholera.

Princeton molecular biologist Bonnie Bassler and graduate student Justin Silpe have identified a virus, VP882, that can listen in on bacterial conversations — and then, in a twist like something out of a spy novel, they found a way to use that to make it attack bacterial diseases like E. coli and cholera.

“The idea that a virus is detecting a molecule that bacteria use for communication — that is brand-new,” said Bassler, the Squibb Professor of Molecular Biology. “Justin found this first naturally occurring case, and then he re-engineered that virus so that he can provide any sensory input he chooses, rather than the communication molecule, and then the virus kills on demand.” Their paper will appear in the Jan. 10 issue of the journal Cell.

A virus can only ever make one decision, Bassler said: Stay in the host or kill the host. That is, either remain under the radar inside its host or activate the kill sequence that creates hundreds or thousands of offspring that burst out, killing the current host and launching themselves toward new hosts.

There’s an inherent risk in choosing the kill option: “If there are no other hosts nearby, then the virus and all its kin just died,” she said. VP882 has found a way to take the risk out of the decision. It listens for the bacteria to announce that they are in a crowd, upping the chances that when the virus kills, the released "kin" immediately encounter new hosts. “It’s brilliant and insidious,” said Bassler.

These E. coli bacteria harbor proteins from the eavesdropping virus. One of the viral proteins has been tagged with a red marker. When the virus is in the “stay” mode (left), the bacteria grow and the red protein is spread throughout each cell. When the virus overhears that its hosts have achieved a quorum (right), the kill-stay decision protein is flipped to “kill” mode. A second viral protein binds the red protein and sends it to the cell poles (yellow dots). All the cells in the right panel will soon die.

“This paper provides an entirely new perspective on the dynamic relationship between viruses and their hosts,” said Graham Hatfull, the Eberly Family Professor of Biotechnology at the University of Pittsburgh, who was not involved in this research. “This study tells us for the first time … that when a phage is in the lysogenic [stay] state, it is not ‘fast asleep,’ but rather catnapping, with one eye open and ears alert, ready to respond when it ‘hears’ signals that cells are getting ready to respond to changes in their environment.”

Bassler, who is also the chair of molecular biology and a Howard Hughes Medical Institute Investigator, had discovered years before that bacteria can communicate and sense one another’s presence, and that they wait to establish a quorum before they act in concert. But she had never imagined that a virus could eavesdrop on this quorum-sensing communication.

“The bugs are getting bugged,” she said with a laugh. “Plus, Justin’s work shows that these quorum-sensing molecules are conveying information across kingdom boundaries.” Viruses are not in the same kingdom as bacteria — in fact, they are not in any kingdom, because they are not technically alive. But for such radically different organisms to be able to detect and interpret each other’s signals is simply mind-boggling, she said. It’s not like enemy nations spying on each other, or even like a human communicating with a dog — those at least are members of the same kingdom (animal) and phylum (vertebrate).

After finding the first evidence of this cross-kingdom eavesdropping, Silpe started looking for more — and found it.

“He just started a brand-new field,” Bassler said. “The idea that there’s only one example of this cross-domain communication made no sense to us. Justin discovered the first case, and then, with his discovery in hand, he went looking more deeply and he found a whole set of viruses that harbor similar capabilities. They may not all be listening in to this quorum-sensing information, but it is clear that these viruses can listen in to their hosts’ information and then use that information to kill them.”

Silpe said he was drawn to work in Bassler’s lab because of her research on bacterial communication. “Communication seems like such an evolved trait,” he said. “To hear that bacteria can do it — her discovery — it was just mind-blowing that organisms you think of as so primitive could actually be capable of communication. And viruses are even simpler than bacteria. The one I studied, for example, only has about 70 genes. It’s really remarkable that it devotes one of those genes to quorum sensing. Communication is clearly not something higher organisms created.”

Once Silpe demonstrated that VP882 was eavesdropping, he began experimenting with feeding it misinformation to trick the virus into killing on command — to turn the predator into an assassin.

VP882 is not the first virus used as an antimicrobial treatment. Viruses that prey on bacteria are called “phages,” and “phage therapy” — targeting a bacterial disease with a phage — is a known medical strategy. But VP882 is the first phage that uses eavesdropping to know when it is optimal to kill its targets, making Silpe’s experiments with salmonella and other disease-causing bacteria the first time that phage therapy has used trans-kingdom communication.

In addition, this virus holds enormous promise as a therapeutic tool because it does not act like a typical virus, Bassler said. Most viruses can only infect a very specific type of cell. Flu viruses, for example, only infect lung cells HIV only targets specific immune-system cells. But the virus VP882 has an “exceptionally broad host range,” Bassler said. So far, Silpe has only performed “proof of principle” tests with three unrelated bacteria: Vibrio cholerae (cholera), salmonella and E. coli. Those diseases have evolved separately for hundreds of millions of years, so the fact that they are all susceptible to this bacterial assassin suggests that many, many more are as well.

Hatfull is optimistic about the utility of this re-engineered virus for antibiotic-resistant bacteria. “Antibiotic resistance is clearly a major global health threat, and there is a clear and evident demand for new strategies and approaches to this problem,” he said. “Although we have admittedly found it tricky even to reach ‘first base’ with basic therapeutic use of naturally occurring phages, we can envisage the possibility of a ‘home run’ if we can engineer phages for therapeutic use that have very specific targeting.” These viral assassins might even slow down the emergence of antibiotic resistant strains, he said.

Bassler gives all credit for the discovery to Silpe. After identifying a new quorum-sensing gene in V. cholerae, he made the choice to search genome databases for that gene. It showed up in some cholera-related strains and exactly one virus. Bassler wondered if that could be a meaningless data artifact, but Silpe wanted to get a specimen of the virus and run experiments.

“He was gung-ho, and I thought, ‘What the heck, give this kid a little rope. If this isn’t working soon, we can always move on,’” she said. “His was a crazy idea, because there’s never, ever been evidence of a virus listening in on bacterial host information to decide whether to stay put or kill. But this lab was built on crazy ideas, like bacteria talking to each other, and we’ve kind of made a living out of it. … Of course, that’s the beauty of science, and science at Princeton, that you have enough resources to play those hunches out, and see if there’s a ‘there’ there. And this time, there was a big ‘there’ there.”


Phage Therapy Revisited: The Population Biology of a Bacterial Infection and Its Treatment with Bacteriophage and Antibiotics

Phage therapy is the use of bacterial viruses (bacteriophage) to treat bacterial infections. It has been practiced sporadically on humans and domestic animals for nearly 75 yr. Nevertheless, phage therapy has remained outside the mainstream of modern medicine, presumably because of doubts about its efficacy, and possibly because it was eclipsed by antibiotics and other chemotherapeutic agents. In this report, we develop the study of phage therapy and antibiotic therapy as a population biological phenomenon-the dynamic interaction of bacteria with a predator (phage) or a toxic chemical (antibiotic) inside a host whose immune and other defenses also affect the interaction. Our goal is to identify the conditions under which phage and antibiotics can successfully control a bacterial infection and when they cannot. We review data published in the 1980s by H. Williams Smith and J. B. Huggins on the use of phage and antibiotics to control lethal, systemic infections of Escherichia coli in experimentally inoculated mice. We show that some of their observations can be accommodated by a quantitative model that invokes known or plausible assumptions about host defenses and the interactions of bacteria with phage and antibiotics some observations remain unexplained by the model. Our analysis identifies several hypotheses about the population dynamics of phage and antibiotic therapy that can be tested experimentally. Included among these are hypotheses that account for variation in the efficacy of the different phages employed by Smith and Huggins and why, in their study, phages were more effective than antibiotics.


PHAGE-BASED VACCINOLOGY

Recombinant DNA technology allows synthesis of vaccine candidates that are subunits of pathogens. However, such vaccines have limited immunogenic features and require adjuvants or effective delivery systems for proper activation of the immune system (Petrovsky and Aguilar 2004 Barrett and Stanberry 2008). Thus, phages are now being evaluated as vaccine delivery agents because of their inherited ability to stimulate humoral and cell-mediated immunity (Burdin et al. 2004). Two strategies are often combined to produce phage vaccines: (1) phage display, when virions are decorated with peptides selected for their ability to bind antigen-presenting cells and (2) phage DNA vaccines, when viral DNA is engineered to carry a foreign antigen gene under the control of a strong eukaryotic promoter and has the ability to deliver this element to mammalian cells (Clark and March 2004a Zanghi et al. 2007).

Filamentous phage M13 has been the first virus manipulated to express a melanoma-specific tumor antigen fragment and has been successfully used to raise an immune response capable of reducing tumor growth in animal models (Benhar 2001 Fang et al. 2005). Currently, several vaccines for infectious diseases are prepared by using the T4 phage display system, which has shown promising results in animal models (Jiang et al. 1997). Similarly, phage T7 has been engineered to display vascular endothelial growth factor (VEGF) and has been successfully used to break immunologic tolerance and produce a strong immune response against Lewis lung cell carcinoma (Li et al. 2006).

Alternatively, phage can be exploited to transfer genes into mammalian cells. In these vectors, the antigens, under the control of a eukaryotic promoter, are cloned inside of a nonessential region of a phage genome. When injected in a mammalian system, these phage particles, acting as a DNA vaccine, can induce potent immune response by expressing foreign antigen inside of anaphase-promoting complexes (APCs) or other cells (Clark and March 2006). Several λ-based DNA vaccines for infectious diseases have been prepared that have shown promising results in animal models (Clark and March 2004b March et al. 2004). It should be noted that these viruses are manipulated to penetrate mammalian cells and, in the absence of engineering, phages are only capable of infecting bacteria.


Conclusion

Phage therapies for Shigella spp. and other pathogenic bacteria have been studied and applied for about a century, but phage therapy as an antibacterial treatment in general has not received much attention due to lack of clinical knowledge and public awareness of phages. However, given that the development of novel antibiotics is laborious, time-consuming and costly, it makes eminent sense to seek alternative antimicrobial approaches to combat drug resistant pathogens. While it inevitably has some drawbacks, phage-based biocontrol and bacteriophage therapy are very promising approaches to combat the challenge of pathogenic bacterial infections, particularly when the search for new antibiotics is stagnating. The potential of phage therapy has been acknowledged and revisited by many scientists over the last few decades, and there has been a rejuvenation of research into phage therapy. Moreover, phages have many unexploited potentials as an alternative to antibiotics, both due to the range of intrinsic variation in their mode of action, also due to almost unlimited variety of phages and their ability to evolve in situ to successfully deal with bacterial resistance. The FDA has approved bacteriophages as GRAS and allowed the application of phages as food additives in 2006, which is a significant boost to phage therapy research.

Nevertheless, the therapeutic application of phages still requires extensive studies, judiciously performed clinical trials, and importantly well-defined regulatory guidelines. Currently, phage therapy is encouraged in many parts of the world because policymakers consider growing MDR as a serious health problem. This awareness should further encourage researchers to study the biological properties of phages, which eventually increases their safety and efficacy. Furthermore, genetically modified phages could help to solve the issues of patent filing and as a result increase the interest of pharmaceutical and biotechnology companies to produce phage-products. Finally, cocktails of natural phages and genetically modified phages could open new perspectives for successful phage therapy in the future, particularly against the major challenge of Shigella and Shigella-like multidrug resistant bacteria.