Complexity, challenges and costs of implementing phage therapy

Future MicrobiologyVol. 17, No. 9 EditorialOpen AccessComplexity, challenges and costs of implementing phage therapySebastian Leptihn & Belinda LohSebastian Leptihn *Author for correspondence: E-mail Address: Leptihn@intl.zju.edu.cnhttps://orcid.org/0000-0002-4847-4622Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, PR ChinaUniversity of Edinburgh Medical School, Biomedical Sciences, College of Medicine & Veterinary Medicine, The University of Edinburgh, 1 George Square, Edinburgh, EH8 9JZ, UKSearch for more papers by this author & Belinda Loh **Author for correspondence: E-mail Address: belinda.loh@izi.fraunhofer.dehttps://orcid.org/0000-0003-1364-6911Fraunhofer Institute for Cell Therapy & Immunology (IZI), Department of Vaccines and Infection Models, Perlickstr. 1, Leipzig, 04103, GermanySearch for more papers by this authorPublished Online:11 Apr 2022https://doi.org/10.2217/fmb-2022-0054AboutSectionsPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack Citations ShareShare onFacebookTwitterLinkedInReddit Keywords: antimicrobial resistancebacterial infectionbacterial pathogensbacteriophagebiological antibioticsphage bankphage therapytherapeutic phagePhage therapy is a fascinating and promising concept of a directed process that happens naturally many billion times every second in every ecosystem, from our digestive tract to the wide oceans, where a sheer unimaginable number of bacteria are killed by viruses every day [1]. In human medicine, this elimination of bacteria is guided as viruses are being selected to target specific bacteria that cause a disease. Phages are first isolated and characterized for efficient elimination of a pathogen. A phage solution could then be administered to the patient, akin to how it was done in the past before the advent of antibiotics [2].Yet, when outlining a roadmap of the challenges of phage therapy in our day, one comes to realize that there are multiple roadblocks presented by our structured and organized world. One is the ambiguous character of bacteriophages being non-living entities, but are yet not pure biological macromolecular complexes (such as therapeutic proteins). This creates a challenge for regulatory bodies as legislative approval processes are complex, costly and time intensive for medical treatments or therapeutic compounds. In addition, as this approach uses ‘live viruses’ for treatment, patients might object to such therapies due to unfounded fears and the lack of information. However, in this opinion piece, we will focus on the scientific and medical hurdles of phage therapy as this is more tangible than the psychology of the human mind.Building a phage collectionWhen using the term ‘precision medicine’ in phage therapy, one could say it is a buzzword to distract from the challenges phage therapy presents, one of them being their extreme host specificity. Depending on the host bacteria, some phages are highly selective, infecting less than 1% of tested strains, while others kill around 5–15% of bacterial isolates. Most studies report low numbers of experimentally tested bacteria, not allowing for statistically significant conclusions of their findings when describing a phage’s host range [3]. What does this mean for the use of phages in clinical practice? Assuming the worst case scenario where a single phage would only infect 1% of clinical isolates, a hypothetical phage therapy center would require at least 300 phages at hand, ready for each and every pathogenic species when a patient comes in for treatment. To explain this number, we need to take a deeper look at academic and medical research. Fundamental research studies as well as applied clinical practice have demonstrated that using formulations containing multiple phages (with three or more, also known as phage cocktails) decrease the likelihood of phage resistance [4–6]. Resistance to phages occurs rapidly and is another bottleneck that impedes the implementation of phage therapy in the short term. Phage resistance can, among other mechanisms, be mediated by minute changes in genes that cause ever so slight alterations to the receptors on the bacterial surface. A collection of 300 phages seems reasonable at first glance. However, to allow for a margin of variation, and if phage resistance occurs despite the use of cocktails, possibly a second three-phage preparation may be required, increasing the number to 600. A concrete example of phage therapy is the famous treatment of Steffanie Strathdee’s husband who contracted an infection with a multidrug-resistant Acinetobacter baumannii strain [7,8]. After only 8 days of therapy, the strain developed resistance to two phage cocktails, each containing four phages, while the combination of phages with antibiotics was eventually successful and led to a full recovery of the patient. The administration of antibiotics, which had no effect on the original pathogen, was based on the growing evidence that virulence and antibiotic resistance often decreased in phage-resistant strains [9–11]. Antibiotic resensitization and the complex effects of synergy when using phages and antibiotics together deserves more attention in research. The antibiotic pill is not the cherry on the cocktail glass, but is likely to become a main ingredient of a cocktail in phage therapy.A collection of phages for the most notorious pathogens, those of the ESKAPE group only, would thus require a collection of 3600 phages. This does not sound like a Herculean task, but to establish such a phage bank, one would require thoroughly characterized phages. This includes confirming that they are lytic and that they contain no virulence factors, which could be done rapidly by genome analysis. Ideally, information regarding which receptors the phage targets on a host cell should also be available; this would prevent the use of phages that target the same receptor, thus reducing the number of points of attack. Another caveat is to avoid porins as receptors as mutations in these genes might not only abolish binding of the phage particles, but might also reduce uptake of certain antibiotics, thus leading to phage–antibiotic co-resistance [12]. However, many outer membrane proteins are also virulence factors, for example, facilitating attachment [13–16] and their mutation or genomic deletion as a mechanism of phage resistance may decrease virulence. Hence, fully characterized phages are required to make informed decisions in clinical practice.Phages ready for useThe next issue deals with the availability of the phages for immediate use. Producing a therapeutic phage formulation is tedious as molecules from the hosts, in particular lipopolysaccharides and other toxins that might elicit a negative response in the patient, have to be removed in order to obtain a highly pure and concentrated solution that can be administered. Producing such a solution is expensive and requires good manufacturing practice facilities. Would it be feasible to have multiple doses of such phage solutions ready at a center’s disposal? One argument that speaks against this is the stability of phages in solutions, which at present is the most commonly used administration method. In liquid, phage titers have been shown to decrease over time which is less than optimal for dosing. Some phages are intrinsically unstable that keeping a therapeutic solution of them would not be feasible. Here, encapsulation techniques might provide a solution. Embedding phages within a material shows promise not only for targeted delivery but also to keep phages intact for long durations. Lyophilization might be one option for long term storage of large quantities of phages, yet it is not possible for all phages. Here, research and empirical testing for each phage is crucial and many diverse methods have been developed in the past [17].A large library would also require the rapid identification of suitable phages which target the strain that causes the infection, a process that one might call ‘phage matching’. A possible but impractical approach is the manual screening of phages on bacterial culture plates. The implementation of more rapid techniques is feasible with current technology and could include pipetting robotic platforms or microfluidics.Standardization of phage therapeutics: synthetic phagesMany problems regarding the testing and approval of therapeutic phages may be overcome by a single approach: the use of a few fully characterized phages with modular structures containing replaceable, engineered receptor binding domains that allow the infection of multiple bacteria. ‘Building’ a one-size-fits-all phage would not be necessary, but constructing one where we only have to choose the receptor binding domains to generate an array of different phages, would prove valuable. Such a phage would ideally be stable in situ (i.e., the site of infection or in solution e.g., the blood stream) and can be incorporated in formulations for storage and targeted delivery, while the phage would also replicate fast with a large number of progeny from each life cycle. The possibility to engineer phages with receptor binding proteins that allow the virus to target a broader range of host bacteria has been shown in proof-of-principles studies [18,19]. This is where fundamental research goes hand in hand with applied studies: phage discovery allows the discovery of novel phages more suitable than T7 or T4, structural biology provides us with the information needed to design novel receptor binding proteins and bioinformatic advances including the revolution in structure prediction by AlphaFold 2.0 [20], will allow us to model fusion proteins using synthetic biology and genome engineering.Do we need phage therapy today?It is obvious that every available opportunity should be pursued, especially since antibiotics are becoming ineffective due to antimicrobial resistance (AMR) [21,22]. At the point of writing, medical doctors still have effective compounds at their disposal in most cases. Thus, an infection even with a highly resistant strain can be cured as they are rarely pan-resistant, meaning that none of the antibiotics have an effect. However, we should not approach AMR with the mindset that ‘we will cross that bridge when we come to it’. Instead, we should plan for the inevitable future.The above challenges are likely to be solved the more pressing AMR becomes. Once countries truly run out of antibiotics and fatalities are not limited to the old and immunocompromised, governments are likely to create the legal framework to allow the implementation of phage therapy. Financial incentives are currently low, as naturally occurring phages cannot be patented and approval of phages is extremely cost-intensive for human clinical use. Yet, instead of waiting for a slow ‘industrial evolution’ currently occurring with a few niche companies, governments should implement publicly funded bodies consisting of central phage banks and treatment centers to tackle the frightening perspective of slipping back into the era before antibiotics were available.Open accessThis work is licensed under the Creative Commons Attribution 4.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.Financial & competing interests disclosureThe authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.No writing assistance was utilized in the production of this manuscript.References1. 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To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.Financial & competing interests disclosureThe authors have no relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript. This includes employment, consultancies, honoraria, stock ownership or options, expert testimony, grants or patents received or pending, or royalties.No writing assistance was utilized in the production of this manuscript.PDF download