Talk:WikiJournal of Medicine/Phage Therapy

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WikiJournal of Medicine
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WikiJournal of Medicine is an open-access, free-to-publish, Wikipedia-integrated academic journal for Medical and Biomedical topics. <seo title=" WJM, WikiJMed, Wiki.J.Med., WikiJMed, Wikiversity Journal of Medicine, WikiJournal Medicine, Wikipedia Medicine, Wikipedia medical journal, WikiMed, Wikimedicine, Wikimedical, Medicine, Biomedicine, Free to publish, Open access, Open-access, Non-profit, online journal, Public peer review "/>

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Article information

Authors: Joana Azeredo[a][i] ORCID iD.svg, Jean-Paul Pirnay[b] ORCID iD.svg, Diana Priscila Pires[a] ORCID iD.svg, Mzia Kutateladze[c] ORCID iD.svg, Krystyna Dabrowska[d] ORCID iD.svg, Rob Lavigne[e] ORCID iD.svg, Bob G Blasdel[f] ORCID iD.svg

Joana Azeredo; Jean-Paul Pirnay; Diana Priscila Pires; Mzia Kutateladze; Krystyna Dabrowska; Rob Lavigne; Bob G Blasdel (15 December 2021), "Phage Therapy", WikiJournal of Medicine, WikiJournal of Medicine, 8 (1): 4, doi:10.15347/WJM/2021.004, ISSN 2002-4436, Wikidata Q100400597





 


Plagiarism check

Artículo bueno.svg Pass. Report from WMF copyvios tool: Multiple sentence sections were found to overlap with previous publications. The majority of these are trivial (e.g. "the Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Wrocław") or hard-to-paraphrase representations of ideas (e.g "To investigate the safety, tolerability, and preliminary efficacy of ascending multiple intranasal doses of") and do not constitute plagiarism. However, paragraph 11 of Clinical experience and randomized controlled trials is probably too closely paraphrased from the source (overlap). Even though the source is CC-BY, it either needs to be explicitly attributed or some additional editing will be useful to avoid too closely paraphrasing. T.Shafee(Evo﹠Evo)talk 02:15, 10 August 2020 (UTC)[reply]

Editor comments


Comments by Thomas Shafee ORCID iD.svgWikidata-logo.svgWikimedia Community Logo.svg ,

These editorial comments were submitted on , and refer to this previous version of the article

Overall the submission is in great shape and ready to be sent for review.

Minor admin

Where possible, please include author ORCID numbers by editing the top section.

Optional suggestions

It might be worthwhile including schematics or diagrams for a few concepts, either by generating a new image or reusing a creative commons licensed one. For example, for routes of administration (e.g. Fig6 from this CC-BY paper), and/or combined therapies and other approaches (somewhat akin to Fig 1 from this paper).

Peer review 1

reviewer-annotated pdf file.
reviewer-annotated pdf

Review by Felix Bröcker Wikidata-logo.svg ,

These assessment comments were submitted on , and refer to this previous version of the article

The article is overall well-written and includes the relevant information and citations. The language could be improved with the help of a native speaker. I included my suggestions for corrections/improvements in the attached word file as comments.

Response

All suggestions were included in the text with the exception of :

Reviewer’s comment 75: It might be helpful to include some information here about the experience of GMP manufacturing in the PhagoBurn project – as far as I know a lot has been learned but there were some issues with low activity of the GMP manufactured phages(?)

Answer: There were indeed stability issues with the PhagoBurn GMP phage product (as reported in the LID paper), but no details as to what caused these issues have been officially released (e.g. in publications) by Pherecydes, so difficult to elaborate on this.

Reviewer’s comment 90: No data on efficacy?

Answer: In fact no, because we are reporting a safety assay

Peer review 2 & 3

Note: Peer reviewers 2 & 3 shared the task of reviewing the submission, commenting on different aspects of the work.

reviewer-annotated pdf file.
reviewer-annotated pdf

Review by Ry Young ORCID iD.svgWikidata-logo.svg , Center for Phage Technology, Texas A&M University, USA

These assessment comments were submitted on , and refer to this previous version of the article

Comments submitted in attached PDF as annotations.

Replacement text suggestions for edits of WikiJournal article on phage therapy [see attached PDF]

replacement paragraph A

...companies. In an era lacking even a basic understanding of the nature of bacteriophages, phage preparations were marketed as treatments of implausible ailments such as gallstones, herpes, kidney stones and various cancers. Commercial preparations even from major pharmaceutical companies were found to be devoid of phages active against the target pathogens (ref). Sometimes these defects were due to practical considerations, like deleterious sterilization procedures or inactivation in storage. However, some phage preparations were targeted against the wrong pathogen or were restricted to only a limited set of strains of the right pathogen. Nevertheless, even decades after the 1934 Eaton/Bayne-Jones report, phage therapy was still in sporadic use in the West into the 1950s and 1960s, and only ended in France in the 1990s.

reference =

replacement paragraph B

How do phages work?

Many types of phages are known but the phages used for therapeutics belong to the order Caudovirales, by far the most abundant type. These phages have double-strand DNA (dsDNA); the size of the genomic DNA (gDNA) ranges from ~ 15 kb to >700 kb (kb = 1000 base pairs, or about one typical gene). Caudovirales means “tailed viruses”, because the gDNA is encapsidated in a protein “head” with a tail (see Figure 1) that, in general, serves as an apparatus for recognizing a feature, or “receptor”, on the surface of a particular bacterial host. After the virion binds to this receptor, the gDNA is ejected through the tail apparatus into the cytoplasm of the bacterial cell. The viral genes are then expressed by the host machinery, leading to a program of DNA replication, morphogenesis of progeny virions, and, eventually, lysis of the cell. As an example, typical phages of E. coli release 100 to 300 progeny virions after an infection cycle of 15 to 45 minutes. This rate of multiplication, unmatched in biology, means that, if sufficient host cells and nutrients are present, one phage particle can generate billions in just a few hours. In addition to this lytic, vegetative pathway, some phages, designated as “temperate” or “lysogenic”, have the capability of shutting off the infection cycle and assuming a dormant form. This form, called a prophage, can integrate into the host chromosomal DNA or form a self-replicating plasmid. The host cell carrying a prophage, called a “lysogen”, has the advantage that it is immune to infections of the same phage. However, although the lysogenic state can last indefinitely, the prophage can also activate spontaneously or after stress applied to the bacterial host. This activation, known as “lysogenic induction” results in viral replication, virion morphogenesis and lysis of the host, just as in the normal lytic cycle.

paragraph C (to be inserted after “...or cell damage78.” in the section Safety aspects.

Recently, however, it was reported that filamentous temperate phages of P. aeruginosa can be endocytosed into human and murine leukocytes, resulting in transcription of the phage DNA. In turn, the product RNA triggers maladaptive innate viral pattern-recognition responses and thus inhibits the immune clearance of the bacteria. [ref PMID= 30923196] Whether this also applies to dsDNA phages like the Caudovirales has not yet been established; this is obviously an important question to be addressed as it may affect the overall safety of phage therapy.

para D (to substiute for boxed para in Safety section:

....phage therapy. It is important to note that many phages, especially temperate phages, carry genes that can affect the pathogenicity of the host. Even the famous lambda, a temperate phage of the E. coli K-12 laboratory strain, carries two genes that provide potential virulence benefits to the lysogenic host, one that increases intestinal adherence and the other that confers resistance to complement killing in the blood. For this reason, temperate phages are generally to be avoided as candidates for phage therapy, although in some cases, the lack of lytic phage candidates and emergency conditions may make such considerations moot (ref PMID = 31068712). Another potential problem is generalized transduction, a term for the ability of some phages to transfer bacterial DNA from one host to another. This occurs because the systems for packaging of the phage DNA into capsids can mistakenly package host DNA instead. Indeed, with some well-characterized phages, up to 5% of the virus particles contain only bacterial DNA; thus in a typical lysate, the entire genome of the propagating host is present in more than a million copies in every milliliter. For these reasons, it is imperative that any phage to be considered for therapeutic useage should be subjected to thorough genomic analysis and tested for the capacity for generalized transduction.

Response

All suggestions were included in the text


reviewer-annotated pdf file.
reviewer-annotated pdf

Review by Jason Gill ORCID iD.svgWikidata-logo.svg , Center for Phage Technology, Texas A&M University, USA

These assessment comments were submitted on , and refer to this previous version of the article

Comments submitted in attached PDF as annotations. My comments are confined to pages 4-13 of the attached pdf.

Response

All suggestions were included in the text

Peer review 4

reviewer-annotated pdf file.
reviewer-annotated pdf

Review by Steffanie Strathdee ORCID iD.svgWikidata-logo.svg , University of California San Diego

These assessment comments were submitted on , and refer to this previous version of the article

First para:

“This therapeutic approach emerged in the beginning of the 20th century but was rapidly surpassed by the use of antibiotics.” Comment: I suggest adding in most parts of the world because antibiotics were slow to penetrate Eastern Europe and the Soviet Union since penicillin was treated as a war secret. Source: Lax, Eric. The Mold in Dr. Florey’s Coat: The Story of the Penicillin Miracle . New York: Henry Holt, 2004.

Response

Added “in most part of the world.” Notably, the popular and even academic literature on this subject is plagued with inaccurate assumptions made by non-experts. In the immediate post-war period, several pilot plants for the production of penicillin using deep fermentation techniques were designed and shipped to Eastern Europe through the UNRRA framework. Thus, from the early days of global antibiotic use, the Soviet Union did in fact have access to penicillin production, related beta-lactams as they were developed, and detailed knowledge of deep fermentation techniques as they existed in the ‘40s. However, while Soviet engineers were able to optimize those plants to produce 24/7, they were both unable to successfully replicate them and politically unable to acquire necessary infrastructure for this from the West. This meant that access to beta-lactams beyond the maximum capacity of these plants, as well as more advanced antibiotics as they were developed, required the use of limited foreign currency. It would thus perhaps be more accurate to say that antibiotics were not available in quantities considered necessary for a functional health system in the West.

History of Phage Therapy

“Bacteriophage were first described by Frederick Twort in 1915.[1]” Comment: True but Twort did not recognize the ‘bacteriolytic agent’ as a virus, so it is misleading to say Twort ‘described’ it. I suggest rephrasing to reflect that like others before him, including Hankin in 1896, Twort witnessed bacteriophage activity in 1915 but thought it could be an enzyme or a virus. Source: Summers, W. C. “Bacteriophage Therapy.” Annual Review of Microbiology 55 (2001): 437– 451.

Response

Added “In 1915, Frederick Twort, a medically trained bacteriologist from England, reported a bacteriolytic phenomenon and advanced the hypothesis that it may be due to a virus. (include ref from twort’s paper: Twort, F. W. (1915). "An Investigation on the Nature of Ultra-Microscopic Viruses". The Lancet. 186 (4814): 1241–1243. doi:10.1016/S0140-6736(01)20383-3.

Add: d’Herelle is widely acknowledged as the discoverer of the bacteriophage. He and his wife derived the name, derived from the Greek word “phageîn”, meaning ‘to devour’. Source: Summers, W. C. “Félix Hubert d’Hérelle ( 1873– 1949): History of a Scientific Mind.” Bacteriophage 6, no. 4 (2016): e1270090.

Response

This is still a controversial issue, so we decided not to mention.

“However, with the sober hindsight provided by a deeply critical and widely read three-part report by two physicians Eaton and Bayne-Jones in 1934[7], it became clear that this period was largely characterized by inconsistent results, unrealistic claims, and unreliable companies.” Comment: This is accurate but it is worth adding the sources for each of the three reports. Also, it should be noted that these reports are now regarded as highly biased by today’s standards. First, one of the authors was d’Herelle’s replacement after he was fired from Yale and was likely influenced by this. Second, only the first 100 publications were reviewed, no non-English publications were included, and these were primarily negative reports. Source: Summers, W. C. “The Strange History of Phage Therapy.” Bacteriophage 2, no. 2 (April 1, 2012): 130– 133.

Response

This is a very interesting point, but maybe not relevant for a larger audience, therefore we decided not to include. Notably, the review series was not exclusively critical, being quite positive about various phage treatments for staph infections. However, even if the authors were motivated by a hypothetical personal bias, they lay out a rigorous, convincing, and influential case for the ineffectiveness of most phage therapy as it then existed in the Anglophone world.

This section should include mention that phage continued to be studied as tools to uncover life processes. Phage were instrumental in the advent of genetic engineering, cancer biology and the discovery of CRISPR. However, at least in the West, the application of phage for phage therapy was relegated to the backburner due to the advent of penicillin and subsequent antibiotics and the three damning reports already referred to. Source: Summers, W. C. “The Strange History of Phage Therapy.” Bacteriophage 2, no. 2 (April 1, 2012): 130– 133.

Response

Added. “Phages were instrumental in the advent of genetic engineering, cancer biology and the discovery of CRISPR.”

Phage therapy in the former Soviet Union

This section is accurate but there are a few important omissions.

I suggest mentioning that the geopolitical bias against Russia around the time of WWII contributed to disdain regarding phage therapy among researchers and clinicians in the West, for many decades. Source: Summers, W. C. “The Strange History of Phage Therapy.” Bacteriophage 2, no. 2 (April 1, 2012): 130– 133.

I suggest spelling out RCT as “randomized clinical trial”. Comment: In referring to the absence of such trials, it is worth mentioning that since phage therapy is largely considered standard of care in the Republic of Georgia and Poland, it could be argued that conducting randomized trials with a control group would be considered unethical in these settings.

Response

Randomized Control Trial was spelled out. The comment was not included because, in fact, the current generation of MDs do not consider phage therapy a standard of care even in Georgia and Poland. Although this has been widely repeated, it has not been generalizably true for some time.

It is worth noting that phage therapy in the Republic of Georgia and Poland typically relies on crude phage lysate, and as a result intravenous phage therapy is not usually done in these settings.

Response

It is true that conventional phage preparations of the Eliava Institute (such as Pyophage and Intestiphage) are not presently formulated for intravenous use, in fact they are prescribed as oral treatments. However, phage products for phages infecting gram-positives have historically been routinely produced to these standards and in the late 1980s the Eliava Institute briefly made phage products against gram negative bacteria that were specifically formulated for intravenous use in response to an epidemic in Moscow. More recently, the Eliava Institute also now produces more purified products (e.g. phage sb-1), which would be likely to meet the standards currently applied by the FDA for intravenous use of IND phage products. So, this cannot be generalised.

The intravenous formulation of phage products has been readily achievable globally by groups with genuine expertise in the pharmacology of biologicals for nearly a century. This may have been a notable achievement for an academic research lab in an extreme circumstance, but we do not feel that it otherwise meets the notability criteria of Wikipedia.

Bacteriophage Application in Phage Therapy

This section is largely accurate with one possible exception:

“In this case, if the bacterial pathogen is not sensitive to the phages in the mixture, it will not cause any adverse reaction to the patient and will be easily cleared from the body.” Comment: While adverse reactions have not been observed, it is possible that treating with phage that are not matched to the bacterial pathogen in question could disrupt the microbiome. Therefore this sentence should be tempered to reflect that in such cases “adverse reactions have not been documented”.

Response

Rephrased to “it will most probably not cause any serious adverse reaction to the patient”

This section would also be strengthened by adding a few details.

Phage are cleared from the human body by the reticuloendothelial system, primarily the liver and the spleen. Source: Merril, C. R., D. Scholl, and S. L. Adhya. “The Prospect for Bacteriophage Therapy in Western Medicine.” National Review of Drug Discovery 2, no. 6 (Jun 2003): 489– 497.

Response

Added “reticuloendothelial system, primarily the liver and the spleen”.

“Phages also can be used as a mono-phage preparation or in combination with other similar or tangentially related, even rather difficult phages in mixture (again, a "cocktail").” Comment: True, but it is important to note that phage cocktails are preferred, which target different receptors in an attempt to thwart the ability of the bacterial host to generate resistance. Source: Schooley RT, Strathdee S. Treat phage like living antibiotics. Nat Microbiol. 2020 Mar;5(3):391-392. doi: 10.1038/s41564-019-0666-4.

Response

This concern is already addressed in the parts “Bacteriophage application in Phage Therapy” and “Development of resistance”. Nevertheless, it is not certain if cocktails are really the best option in view of avoiding phage resistance. There is no relevant evidence concretely demonstrating this. In vitro, it was shown that resistance to a cocktail will inevitably appear (later than against single phages), but that this resistance is more generic and is bound to compromise further use of phages. Using single phages serially, switching before resistance ensues, could be more interesting. But, this is based on preliminary in vitro results. See:

Hall, A. R., De Vos, D., Friman, V. P., Pirnay, J. P., & Buckling, A. (2012). Effects of sequential and simultaneous applications of bacteriophages on populations of Pseudomonas aeruginosa in vitro and in wax moth larvae. Applied and environmental microbiology, 78(16), 5646-5652.

Advantages of Phage therapy

A few edits:

3. “at the site of infection…” Comment: add an ‘s’ after ‘site’ since there can be more than one site of infection, especially if the infection is systemic.

Response

Done

5. Sources should be added regarding biofilm activity. There are now a number of case reports where phage therapy was successfully used to treat infected hardware (e.g., LVADs, prosthetic joint infections). Sources: Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S, Schooley RT. Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States. Open Forum Infect Dis. 2020 Aug 27;7(9):ofaa389. doi: 10.1093/ofid/ofaa389.

Cano EJ, Caflisch KM, Bollyky PL, Van Belleghem JD, Patel R, Fackler J, Brownstein MJ, Horne B, Biswas B, Henry M, Malagon F, Lewallen DG, Suh GA. Phage Therapy for Limb-threatening Prosthetic Knee Klebsiella pneumoniae Infection: Case Report and In Vitro Characterization of Anti-biofilm Activity. Clin Infect Dis. 2020 Jul 23:ciaa705. doi: 10.1093/cid/ciaa705.

Response

To address this comment we added: “There are now a number of case reports where phage therapy was successfully used to treat biofilm associated infections (refs doi. 10.3390/antibiotics9070377; doi: 10.1093/cid/ciaa705, doi: 10.1093/ofid/ofaa389)

Add 8. Phage can be synergistic with antibiotics. Sources: Schooley, R. T., B. Biswas, J. J. Gill, A. Hernandez- Morales, J. Lancaster, L. Lessor, J. J. Barr, et al. “Development and Use of Personalized Bacteriophage- Based Therapeutic Cocktails to Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection.” Antimicrobial Agents and Chemotherapy. 2017 Sep 22;61(10):e00954-17. doi: 10.1128/AAC.00954-17.

Kortright KE, Chan BK, Koff JL, Turner PE. Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria. Cell Host Microbe. 2019 Feb 13;25(2):219-232. doi: 10.1016/j.chom.2019.01.014.

Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S, Schooley RT. Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States. Open Forum Infect Dis. 2020 Aug 27;7(9):ofaa389. doi: 10.1093/ofid/ofaa389.

Segall AM, Roach DR, Strathdee SA. Stronger together? Perspectives on phage-antibiotic synergy in clinical applications of phage therapy. Segall AM, Roach DR, Strathdee SA. Curr Opin Microbiol. 2019 Oct;51:46-50. doi: 10.1016/j.mib.2019.03.005.

Response

The reference doi: 10.1016/j.mib.2019.03.005 was added. The other articles are not specifically addressing the still putative synergy between antibiotics and phages.

Current Challenges to Phage Therapy

1. Add a sentence that reflects that this challenge can conceivably be overcome with the development of a large, ever-expanding phage library that maps on to a repository of bacterial pathogens.

Response

This is an interesting view but not generally accepted as commercially sustainable and is rather speculative for an encyclopaedic article

4. Add that bacterial resistance to phages can be overcome by developing a second generation phage cocktail that targets the bacterial mutant, as reported in several case reports. Sources: Schooley, R. T., B. Biswas, J. J. Gill, A. Hernandez- Morales, J. Lancaster, L. Lessor, J. J. Barr, et al. “Development and Use of Personalized Bacteriophage- Based Therapeutic Cocktails to Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection.” Antimicrobial Agents and Chemotherapy. 2017 Sep 22;61(10):e00954-17. doi: 10.1128/AAC.00954-17.

Response

Added “bacterial resistance to phages can be overcome by developing a second generation phage cocktail that targets the bacterial mutant”

Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S, Schooley RT. Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States. Open Forum Infect Dis. 2020 Aug 27;7(9):ofaa389. doi: 10.1093/ofid/ofaa389.

6. “Current protocols are based on long-term experience of doctors from FSU countries, or currently, individual doctors who are selecting the protocols by their individual choice and opinion.” Comment: This was true until recently as there are an increasing number of protocols being published by Western researchers/physicians.

Response

Rephrased to make it more clear. Nevertheless, the protocols, which are recently published by Western physicians, are most often 100% based on FSU protocols whether this is adequately credited or otherwise

Sources: Schooley, R. T., B. Biswas, J. J. Gill, A. Hernandez- Morales, J. Lancaster, L. Lessor, J. J. Barr, et al. “Development and Use of Personalized Bacteriophage- Based Therapeutic Cocktails to Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection.” Antimicrobial Agents and Chemotherapy. 2017 Sep 22;61(10):e00954-17. doi: 10.1128/AAC.00954-17.

Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S, Schooley RT. Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States. Open Forum Infect Dis. 2020 Aug 27;7(9):ofaa389. doi: 10.1093/ofid/ofaa389.

Cano EJ, Caflisch KM, Bollyky PL, Van Belleghem JD, Patel R, Fackler J, Brownstein MJ, Horne B, Biswas B, Henry M, Malagon F, Lewallen DG, Suh GA. Phage Therapy for Limb-threatening Prosthetic Knee Klebsiella pneumoniae Infection: Case Report and In Vitro Characterization of Anti-biofilm Activity. Clin Infect Dis. 2020 Jul 23:ciaa705. doi: 10.1093/cid/ciaa705.

6. Spell out “FSU”

Response

FSU (Former Soviet Union) was spelled out

8. “In order to prepare therapeutic phages for treatment, it is crucial to select virulent phages and to "train" them to enhance their lytic activity, stability and host range.” Comment: This is an over-generalization as natural lytic phage that have not been trained have been successfully used for phage therapy. I suggest this statement be tempered by saying “which may need to be ‘trained…”

Response

The sentence has been deleted for clarity

Phage Therapy Approaches:

This section omits a number of key points.

First, it should be made clear up front that there are three types of phage preparations that can be used to treat bacterial infections: 1) natural; 2) genetically modified; 3) synthetic.

Response

In this section we described two phage therapy approaches: “One size fits all” and “precision medicine” that can be performed with both natural and engineered phages. Additionally both can be prepared synthetically (in cell free transcription / translation systems). This is already clarified through several parts of the article, so we do not see the need to add upfront this section.

This section should also mention work by Chan and Turner that uses phage to re-sensitize bacterial isolates to antibiotics. In this way, phage is used indirectly, which is a departure from approaches that use lytic phage to directly kill the bacterial pathogen. Sources: Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Phage treatment of an aortic graft infected with Pseudomonas aeruginosa. Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Evol Med Public Health. 2018 Mar 8;2018(1):60-66. doi: 10.1093/emph/eoy005

Response

This is in vitro work and thus the relevance is still perhaps too speculative to be authentically appropriate for a general audience. The considered phage resistant bacterial isolates were produced in vitro (in conditions where virulence and antibiotic resistance are not necessary) and it is unlikely that these phage resistant mutants will be selected in vivo (because, indeed, not virulent and antibiotic sensitive). It is highly likely that in vivo phage therapy will select for other, virulent, antibiotic resistant phage resistant mutants. They re-sensitise bacteria that are likely not relevant in actual in vivo phage therapy. Therefore, we did not include this work.

Kortright KE, Chan BK, Koff JL, Turner PE. Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria. Cell Host Microbe. 2019 Feb 13;25(2):219-232. doi: 10.1016/j.chom.2019.01.014.

This section should also mention the potential for natural phages to be genetically modified to optimize aspects of phage lifestyle. Indeed, this section should also refer to the first in human use of genetically modified phage to treat a bacterial infection. Source: Dedrick R et al. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nat Med . 2019 May;25(5):730-733. doi: 10.1038/s41591-019-0437-z. Epub 2019 May 8.

Response

This study has already been mentioned in the section “biotechnological advances in phage therapy”

I suggest that this be added prior to the sentence below.

“In the future, synthetic biology approaches (e.g. structure-guided design) could generate phages with more predictable and extended host ranges.”

Additional Comments: There are several biotech companies that are already conducting early stage clinical trials of genetically modified phage or even synthetic phage to treat bacterial infections in animals and humans, so this should be mentioned, as the field is moving rapidly.

Response

It is true that some companies are thinking of this, but not sure what can be mentioned formally without consent of those companies (or with references).

This section also describes the Phagoburn trial in an exceptionally positive light, when this trial suffered from a number of shortcomings. It would behoove the readers if these shortcomings could be described so this section is more balanced.

Response

Not sure it is that positive. It clearly mentions the instability problems and the low efficacy, as compared to the control.

The following section is opinion and not entirely correct in this reviewer’s opinion: “However, this concept is not compatible with most (Western) medicinal product (drugs in the US) development and licensing pathways, which require several years and millions of euros (dollars) to complete, even when considering abbreviated pathways, and this for every phage in the bank. Moreover, it is very difficult to imagine how existing medicinal product pathways will be able to cater for the ad hoc adaptation of banked phages, or the application of newly acquired or isolated (from the environment) phages.” Comment: At least one phage company in the US has successfully obtained FDA approval and patented their phage bank, allowing them to personalize phage cocktails to bacterial isolates using any phage in the bank, for individual cases and outbreaks. Source: https://www.businesswire.com/news/home/20201118005567/en/FDA-Clears-Expanded-Access-IND-for-APT%E2%80%99s-PhageBank%E2%84%A2-Therapy-to-Combat-COVID-19-related-Bacterial-Infections

Response

This part was rephrased. Nevertheless, no phage product has possessed marketing authorization from the FDA since this was removed from SPL in 1994. The plans for seeking marketing authorization that have been described by APT are remarkably speculative for the generalist audience of this encyclopaedia article and would also be difficult to accurately describe without being either inappropriately critical or inappropriately uncritical.

Further, the para that begins with “It might be wise to develop both options…” mentions only the Eliava institute, but a growing number phage therapy centers, companies and programs in North America now operate using a similar approach. Sources: https://medschool.ucsd.edu/som/medicine/divisions/idgph/research/center-innovative-phage-applications-and-therapeutics/Pages/default.aspx https://www.bcm.edu/research/labs-and-centers/research-centers/tailor

Response

Added : ”a growing number phage therapy centers, companies and programs in North America now operate using a similar approach (e.g. Center for Innovative Phage Applications and Therapeutics)”

Phage Therapy against Infectious Biofilms

This section is mostly accurate but the statement “the total eradication of biofilms seems to be a nearly impossible task” contradicts the next section where it is stated that “ some combinations of phages and antibiotics have been shown to almost eradicate bacterial biofilms”. Indeed, the former sentence should be omitted since there are several cases in which phage therapy was successfully used in vivo to treat biofilms on infected hardware devices in humans: Sources: Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S, Schooley RT. Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States. Open Forum Infect Dis. 2020 Aug 27;7(9):ofaa389. doi: 10.1093/ofid/ofaa389.

Cano EJ, Caflisch KM, Bollyky PL, Van Belleghem JD, Patel R, Fackler J, Brownstein MJ, Horne B, Biswas B, Henry M, Malagon F, Lewallen DG, Suh GA. Phage Therapy for Limb-threatening Prosthetic Knee Klebsiella pneumoniae Infection: Case Report and In Vitro Characterization of Anti-biofilm Activity. Clin Infect Dis. 2020 Jul 23:ciaa705. doi: 10.1093/cid/ciaa705.

Response

Replaced “The total eradication of biofilms is difficult to achieve”

Phage-Antibiotic Combination

This section is missing a number of case reports where antibiotics and phage had demonstrated synergy in treating human bacterial infections. Sources: Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Phage treatment of an aortic graft infected with Pseudomonas aeruginosa. Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Evol Med Public Health. 2018 Mar 8;2018(1):60-66. doi: 10.1093/emph/eoy005

Kortright KE, Chan BK, Koff JL, Turner PE. Phage Therapy: A Renewed Approach to Combat Antibiotic-Resistant Bacteria. Cell Host Microbe. 2019 Feb 13;25(2):219-232. doi: 10.1016/j.chom.2019.01.014.

Schooley, R. T., B. Biswas, J. J. Gill, A. Hernandez- Morales, J. Lancaster, L. Lessor, J. J. Barr, et al. “Development and Use of Personalized Bacteriophage- Based Therapeutic Cocktails to Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection.” Antimicrobial Agents and Chemotherapy. 2017 Sep 22;61(10):e00954-17. doi: 10.1128/AAC.00954-17.

Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S, Schooley RT. Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States. Open Forum Infect Dis. 2020 Aug 27;7(9):ofaa389. doi: 10.1093/ofid/ofaa389. Early clinical experience of bacteriophage therapy in 3 lung transplant recipients.

Aslam S, Courtwright AM, Koval C, Lehman SM, Morales S, Furr CL, Rosas F, Brownstein MJ, Fackler JR, Sisson BM, Biswas B, Henry M, Luu T, Bivens BN, Hamilton T, Duplessis C, Logan C, Law N, Yung G, Turowski J, Anesi J, Strathdee SA, Schooley RT.Am J Transplant. 2019 Sep;19(9):2631-2639. doi: 10.1111/ajt.15503.

Response

Some references were added, however the majority of cited work is not specifically related to antibiotic/phage synergism.

Biotechnical Advances in Phage Therapy

“The success of phage therapy is highly dependent on the safety of phage preparations…” Comment: The authors have previously stated that treatment with natural phages is safe, which this reviewer agrees with. This sentence should be modified to make it explicit that this refers to genetically modified and synthetic phage preparations.

Response

There is a difference between safety of phages and safety of phage preparations, here we are highlighting the aspects related to the phage preparations.

“However, no strictly virulent phages have been found for some bacterial species such as C. difficile,[36] which might limit the use of phage therapy in some fastidious bacteria.” Comment: This may be the case for natural phages, but this sentence should be modified to indicate that in such cases genetically modified and synthetic phage preparations could overcome this limitation.

Response

Rephrased: might limit the use of phage therapy, with natural phages, in some fastidious bacteria

“A group of phage researchers have set some quality and safety requirements for sustainable phage products. One of them is that phages encoding for lysogeny, virulence factors or antibiotic resistance should not be considered suitable for therapy.[35] Comment: Revise this sentence to indicate that more than one group has developed guidelines for phage therapy. Sources: Philipson CW, Voegtly LJ, Lueder MR, Long KA, Rice GK, Frey KG, Biswas B, Cer RZ, Hamilton T, Bishop-Lilly KA. : Characterizing Phage Genomes for Therapeutic Applications. Viruses. 2018 Apr 10;10(4):188. doi: 10.3390/v10040188.PMID: 29642590

Luong T, Salabarria AC, Edwards RA, Roach DR. : Standardized bacteriophage purification for personalized phage therapy. Nat Protoc. 2020 Sep;15(9):2867-2890. doi: 10.1038/s41596-020-0346-0. Epub 2020 Jul 24.PMID: 32709990

Response

Rephrased to “the Phage Research community has begun to …”

“…several purifications methods have been developed and optimized to ensure phages' safety.” Add an additional source: Luong T, Salabarria AC, Edwards RA, Roach DR. : Standardized bacteriophage purification for personalized phage therapy. Nat Protoc. 2020 Sep;15(9):2867-2890. doi: 10.1038/s41596-020-0346-0. Epub 2020 Jul 24.PMID: 32709990

“The tremendous potential of phage engineering was already proved in clinical practice as synthetic phages were successfully used to treat a 15-year-old patient with a disseminated drug-resistant Mycobacterium abscessus infection.[41] Comment: Correct this sentence as this case involved genetically modified phage, NOT synthetic phage. Also, as noted earlier, this was a ‘first in human’ case, and the first time a human Mycobacterium infection was treated with phage therapy, which lends hope that Mycobacterium tuberculosis, the world’s most serious bacterial pathogen, could one day be treated with phage therapy.

Response

Changed to engineered phages

Clinical Experience and Randomized Trials

This section would benefit from adding a source that refers to how clinical trials of phage preparations should be treated as ‘living antibiotics”. Source: Schooley RT, Strathdee S. Treat phage like living antibiotics. Nat Microbiol. 2020 Mar;5(3):391-392. doi: 10.1038/s41564-019-0666-4.

Response

We are not sure where in this section we could include the source.

This section should also note that NIH has funded two clinical trials, signaling increasing interest in phage therapy in the US. Sources: https://www.nih.gov/news-events/news-releases/nih-renews-funding-antibacterial-resistance-leadership-group http://outbreaknewstoday.com/bacteriophage-therapy-intralytix-receives-multimillion-dollar-grant-for-shigella-preparation-93652/

“The pharmaceutical industry has so far demonstrated little to no interest in phage therapy.” Comment: This is no longer true so this sentence should be tempered. Janssen has invested $800 million USD in a genetically modified phage approach being used by Locus Biosciences.

Response

This paragraph was rephrased.

This section should also note that in 2018, based on experience with a growing number of successful patients treated with phage therapy, the first dedicated phage therapy center was launched in the US. Sources: https://medschool.ucsd.edu/som/medicine/divisions/idgph/research/center-innovative-phage-applications-and-therapeutics/Pages/default.aspx

Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S, Schooley RT. Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States. Open Forum Infect Dis. 2020 Aug 27;7(9):ofaa389. doi: 10.1093/ofid/ofaa389.

Additionally, a phage therapy center has been operating in Belgium which deserves mention. Source: https://pubmed.ncbi.nlm.nih.gov/30884879/

Response

Added “It should be highlighted that in 2018, based on experience with a growing number of successful patients treated with phage therapy, the first dedicated phage therapy center was launched in the US. (doi: 10.1093/ofid/ofaa389), additionally a phage therapy center has been operating in Belgium https://pubmed.ncbi.nlm.nih.gov/30884879/”

Development of Resistance to Phages

This section should mention that bacterial resistance to phages can be overcome by developing a second generation phage cocktail that targets the bacterial mutant, as reported in several case reports. Sources: Schooley, R. T., B. Biswas, J. J. Gill, A. Hernandez- Morales, J. Lancaster, L. Lessor, J. J. Barr, et al. “Development and Use of Personalized Bacteriophage- Based Therapeutic Cocktails to Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection.” Antimicrobial Agents and Chemotherapy. 2017 Sep 22;61(10):e00954-17. doi: 10.1128/AAC.00954-17.

Aslam S, Lampley E, Wooten D, Karris M, Benson C, Strathdee S, Schooley RT. Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States. Open Forum Infect Dis. 2020 Aug 27;7(9):ofaa389. doi: 10.1093/ofid/ofaa389.

Response

This comment was already addressed before

Regulatory Aspects

General Comment: At least one phage company in the US has successfully obtained FDA approval and patented their phage bank, allowing them to personalize phage cocktails to bacterial isolates using any phage in the bank, for individual cases and outbreaks. Source: https://www.businesswire.com/news/home/20201118005567/en/FDA-Clears-Expanded-Access-IND-for-APT%E2%80%99s-PhageBank%E2%84%A2-Therapy-to-Combat-COVID-19-related-Bacterial-Infections

Response

This comment was also addressed before

Additional notes in attached PDF

Post-review editorial comments


Comments by Thomas Shafee ORCID iD.svgWikidata-logo.svgWikimedia Community Logo.svg ,

These editorial comments were submitted on , and refer to this previous version of the article

Following author responses to reviewer comments R4 had these additional comments (paraphrased):

R4: Current Challenges to Phage Therapy - Add a sentence that reflects that this challenge can conceivably be overcome with the development of a large, ever-expanding phage library that maps on to a repository of bacterial pathogens.
Author Response This is an interesting view but not generally accepted as commercially sustainable and is rather speculative for an encyclopaedic article
R4: Phage Therapy Approaches - This section should also mention work by Chan and Turner that uses phage to re-sensitize bacterial isolates to antibiotics. In this way, phage is used indirectly, which is a departure from approaches that use lytic phage to directly kill the bacterial pathogen. Sources: Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Phage treatment of an aortic graft infected with Pseudomonas aeruginosa. Chan BK, Turner PE, Kim S, Mojibian HR, Elefteriades JA, Narayan D. Evol Med Public Health. 2018 Mar 8;2018(1):60-66. doi: 10.1093/emph/eoy005
Author Response This is in vitro work and thus the relevance is still perhaps too speculative to be authentically appropriate for a general audience. The considered phage resistant bacterial isolates were produced in vitro (in conditions where virulence and antibiotic resistance are not necessary) and it is unlikely that these phage resistant mutants will be selected in vivo (because, indeed, not virulent and antibiotic sensitive). It is highly likely that in vivo phage therapy will select for other, virulent, antibiotic resistant phage resistant mutants. They re-sensitise bacteria that are likely not relevant in actual in vivo phage therapy. Therefore, we did not include this work.

To gain additional input on the disagreement, I checked with the other reviewers and received these responses (paraphrased):

R1:Regarding point 1 there are various companies investing in phage banks (see a recent review here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901949/) so I would agree with Reviewer 4 here. There definitely is commercial interest in developing such phage banks.
R1:Regarding the second point: The authors already describe approaches that are mainly backed by in vitro studies, such as the potential use of phages against biofilms. Therefore, I don't see why phage-mediated sensitization to antibiotics should not be mentioned. I suggest to include a sentence or two on the potential for re-sensitization in the "Phage-antibiotic combination" parapgraph.
R3:Re the first objection, the article itself states that phage libraries are part of the current practice (“After identification of the pathogen (infectious agent), the bacteria should be checked in vitro against a library of phages to select the most effective phage for therapeutic application.”).  It does not seem like much of a stretch to state that library building can be an ongoing process.
R3:For the second comment, the authors are free to mention that the approach and mechanism are still speculative but the Chan et al. citation would fit in the “Phage-antibiotic combinations” section. Phage-antibiotic synergy is not a fringe topic (73 results in pubmed, most from the last 5 years) but the mechanisms for the observed effects are not well understood; the Chan et al. paper presents one plausible-sounding hypothetical mechanism.

Therefore, I'd summarise by recommending that the authors aim to address the recommendations as best possible.

T.Shafee(Evo﹠Evo)talk 05:57, 17 June 2021 (UTC)[reply]