Phage research


Will phage therapy be a mainstream antibacterial tool in future? If so, what are the approaches to make them practical?

Dr. Jean-Paul Pirnay

Senior Researcher, Queen Astrid Military Hospital in Brussels

Synopsis

In an article titled “Phage Therapy in the Year 2035” in Frontiers in Microbiology under Advances in Phage Therapy: Present Challenges and Future Perspectives by Dr. Jean-Paul Pirnay enlightens a hypothesis and theory article on the path forward that is required to make the bacteriophages as a personalized treatment option for the multidrug-resistant infections. In this piece, he explains the peculiarities and inadequacies of the phages in today’s context. Further, he illuminates the two approaches (one-size fits all and personalized concept) briefly along with the synthetic biology approach to reduce phage resistance. He concludes by envisioning the phage supply chain management that includes various stakeholders, artificial intelligence, bacteriophages, and distributed ledger technology requiring community effort to make it authentic.

Why is phage therapy needed?

  • The leading peril of both community and hospital-acquired multi-drug resistant bacteria infections is emerging globally.
  • Most of the clinically pathogenic bacteria have developed resistance to almost all the available antibiotics making them pan drug-resistant.
  • Bacteriophages, the rivals of bacteria are a potential therapeutics to combat the multi-drug resistant pathogens are ubiquitous and the most abundant species on the earth.
  • Complying with lytic phages is essential for successful phage therapy.
  • Since the co-discovery of the bacteriophages by Frederick Twort, and Felix d’Hérelle in 1915 and 1917 and later George Eliava devoted his research by establishing Eliava Institute in Tbilisi, Georgia in 1923, extensive phage therapy research was in progress but camouflaged universally.
  • The encumbrance of resistant infections has reintroduced the interest in phage therapy.

A narrative fiction

  • An ambiguous backdrop in the futuristic world in the year 2035, a retired microbiologist Dr. John Iverian is stung by a bug (Halyomorpha halys).
  • He did not treat the wound, but the next morning, it turns into a necrotic would with infection as predicted by the home management system (Osuri).
  • With concern, he initiated the Phage-BEAM device (Bedside Energized Anti-Microbial) by gently removing the sterile cotton swab by gently swabbing the wound and inserted into the “sampling” area which extracts the total DNA and determines the complete metagenome data.
  • The sequenced data is sent to the “Phage XChange” server (AI-driven algorithm) predicts the phage that will lyse the infecting bacteria (identified in the metagenome) with a minimum immune reaction in the patient.
  • Osuri predicted the bacterial strain to be Streptococcus pyogenes strain FE-2033 (imminent threat to public health).
  • The device will be able to synthesize the ready-to-use therapeutic phage product in one hour, and phage suspension was prepared in the form of a hydrogel-based wound dressing containing synergistic antibiotics.
  • He applied for once a day for the next seven days, and the wound was almost completely healed without leaving his home.

Peculiarities of bacteriophages

The bacteriophages exhibit quite a few unique properties, they are;

  1. Specific to the bacteria they infect.
  2. Spare the beneficial bacteria.
  3. Phages multiply only in the presence of the host.
  4. Both bacteria and phages work mutually where they involve in selective effect resulting in “antagonistic coevolution”.

Dualistic Approaches in phage therapy

One-size-fits-all is an approach that contains broad-spectrum phage cocktails active against Gram-positive and Gram-negative bacteria commonly stumbled upon, causing various infectious diseases. This is one of the difficult methods to develop as it contained a large number of phages. An example of this approach was the PhagoBurn trail; its success was due to the prior recognized susceptible bacteria. With progressing treatment and identifying phage resistance, new phages must be supplemented to the cocktail.

The personalized concept is the one in which one or more phages are selected from a phage bank or previously characterized backgrounds. It is more sustainable with less selection pressure contributing to the phage resistance. However, logistical constraints and licensing paths remain a limitation.

Synthetic biology

Synthetic biology approaches such as yeast-based platforms, cell-free transcription-translation (TXTL) systems, and genetic engineering strategies must be developed to satisfy the precision and personalized phage therapy. Links between bacterial genomes and infecting phage genomes must be established using the Deep Learning process. The shortcomings are a massive amount of data linking the lytic phage genomes to the host must be generated that is currently unavailable. The researchers and institutes are not profound to submit their data to a single centralized database. The absence of quick, reliable, and cheap synthesis of large DNA molecules are a few constraints that need to be taken care of. The de novo synthesis of phage genomes requires assembling several genome fragments using yeast artificial chromosomes, cell-free phage production systems, or chemical assembly.

Concluding remarks

  • With the use of synthetic phages, there is no need for the maintenance of phage banks or the transfer of bacterial isolates throughout the world for the phage search.
  • It would be easy to combat epidemic outbreaks and bioterrorism.
  • Lethal strains requiring higher biosafety conditions can be cultured in safe and less feasible environments.
  • The negative impact, such as endotoxins on patients, could be minimized or evaded.

Take-home message

  • The emerging studies on the efficacy of bacteriophages in treating the multi-drug resistant infection prove them to be an alternative to antibiotics.
  • To make the treatment from bench to bedside, several strategies have to be worked out to accomplish practicability.
  • Aspects of phage and bacterial receptor interaction, artificial intelligence, distributed ledger technologies, genome data on bacteria and phages, stakeholders (Sponsors, community, researchers, patients), and phage synthetic techniques have to be constituted to make this therapy a reality to every patient.

A chronicle of a teenager who underwent phage therapy against Mycobacterium infection

A rejoiced mom reiterates the saga of how she saved her daughter from a superbug infection, Mycobacterium abscessus, and the post-therapeutic life of Isabella. When the antibiotics failed, once a forgotten therapy (The Phage Therapy) came to their rescue. Like any other mom, Jo Carnell-Holdaway was desperate to save her child from the suffering that is when she found about this therapy online and highlighted it to the hospital team. Immediately they contacted a team of researchers at the University of Pittsburgh to facilitate the treatment procedure. After a resilient period of selection and identifying the right phages for therapy, the cure was initiated. The treatment turned out to be successful, and presently she is enjoying her healthy life, such as socializing with friends and pursuing her education.

The Flashback:

Isabelle Holdaway is a 15-year old teenager hailing from Kent, England. Isabelle was diagnosed with a lung illness-causing cystic fibrosis at 11 months from birth, since then, she was under antibiotics, but in September 2017 she had undergone a double lung transplant due to which she was on immuno-suppressant drugs to evade transplant rejection. This caused her to contract with Mycobacterium abscessus, a bacterial infection, which started rapidly spreading, causing sores and swollen nodules across her body. Her pediatrician, Dr. Helen Spencer at Great Ormond Street Hospital in London, was concerned about the path of the consequence as the failure of standard treatments that could lead to death as in previous cases. On hearing Isabelle’s mother on the viruses that kill bacteria, the doctor decided to take a chance in saving the precious life. So she contacted Dr. Graham Hatfull at the University of Pittsburgh, who has more than a decade long experience in working with phages against Mycobacterium, suitable phages were screened against the particular strain that they are dealing with from a collection of more than 15,000 phages at their lab facility. After months of strenuous investigation, they found three phages that can infect them. This excited them, but there came a hindrance where out of three phages, two were found to be temperate, wherein they could enter a lifecycle that discontinuities their virulent capacity and integrate their genome into the bacteria and cause repression. With the rich experience in molecular understanding and genome editing, Dr. Hatfull decided to knock out the particular gene responsible for the respective consequence by genetic engineering, and he succeeded in it. The treatment was initiated as a phage cocktail intravenously twice a day from June 2018, and her condition started to improve after 72 hours. After constituting for six weeks, the infection significantly reduced to few trace amounts of lesions, and liver scans indicated that the infection had vanished. The pediatrician believes over time; the infection could be cleared out of the system. The phages were isolated from Aubergine of decomposing vegetables in Durban, South Africa. The results of the study have been published in the Journal “Nature Medicine”.

Currently, she is pursuing arts and product design while preparing for the A-levels and equipping her driving skills. She is keen to travel to the USA to meet the team that helped her with the preparation of the bacteriophages for phage therapy.

References:

https://www.mirror.co.uk/news/uk-news/mum-helped-save-daughter-deadly-22038281

https://usatodaypost.com/mum-helped-save-her-daughter-from-deadly-bug-thanks-to-a-rotting-aubergine/

https://edition.cnn.com/2019/05/09/health/cystic-fibrosis-teen-engineered-bacteriophage-study/index.html

https://www.sciencemag.org/news/2019/05/viruses-genetically-engineered-kill-bacteria-rescue-girl-antibiotic-resistant-infection#

https://www.gosh.nhs.uk/news/first-use-pioneering-phage-virus-therapy-treat-patient-cystic-fibrosis

https://www.theguardian.com/science/2019/may/08/teenager-recovers-from-near-death-in-world-first-gm-virus-treatment


A brief history about the superheroes: the bacteriophages

Bacteriophages (phages) are viruses of the bacteria which have the capability to infect and kill bacteria. Based on their life-cycle, they are classified into lytic and temperate phages. The history of works relating to bacteriophages dates back to the year 1896 where an English chemist Ernest Hankin reports the bactericidal activity of waters collected from the Indian rivers Jumna and Ganga on Vibrio cholerae [1]. Twenty years later, the discovery of the bacteriophages was credited to two independent researchers, an English microbiology Fedrick Twort in 1915 [2] and a French Canadian microbiology Felix d’Herelle in 1917 [3] who observed a filterable and transmissible agent that caused the bacterial lysis. The term “bacteriophage” was coined by Felix d’Herelle [4]. Initially, d’Herelle tested the efficacy of the suspension on himself, his friends, and family, and then he gave it to patients suffering from dysentery and cholera. Since then, he focused on investigating other infections relating to Salmonella, Shigella, Pasteurella, etc.. The first report on the phage therapy was published in 1921 [5]. A review by Richard Sharp summarises the biology and history of the bacteriophages wherein; he elucidated the initial report by Hankin to the early interest by the medical and industrial sector in pursuing bacteriophages, the development of molecular understandings such as the experiments by Hershey and Chase on the validation of nucleic acid to be the genetic material and discoveries of Salvador Luria and his colleagues on the replication mechanism of the phages, finally he concludes on the isolation and characterization of the bacteriophages [6]. William Summers has complied with the early works of literature on phage therapy [7], and Altamirano, F.L.G., and Barr, J.J (2019) have covered the key points to consider for successful phage therapy in the post-antibiotic era [8].

Since the discovery of phages, the curiosity to study its therapeutic potential grew in an exponential way to several nations such that in 1932 bacteriophages were used extensively to control cholera outbreaks in India [9]. Later few pharmaceutical companies in France and the USA, such as L’Oréal [10] and Eli Lilly Company, produced commercial phage preparations, a review paper has summarised the companies involved in bacteriophage-based preparations [11]. The discovery of antibiotics by Alexander Fleming in 1928 led to the downfall of bacteriophages, especially in the Western world [11]. Although in the demise of bacteriophage research in the antibiotic era, few Eastern nations such as Poland, Georgia, and Russia continued the phage research and it is still in practice. In 1923, Georgian microbiologist George Eliava constituted a dedicated institution for phage therapy and its research entitled Eliava Institute of Bacteriophage, Microbiology, and Virology in Tbilisi, Georgia. In the last three decades, there has been a void in the discovery of antibiotics, and due to the misuse and overuse of the antibiotics the bacteria have acquired resistance to multiple antibiotics, this is causing severe problems in almost all sectors right from aquaculture, environment, food, etc., Owing to this frightening concern, researchers all over the world are searching for alternative therapies to combat these deadly superbugs while the incident rates of resistant infections are on the rise.

In these hard-times, bacteriophage-based therapy seems convincing based on the preliminary studies, and its re-emergence has been the saviour of people’s lives. Two of the critical studies in treating drug-resistant infections in recent times have spurred the interest in pursuing this in clinical scale. In 2015, a patient with multi-drug resistant infection was successfully treated with bacteriophages in San Diego, California [12]. In another instance, a 15-year old patient with a double lung transplant contracted with a Mycobacterium infection, and all the antibiotics failed to clear the infection while three bacteriophages were recombinantly engineered to eradicate them successfully [13].

In conclusion, the bacteriophages are natural rivals of the bacteria and have been evolving since its inception. Even though its potential was concealed during the antibiotic era, the recent problems due to the antibiotic resistance infections have made us look back and re-discover its inherent ability to combat the deadly pathogens. Studies must be encouraged towards learning their capability in the clinical setting as an alternative strategy to fight a war against the untreatable micro-organisms that are resistant to antibiotics.

References

[1] Hankin, E., 1896. The bactericidal action of the waters of the Jumna and the Ganges on Vibrio cholerae. Ann Inst Pasteur, 10, p.511.

[2] Twort, F.W., 1921. THE ULTRA-MICROSCOPIC VIRUSES. The Lancet, 198(5108), p.204.

[3] d’Herelle, M.F., 1961. Sur un microbe invisible antagoniste des bacilles dysentériques. Acta Kravsi.

[4] Duckworth, D.H., 1976. ” Who discovered bacteriophage?”. Bacteriological reviews, 40(4), p.793.

[5] d’Herelle, F. and LeLouet, G., 1921. Sur la vaccination antibarbonique par virus atténué. CR Soc. Biol. Paris, 85, pp.1011-13.

[6] Sharp, R., 2001. Bacteriophages: biology and history. Journal of Chemical Technology & Biotechnology, 76(7), pp.667-672.

[7] Summers, W.C., 2001. Bacteriophage therapy. Annual Reviews in Microbiology, 55(1), pp.437-451.

[8] Altamirano, F.L.G. and Barr, J.J., 2019. Phage therapy in the postantibiotic era. Clinical microbiology reviews, 32(2), pp.e00066-18.

[9] Morison, J., 1932. Bacteriophage in the Treatment and Prevention of Cholera. Bacteriophage in the Treatment and Prevention of Cholera.

[10] Summers, W.C., 1999. Felix dHerelle and the origins of molecular biology. Yale University Press.

[11] Monk, A.B., Rees, C.D., Barrow, P., Hagens, S. and Harper, D.R., 2010. Bacteriophage applications: where are we now?. Letters in applied microbiology, 51(4), pp.363-369.

[12] Schooley, R.T., Biswas, B., Gill, J.J., Hernandez-Morales, A., Lancaster, J., Lessor, L., Barr, J.J., Reed, S.L., Rohwer, F., Benler, S. and Segall, A.M., 2017. Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection. Antimicrobial agents and chemotherapy, 61(10), pp.e00954-17.

[13] Dedrick, R.M., Guerrero-Bustamante, C.A., Garlena, R.A., Russell, D.A., Ford, K., Harris, K., Gilmour, K.C., Soothill, J., Jacobs-Sera, D., Schooley, R.T. and Hatfull, G.F., 2019. Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus. Nature medicine, 25(5), pp.730-733.

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