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Widespread antibiotic-resistant bacteria are threatening the arsenal of existing antibiotics. Not only are antibiotics less likely to be effective today, but their extensive use continues to drive the emergence of multidrug-resistant pathogens. A new-old antibacterial strategy with bacteriophages (phages) is under development, namely, phage therapy. Phages are targeted bacterial viruses with multiple antibacterial effector functions, which can reduce multidrug-resistant infections within the human body. This review summarizes recent phage therapy clinical trials and patient cases and outlines the fundamentals behind phage treatment strategies under development, mainly through bench-to-bedside approaches. We discuss the challenges that remain in phage therapy and the role of phages when combined with antibiotic therapy.
Methods
This narrative review presents the current knowledge and latest findings regarding phage therapy. Relevant case reports and research articles available through the Scopus and PubMed databases are discussed.
Findings
Although recent clinical data suggest the tolerability and, in some cases, efficacy of phage therapy, the clinical functionality still requires careful definition. The lack of well-controlled clinical trial data and complex regulatory frameworks have driven the most recent human data generation on a single-patient compassionate use basis. These cases often include the concomitant use of antibiotics, which makes it difficult to draw conclusions regarding the effectiveness of phages alone. However, human data support using antibiotics as phage potentiators and resistance breakers; thus, phage adjuvants are a promising avenue for near-term clinical development. Current knowledge gaps exist on the appropriate routes of administration, phage selection, frequency of administration, dosage, phage resistance, and pharmacokinetic and pharmacodynamic properties of the phages. In addition, we highlight that some phage therapies have mild adverse effects in patients.
Implications
Although more translational research is needed before the clinical implementation is feasible, phage therapy may well be pivotal in safeguarding humans against antibiotic-resistant infections.
The ability to control infectious diseases marked a revolution in human health, shifting the global burden of disease from infectious diseases to noncommunicable diseases, which are now considered a leading cause of death.
The 20th century brought an appreciation of bacteriophages (often known simply as phages) and their relationship to infectious diseases, which resulted in the implementation of phage therapy to decrease the incidence of several infectious diseases. From the first successful administration of phages in 1921 at Hôpital des Enfants-Malades, Paris, France, treating children with Shiga dysentery to its widespread use in humans around the world, the effectiveness of phage therapy was highly controversial.
In 1945, a new era began with the golden age of antibiotics, and phage products were taken off the market. However, shortly thereafter, penicillin resistance became a substantial clinical problem. In response, new classes of antibiotics and modifications to old classes were developed and deployed.
On the basis of diverse criteria, such as mortality, prevalence of resistance, treatability and current pipeline, the situation is critical for most difficult-to-treat, community-acquired, health care–associated, and nosocomial infections caused by ESKAPEE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter species, and Escherichia coli) pathogens. We included Mycobacterium tuberculosis to the critical category as an additional priority global health threat. The list is an excellent guide for the prioritization of research and development aimed at discovering new antibacterial therapies, which are critically needed.
The inevitable demise of all available antibiotics has reignited the development of phage therapy. Phages are naturally occurring viruses that infect both gram-positive and gram-negative bacteria. As such, they are generally unaffected by antibiotic resistance and (unlike most antibiotics) are able to target bacteria encased in biofilms.
A substantial volume of preclinical data and an increasing body of clinical evidence indicate the immense therapeutic potential across a wide range of infectious diseases. For decades, the Eliava Institute in Georgia and the Ludwik Hirszfeld Institute in Poland have provided phage therapies to hundreds of nationals and internationals. The Eliava Institute has routinely provided off-the-shelf fixed-phage products and personalized single-patient phage treatments as extempore medications.
Recently, Belgium implemented single-patient phage therapy regulation as magistral preparations (ie, pharmacy compounding), with phage products prepared and deployed by the Queen Astrid Military Hospital.
In the United States, the Food and Drug Administration recently approved multiple phage therapy clinical trials and several phage therapies as expanded access Investigational New Drug (eIND) for patients with an immediately life-threatening condition or serious disease where standard of care has failed.
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
In this review, we summarize the increasing body of clinical data on phage therapy and discuss how phages transition from bench to bedside and beyond. Our aim is to highlight the importance of approaching translational and clinical research from various angles and develop innovative ways to overcome the many challenges with implementing phage therapy.
The Active Agent
Phages are bacteria-restricted viruses that exploit all natural environments, including the human body.
Although phages come in a variety of morphologic structures and genome types, most discovered phages are nonenveloped icosahedral head and tail in structure and have double-stranded DNA genomes. Viral tails are unique to phages and can be contractile, short noncontractile, or long noncontractile, which allow for viral classification as myoviruses, podoviruses, and siphoviruses, respectively.
Together with their enormous abundance, great diversity, and relative ease of isolation, phages provide an unlimited source of antibacterial agents against all human bacterial pathogens (Fig. 1).
When virulent double-stranded DNA phages infect susceptible host bacteria in vitro, the number of phages in the culture supernatant does not increase until after, generally, 30–40 min at 37 °C. This period is required for a phage particle to inject its genome into the host cell, hijack host metabolism, express its viral genes, assemble phage particles, and release progeny into the environment (Fig. 1). Cell lysis is the result of viral endolysins cleaving bonds within the cell wall peptidoglycan, which causes the cell wall to destabilize and osmotic rupture to occur under the high internal pressure.
A successful infection by a virulent phage always leads to cell lysis.
Figure 1Lytic infection cycle of virulent phages. Step 1: adsorption: attachment of tail fibers onto a specific receptor on the bacterial cell wall. Step 2: injection: viral DNA penetrates the host through a hollow tube in the tail. Step 3: protein synthesis and host hijacking. Viral genes direct the synthesis of viral proteins using the machinery of the host. Steps 4 and 5: viral genome synthesis and assembly. Step 6: release: mature viral particle (virion) release occurs via viral peptidoglycan hydrolases (endolysins) that mediate host cell lysis, which liberates up to 200 infectious phages.
By contrast, infection by a temperate phage can lead to lysogeny. That is, temperate phages infect bacteria as a symbiotic prophage and replicate along with the bacterial chromosome during bacterial cell division. When exposed to environmental cues or stressors, the prophage resumes a lytic cycle to create phage particles.
An inherent capacity of prophages to mediate the transfer of genes between bacteria by specialized transduction—an event that may increase bacterial virulence or promote antibiotic resistance—generally disqualifies temperate phages for therapeutic purposes. However, advances in synthetic biology have provided new opportunities for the use of temperate phages as a therapy against bacterial infections by removing so-called lysogeny genes from their genome.
The parasitic and enzymatic bacterial killing by phages are different from the antibacterial mode of action by all other drugs, which allows them to be effective against most MDR bacteria (Fig. 2). In addition, self-replication in the presence of susceptible bacteria provides density-dependent dosing at the site of infection. Reducing the number of daily doses through extended-release drugs can reduce the relapse of disease, symptoms associated with drug therapy (ie, drug-related problems), patient nonadherence, and costs.
However, the association between the number of phage doses per day and relapse in infections remains uninvestigated .
Figure 2Phages as potential antibiotic adjuvants. (A) There are 4 main mechanisms of antibiotic resistance: (1) excretion by activation of efflux pumps, (2) decreased uptake by changes in the outer membrane permeability, (3) modifications on the drug target, and (4) enzymatic inactivation of the drug. (B) Phages can potentiate the antibiotics by altering the physiologic activities exhibited by phage sensitive and resistant bacteria by (1) direct blockade or mutation of drug efflux mechanism, (2) enhancement of drug uptake through cell wall mutations (untested), and (3) inhibition of antibiotic resistance elements.
Figure 3Summary of the phage therapy clinical trials and compassionate use case reports from 2005 to 2020. Case reports are categorized by the site of infection and target pathogen. The color coding represents the primary route of phage administration in each case report.
A unique aspect of phage therapy is the potential for low-dose phage treatments, relying on self-replication to bring up the phage concentration at the site of infection. For self-dosing to occur, target host cell densities need to be over a replication threshold of ≥104/CFU/mL.
Phage infection can only take place after the viral tail fibers bind irreversibly to specific receptors on the bacterial cell wall, including lipopolysaccharide (endotoxin), teichoic acid, pili, outer membrane proteins, efflux pumps, and polysaccharide. This stringent compatibility causes phages to be specific against bacterial targets and prevent tropism for mammalian cells. Nevertheless, phages can rapidly translocate throughout the body, even penetrating compartments previously considered sterile.
However, despite the increasing number of clinical applications, there is a limited understanding of the interactions between phages and human cells.
Clinical Data
It is well recognized that all recipients of phage therapy have so far been treated empirically, with incomplete information on, for example, the phages, adequate route of administration, dosing, duration, and antibiotic compatibility. Figure 1, Figure 3 and the subsections below briefly summarize select phage therapy clinical trials and single-patient reports between 2005 and 2020 grouped by route of administration. Further case data are summarized in Supplemental Table 1. With limited clinical trial data, lessons learned from personalized case studies under eIND have advanced medicinal phage technologies and highlighted potential risks and challenges, which we review in subsequent sections.
Oral Route
A randomized, double-blind, and placebo-controlled Phase I study of oral ingestion 3 times daily for 2 consecutive days of a single phage targeting E coli at a low dose of 9.0 × 105 and high dose of 9.0 × 107 PFU per dose caused no adverse effects in healthy adults.
In another safety study, no serious adverse effects were found after oral ingestion of a 10-phage mix (cocktail) targeting E coli at 1.5 × 107 to 1.5 × 108 PFU per dose in both adults and children. However, increased aspartate aminotransferase levels were observed in children, and some adults reported transient abdominal pain, dyspepsia, and toothache.
In a double-blind, placebo-controlled, crossover trial, healthy adult daily dietary supplementation with a 4-phage cocktail targeting E coli at 106 PFU per dose had no serious adverse effects after 28 days.
Although recipients had reductions in fecal E coli counts, there was no global disruption of the gut microbiota community, and both short-chain fatty acids and lipid metabolism were largely unaltered, thereby suggesting that phages can alter targeted microbiome species without inducing dysbiosis.
In a randomized controlled trial, oral phage treatment targeting diarrheal E coli in children did not improve acute diarrhea symptoms any more than oral rehydration therapy.
or 3.6 × 108 PFU per dose of a 10-phage cocktail 3 times daily for 4 consecutive days. No adverse events were attributable to oral application. Less than half of the recipients had E coli in their stool, which accounted for <5% of total fecal bacteria.
Eradication of a multidrug-resistant, carbapenemase-producing Klebsiella pneumoniae isolate following oral and intra-rectal therapy with a custom made, lytic bacteriophage preparation.
Phages applied intraoperatively have cured a series of implant-associated MDR and recalcitrant infections. A 1-phage treatment at 1 × 108 PFU in combination with ceftazidime applied directly to an aortic fistula cleared a chronic aortic graft MDR P aeruginosa infection in a 76-year-old.
Similarly, a chronic aortic graft S aureus infection was cured after a 59-year-old patient received 2 × 1010 PFU per dose of a single phage applied via drainage every 12 h for 2 days.
A 2-1-1 phage mix targeting P aeruginosa, S aureus, and E faecium, respectively, cleared an aortic graft multispecies infection in a 52-year-old patient after 2 local phage treatments of 2.5 × 109 PFU administration a day apart. Unfortunately, relapse of a P aeruginosa infection occurred after 17 days.
Left ventricular assist devices (LVADs) are becoming a more frequent life-support intervention, but there has been mixed success of treating LVAD infections with phages. A 62-year-old with fulminant pleural empyema caused by S aureus infection after LVAD implantation was cured after 1-phage local treatments of 2 × 1010 PFU applied via drainage every 12 h for 7 days.
In contrast, a 51-year-old could not be cured of chronic S aureus LVAD infection after 2 weeks of daily local treatments with a 4-phage mix at 1.0 × 1010 PFU applied via drainage. The cause of treatment failure was unknown, but there were no signs of developed phage resistance or phage-neutralizing antibodies after 2 weeks.
Phages have also treated prosthetic joint infections (PJIs). An 80-year-old with type 2 diabetes was cured of a methicillin-sensitive S aureus prosthetic hip infection after debridement and a single local administration of a 6-phage mix at 6 × 1010 PFU in 20 mL of phosphate-buffered saline.
Salvage debridement, antibiotics and implant retention (“DAIR”) with local injection of a selected cocktail of bacteriophages: is it an option for an elderly patient with relapsing Staphylococcus aureus prosthetic-joint infection?.
Treatment also consisted of daptomycin, amoxicillin, and clindamycin to suppress E faecalis and Staphylococcus lugdunensis (also isolated from the joint) and oral amoxicillin/clindamycin for 6 months. The patient's PJI remained infection free for 18 months.
Salvage debridement, antibiotics and implant retention (“DAIR”) with local injection of a selected cocktail of bacteriophages: is it an option for an elderly patient with relapsing Staphylococcus aureus prosthetic-joint infection?.
Similarly, an 80-year-old with a P aeruginosa PJI was cleared with a 100-mL intraoperative treatment of a 3-phage cocktail at 1 × 108 PFU followed by administration of 5 × 108 PFU per dose every 8 h via drainage for 5 days.
In another case, after removal of sacroiliac joint cement and tissue debridement, 4 local administrations of a 4-phage mix of approximately 2.0 × 1010 PFU, colistin, and a compress soaked with approximately 4.0 × 1010 PFU, combined with off-label intravenous ceftolozane/tazobactam, cleared a chronic MDR P aeruginosa PJI.
Innovations for the treatment of a complex bone and joint infection due to XDR Pseudomonas aeruginosa including local application of a selected cocktail of bacteriophages.
Phage intervention allowed for surgical reconstruction after 2 weeks.
A patient with severe P aeruginosa osteomyelitis that received intraoperative phage therapy exhibited no severe adverse events, and wound infection resolved without relapse.
After thorough debridement and irrigation, 10–40 mL of a 107PFU/mL mix of S aureus and P aeruginosa phages rinsed the bone/soft tissue defects. After a contact time of 10 min, a gentamicin and phage–soaked collagen sponge was applied to the infected bone before closure. Postoperative administration of phage occurred for 7–10 days, 3 times per day, with 3 months of concomitant antibiotics.
Under eIND, a 68-year-old patients with diabetes was cured of a disseminated MDR A baumannii infection from necrotizing pancreatitis with combined phage and antibiotic therapies.
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
Treatment consisted of 4-phage 109 PFU per dose given intraoperatively via drainage catheters every 6–12 h. After 36 h, a second 4-phage mix at 109 PFU per dose was administered intravenously at increasing frequency to dosing every 2 h. Phage resistance developed after 10 days. This necessitated switching intravenous treatment to a third 2-phage mix, which was maintained for the remaining 2 weeks of therapy.
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
During debridement surgery and placement of a static vancomycin spacer, 2 intra-articular doses of a single phage at 5.4 × 109 PFU in 10 mL of saline were given. Daily 2.7 × 109 PFU in 50 mL of intravenous saline infusions were continued. However, the patient developed transaminitis after 3 days, prompting phage treatment termination. Aminotransferase and alanine aminotransferase levels returned to normal with continuation of daptomycin use alone. Nonetheless, combined interventions cleared the chronic joint infection, which allowed for distal femoral cemented prosthesis implantation.
In another case, a 62-year-old with a potentially limb-threatening chronic K pneumoniae prosthetic knee infection was treated with intravenous phage therapy after several failed surgical interventions and prolonged antibiotic therapy.
Phage therapy for limb-threatening prosthetic knee Klebsiella pneumoniae infection: case report and in vitro characterization of anti-biofilm activity.
Clin Infect Dis.Jul 2020; 23 ([Epub ahead of print])
The patient received 40 daily 30-min infusions of a single phage at 6.3 × 1010 PFU in 50 mL of normal saline. During phage therapy, the patient experienced improvement in erythema, swelling, pain, range of motion, and function of the knee. The patient reported minor and intermittent pruritus of the lower extremity approximately 2 weeks into the course of therapy but experienced no apparent adverse events from the infusions.
Phage therapy for limb-threatening prosthetic knee Klebsiella pneumoniae infection: case report and in vitro characterization of anti-biofilm activity.
Clin Infect Dis.Jul 2020; 23 ([Epub ahead of print])
After surgical debridement, parenteral administration of 8.5 × 107 PFU in lactated Ringer solution every 2 h through a central catheter, for a total of 98 doses, cleared A baumannii from the site of infection. Two hours after the first dose, the patient exhibited a hypotensive response, but the remaining doses produced no adverse effects. After finishing phage treatment, the patient continued to experience fevers and leukocytosis and died 9 days later.
suggested that surgical drain phage administration might have led to a better outcome.
A 15-year-old patient with cystic fibrosis (CF) who developed a M abscessus airway infection after lung transplant was cured after 32 weeks of treatment with 3-phage mix at 3 × 109 PFU per dose given every 12 h under eIND.
Unconventionally, treatment consisted of temperate phages with modified genomes to remove their ability to undertake lysogeny, instead of traditionally virulent phages.
Similarly, a 26-year-old patient with CF who received a 4-phage mix at 4 × 109 PFU per dose every 6 h for 8 weeks intravenously, in combination with antibiotics, was cured of an MDR P aeruginosa lung infection.
In another case, a 57-year-old with an MDR P aeruginosa airway infection that developed after lung transplant was cleared after a 4-week intravenous course of a 4-phage mix at 4 × 109 PFU per dose given every 12 h concomitantly with inhaled colistin.
In contrast, 10 weeks of intravenous phage and antibiotic therapies could not eradicate a Burkholderia dolosa airway infection that developed after lung transplant.
A 67-year-old with a history of P aeruginosa urinary tract infections (UTIs) was cleared with a 6-phage mix at 2 × 107 PFU instilled directly into the bladder every 12 h for 10 days, in combination with colistin and meropenem. The patient remained free of UTIs for 12 months.
In a single-arm study, antibiotics combined with a 3-phage mix at 3 × 109 PFU in saline per minute for 10–30 min 2 times daily for 14 days had clinical improvement in 8 of the 13 recipients with S aureus infective endocarditis and bacteremia.
In a double-blind, Phase I study, no adverse events occurred after weekly venous leg ulcer topical washes with phages targeting E coli, P aeruginosa, and S aureus.
However, wound healing after 12 treatments of 3.2 × 1010 PFU in 50 mL of saline given weekly was not significantly different from saline-only washing. The lack of clinical improvement was likely caused by the lack of sensitivity of the infecting bacterial isolates to the treatment phages; prior phage sensitivity testing was not performed.
Similarly, a multicenter, double-blind, randomized, Phase I/II study failed to find burn wound clinical improvement after a 12-phage topical treatment of P aeruginosa infections when compared with silver sulfadiazine cream.
Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled, double-blind phase 1/2 trial.
The study had several deficiencies, including elevated endotoxin levels and instability of phages in administered products. The inability to adjust treatment parameters of the clinical trial caused treatment to instead consist of phage counts <103 PFU per dose.
Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled, double-blind phase 1/2 trial.
Phages rely entirely on chance encounters with their bacterial hosts, and providing high-phage doses increases the likelihood of bacterial encounters for both lysis and self-dosing via phage replication.
In a double-blind, Phase I/II trial, topical phage treatment of chronic otitis media caused by P aeruginosa was ineffective overall.
A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy.
For all recipients, phages briefly reduced bacterial counts within the ear canal. Ear swabs also had an abundance of phages, which implies phages replicated at the site of infection. However, infections relapsed in 9 of 12 recipients.
A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy.
A rebound in bacterial counts during treatment is consistent with the emergence of phage resistance, but it was not tested. In another study, intranasal irrigations with a 3-phage mix reduced S aureus in the interim but only cleared infections in 2 of 9 recipients.
Patients exhibited adverse effects, including rhinalgia after 2 treatments of 3 × 108 PFU, oropharyngeal pain after 22 treatments of 3 × 108 PFU, and metabolic acidosis after 28 treatments of 3 × 109 PFU.
In contrast, a 16-year-old with a rare congenital skin disorder called Netherton syndrome had a significant reduction in atopic eczema after daily topical and oral administrations of an undefined mix of Streptococcus, Staphylococcus, Proteus, Escherichia, Pseudomonas, and Enterococcus phages.
The daily treatment regimen consisted of a 20-min application of sterile gauze soaked with the phage mix, followed by phages mixed into ointment cream. The patient also ingested 20 mL of the same phage mix.
Continuous daily treatments occurred for 2 weeks, with 2-week pauses, and after 3 months a second 2-phage cocktail was introduced to address the emergence of phage-resistant S aureus isolates. Patient quality of life improved with decreased skin irritation and increased joint mobility.
A K pneumoniae lung infection during drug-induced immunosuppression after heart transplantation was successfully cleared in a 40-year-old after inhalation of a 2-phage cocktail at 2 × 108 PFU per dose and daily nasogastric ingestion of 1.8 × 109 PFU per dose for 4 days, under the Declaration of Helsinki. After phage therapy, K pneumoniae was undetectable in bronchial lavages but remained in the patient's stool.
Three cases of E faecalis chronic prostatitis were successfully treated with twice-daily intrarectal phage treatments (phages at 108 to 109 PFU per dose given for approximately 1 month). At the end of treatment, all 3 patients' prostates were restored to normal and physiologic function.
Similarly, a 60-year-old patient who received a kidney transplant experience 12 severe episodes of UTI caused by K pneumoniae in the 15 months after transplant. Phage therapy was initiated after the patient's 10th UTI and continued throughout 2 more hospitalizations. Intrarectal phage administration produced no adverse effects on the patient despite hospitalization, and in the 4 years after phage treatment, the patient had no hospitalization for UTIs.
Not all phages are candidates for therapeutic purposes. As mentioned, virulent phages with obliquely lytic replication cycles are preferred (see Fig. 1) because cell lysis is indeterminate and there is a reduced risk of viral mediated horizontal gene transfer via transduction.
permit identification of undesirable gene features to rapidly rule out unsuitable phage strains based on homologies to known genes on existing databases. For example, carrying lysogeny-associated repressors and integrases, bacterial virulence, toxin, and/or antibiotic-resistance genes would disqualify a phage for human therapy.
Continued efforts to improve the quality and accuracy of archived phage genomic information will contribute to increasing the tolerability of phage therapy.
In general, a good phage candidate for therapy is one that infects a wide range of bacterial strains. There is evidence that myoviruses exhibit a broader host range.
In contrast, narrow host range phages may present new therapeutic opportunities. For instance, targeting a prevalent and specific strain of pathogenic bacteria could avoid adverse effects associated with host microbiome dysbiosis.
Another feature important in phage selection is their natural ability to disrupt structured communities of bacterial cells that attach to surfaces and enmesh in biofilm.
Many infectious diseases in humans are the result of, or exacerbated by, biofilms. Self-made exopolysaccharide matrix provides an essential scaffold for biofilm development, promoting bacterial adhesion to surfaces and cohesion as well as hindering diffusion. Although it is often assumed that biofilms confer resistance to phages, most phages readily infect bacteria within biofilms.
Indeed, phages have coevolved with bacterial biofilms; thus, their infection of encased bacteria is expected. For instance, some phage tail fibers and tail-spikes even carry depolymerases that degrade exopolysaccharides to unmask cell receptors on planktonic cells and disrupt the exopolysaccharide matrix of biofilms.
biofilms. In an artificial CF sputum, phages could reduce P aeruginosa biofilm by 3-logs, indicating that phages readily penetrate and lyse bacteria encapsulated in biofilms.
Because phages lyse distal bacteria, interior cells awaken and become more metabolically active because of increased oxygenation and nutrient exposure, thus becoming more sensitive to phage attack. Certain phages, however, poorly penetrate the biofilm matrix,
Although biofilm infections are common and cause clinically significant and potentially fatal infections, much work remains in the quest for effective antibiofilm phages in clinical settings.
The extended storage of phages is another important consideration. Phages keep in short-term cold storage at 4 °C when purified in buffered solution, concentrated, and shielded from light.
Even then, phage counts generally trickle down for months. Cryopreservation can minimize the loss of phages, but phage particles are inactivated with freezing and thawing cycles.
Comparative analysis of different preservation techniques for the storage of Staphylococcus phages aimed for the industrial development of phage-based antimicrobial products.
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled, double-blind phase 1/2 trial.
Well-planned phage combinations have several benefits over use of a single-phage strain. These benefits include, (i) broadening target bacterial strain spectrums, (ii) targeting multiple bacterial species at once, (iii) increasing dose potency by multiple phage strains attacking the same bacterial cell, and (iv) limiting resistance by forcing the target bacterium to evolve resistance to multiple phages simultaneously to survive.
Efficiency of single phage suspensions and phage cocktail in the inactivation of Escherichia coli and Salmonella typhimurium: an in vitro preliminary study.
The drawback is that individual phages generally require a reduction in concentration when mixed into a single dose. There is also the potential that phages will interfere with one another, for example, compete for the same bacterial cell receptor and drive cross-resistance.
The drawback of using a single-phage strain is that it requires careful definition of the etiologic bacterium before therapy. Thus, this approach is primarily for proof of concept, efficacy, and tolerability in vitro and animal studies.
Product Pipelines
Generally, 3 pipelines exist for phage drug products: off the shelf, pharmacy compounding, and on-demand de novo. Off-the-shelf, fixed-phage products are designed to target not-yet-identified pathogens (eg, multiple-phage strains targeting multiple bacterial species) or identified pathogens (eg, multiple phages targeting a single bacterial species). They are manufactured under current Good Manufacturing Practice production, and final products undergo phased clinical safety and efficacy testing.
Fixed products enhance tolerability, quality, and uniformity. However, the clinical usefulness of fixed-phage products is unclear because of, for example, high strain variability of target bacterial pathogens, rapidity of phage resistance, encountering multispecies infections, and varied phage storage stability.
Compounding by a licensed pharmacist with a physician's prescription can create phage medications that are tailored to the individual needs of a single patient.
This approach may be required when the patient's infection isolates are not sensitive to phages in the fixed product, dosage is unavailable, or the fixed-phage product is not well tolerated (see the Drug-Related Problems section below). Compounding also allows the insertion of phages into topical creams, transdermal gels, or other dosage forms.
To implement phage compounding, large and diverse collections of purified phages (phage banks) are a prerequisite.
Indeed, bacterial susceptibility and phage strain diversity have been the driving forces in library construction. For instance, the Queen Astrid Military Hospital has an extensive phage collection. However, only 15 of 260 patient isolates were sensitive to phages in the collection.
Adaptive Phage Therapeutics diverse and well-characterized PhageBank collection also did not contain a phage strain suitable against a patient's K pneumoniae isolate.
Phage therapy for limb-threatening prosthetic knee Klebsiella pneumoniae infection: case report and in vitro characterization of anti-biofilm activity.
Clin Infect Dis.Jul 2020; 23 ([Epub ahead of print])
Thus, proper phage selection criteria and library size have yet to be identified. A potential improvement may be to ensure a diverse collection of phages that use different bacterial receptors.
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
Phage therapy for limb-threatening prosthetic knee Klebsiella pneumoniae infection: case report and in vitro characterization of anti-biofilm activity.
Clin Infect Dis.Jul 2020; 23 ([Epub ahead of print])
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
Phage therapy for limb-threatening prosthetic knee Klebsiella pneumoniae infection: case report and in vitro characterization of anti-biofilm activity.
Clin Infect Dis.Jul 2020; 23 ([Epub ahead of print])
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
Phage PK properties are unique because of their relatively large size (approximately 100 times larger than antibiotics and 10 times larger than antibodies). In addition, phages consist of several different proteins, which can increase their rate of clearance by the mononuclear phagocyte system and neutralization by antiphage antibodies.
Phage efficacy in entering animal or human bodies strongly depends on the route of administration. Oral administration effectively delivers phages to the gastrointestinal tract, and efficiency of gut transit is dose dependent. Fecal phage counts peaked at 3.0 × 104 PFU/g after oral consumption of 1.5 × 107 PFU in mineral water 3 times daily.
Patients orally treated with phages for acute cholera at a dose of 1013 PFU, together with phage propagation at sites of infection, had fecal concentrations of >1011 PFU/g.
This finding suggests that phage passage through the stomach can be efficient. Absorption of phages into the blood, however, was inefficient, reaching only 102 PFU/mL.
For phages to be effective, they must reach the site of infection in sufficient numbers and infect as many target bacteria as possible, without causing patient harm. Conversely, removal of phages from the site of infection is an important factor in terminating action. Phages delivered systemically can penetrate the lumen of murine lungs.
Phages in the plasma and tissues (spleen, kidney, liver, and lung) of rats after a single 1-mL intravenous bolus of 1010 PFU/mL exhibited a half-life of 2.3 and 9 h, respectively.
Continuous infusion of 0.1 mL/h for 24 h of the same phage mix and titer resulted, however, in plasma progressively increased to reach a plateau of 107 PFU/mL after 6 h, which is comparable with the concentration achieved after bolus injection.
In humans, after a dose of 8.5 × 107 PFU in 4 mL of lactated Ringer solution, administered through a peripherally inserted central catheter, phage levels were detectable after 5 min in blood samples but were undetectable after 50 min.
Studies examining the pharmacodynamic properties of phages, defining synergy, additivity, indifference, antagonism, and host immune system interaction, are scarce. The monotherapy versus mix versus phage-antibiotic combination therapy debates have not yet considered the potential additional value of the patient immune system. It is still unclear whether the initial phage dose or phage replication most influences outcomes as well as what is a sufficient level of target bacteria to allow phage replication to overtake bacterial replication.
Thus, the effectiveness of phage therapy likely increases as the infection worsens, inflating the likelihood that phages will encounter a bacterial host. Inefficient outcomes, however, may arise from the tendency for phages to bind to bacterial debris.
With the uniqueness of phage therapy, studying pharmacokinetic and pharmacodynamic properties is challenging. Most proof-of-principle studies of phage therapeutic applications use very high titers of phage to achieve efficacy, which is unlikely to be achieved in humans. However, given the low toxicity of phages, phage therapy should be successful provided that phages reach the site of infection in sufficient numbers and are able to replicate within target bacteria.
Drug-related problems actually or potentially interfere with desired health outcomes, including adverse reactions and emerged resistance. They are relatively common in hospitalized patients and can result in morbidity and mortality as well as increased costs. The range of adverse reactions during phage therapy varies widely (summarized in Table II). A 2-year-old experienced anaphylaxis after intravenously administered phages,
Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled, double-blind phase 1/2 trial.
Phage therapy for limb-threatening prosthetic knee Klebsiella pneumoniae infection: case report and in vitro characterization of anti-biofilm activity.
Clin Infect Dis.Jul 2020; 23 ([Epub ahead of print])
Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled, double-blind phase 1/2 trial.
A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy.
We speculate that adverse reactions can arise because of bacterial lysis by the phages and/or direct phage-mammalian host immune system interactions and/or residual bacterial toxins in phage products.
Phage-induced rapid release of bacterial cell wall components may have immediate adverse effects for the patient. Animal studies have found that phage-induced endotoxin release is significantly lower in lysis-deficient phages compared with lytic phages, which leads to decreased proinflammatory cytokines (eg, tumor necrosis factor α and interleukin [IL] 6).
However, the amount of endotoxin released during antibiotic action is also clinically important. For instance, some classes of β-lactam antibiotics lead to markedly increased levels of free endotoxins, whereas treatment with carbapenems and aminoglycosides produces relatively low amounts of endotoxins. Dufour et al
found that phage-mediated bacterial lysis–released endotoxins were similar to β-lactam antibiotics in vitro.
Direct interactions between phages and the host immune system can induce signaling cascades that can result in elevated cytokines, increased immune cell infiltration, increased phagocytosis, and adaptive immunity activation (T-cell response and antibody production by B cells). Phages stimulate antiviral interferons through activation of Toll-like receptor 9 and play crucial roles in the innate immune system by recognizing microbial DNA as a pathogen-associated molecular pattern.
However, the physiologic and immunologic consequences of harboring internalized phage particles are unclear.
Certain structural proteins of phages can elicit weak humoral responses after prolonged exposure, which can lead to the antibody neutralization of phage particles.
Antibodies against staphylococcal bacteriophages in human sera. II. assay of antibodies in exacerbation and regression of chronic staphylococcal osteomyelitis.
A phage safety trial in humans found no antiphage IgG, IgM, or IgA antibodies detected in the blood of recipients after oral ingestion of phages for 2 consecutive days.
Notably, phage numbers in murine models are significantly higher compared with human therapeutic doses. Although phages appear to induce only weak antibody responses, antiphage antibody responses may lead to the activation of the complement system.
Bacteriophage therapy increases complement-mediated lysis of bacteria and enhances bacterial clearance after acute lung infection with multidrug-resistant Pseudomonas aeruginosa.
Human blood from recipients of phage therapy was found to contain antiphage IgG, IgM, and IgA antibodies in vitro. However, no correlation was found between the induction of phage-neutralizing antibodies and the outcome of phage therapy.
Antiphage antibodies, although likely not harmful to patients, could limit the effectiveness of phages given therapeutically. To date, this problem has not been reported. Identifying immunologic interactions with phages that contribute to the development of adverse reactions may aid in the prevention of problems related to phage therapy.
Phage Resistance
Another complication of phage therapy is that bacteria can thwart phage attack through an arsenal of antiviral mechanisms, targeting almost every step of the phage replication cycle.
These mechanisms include spontaneous chromosomal mutations, the ability to block the entry of phage genetic material (eg, superinfection exclusion), DNA restriction-modification enzymes, abortive infection, and CRISPR-Cas adaptive immunity. A major mechanism that drives phage resistance is spontaneous chromosomal mutations governed by Darwinian dynamics. During treatment of an infection, a small number of mutations will spontaneously arise (rate of approximately 10−8), followed by phage-resistant subpopulation regrowth.
Animal studies have found bacteria can rapidly shrug off phage attack, leading to uncontrolled proliferation of phage-resistant mutants and treatment failure.
However, target bacterial populations are likely to experience large, cyclic swings (predator-prey dynamics) in population size before resistance dominates.
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
Most studies have not adequately tested for the emergence of phage resistance, likely because of successful outcomes. However, cases continue to indicate that resistance emerges during phage therapy,
which might be attributable to unreported treatment failures.
Despite the near certainty that phage resistance will arise, multiple scenarios occur with which phage resistance does not impede a positive therapeutic outcome.
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
If resistance to phage treatment arises, switching to new phages with different binding sites or order of exposure can be therapeutic strategies to improve efficacy.
One approach that has received little exploration is the use of phage adjuvants, also referred to as phage potentiators and resistance breakers. These adjuvants are active compounds with little or no effect on bacterial growth in isolation and when c-administered with phages act to enhance phage activity or block phage resistance. The combination of synergistic antimicrobials are also adjuvants. Chemical antibiotics can act as phage adjuvants by boosting phage particle production. For instance, a subinhibitory concentration of cephalosporin increased an E coli cell's production of the phage particles by 7-fold.
Phage-infected Burkholderia cenocepacia cells produced higher phage counts in the presence of subinhibitory concentrations of meropenem, ciprofloxacin, and tetracycline.
Antibiotics that act by inhibiting cell division (β-lactam, quinolones, and nalidixic acid) or cause an elongated morphologic structure (ciprofloxacin and meropenem) can permit higher production of phage particles.
Likewise, subinhibitory concentration of tetracycline causes cell clustering, which may promote increased phage infections by minimizing lateral travel between adjoined cells, thereby enhancing contact with phage receptors on uninfected cells.
Combining phages with subinhibitory concentrations of ciprofloxacin or meropenem can also inhibit regrowth of phage-resistant mutants in a murine endocarditis model and thus improve the phage therapy outcome.
Bacterial biofilms represent a major obstacle in the fight against bacterial infections because they are inherently refractory to various antibiotics. A potential adjuvant to phage therapy include DNAs that can degrade extracellular DNA, which plays important roles in both the aggregation of bacteria and the interaction of the resulting biofilm with polymorphonuclear leukocytes during an inflammatory response.
Disrupting the mixed-species biofilm of Klebsiella pneumoniae B5055 and Pseudomonas aeruginosa PAO using bacteriophages alone or in combination with xylitol.
Disrupting the mixed-species biofilm of Klebsiella pneumoniae B5055 and Pseudomonas aeruginosa PAO using bacteriophages alone or in combination with xylitol.
For example, some phages infect gram-negative bacteria by binding to TolC or its homologues, a common component of a wide variety of multidrug efflux pumps.
Mutations in the gene encoding of the outer membrane porin M, which is part of the efflux pump complex, impaired phage infection but restored the sensitivity to ciprofloxacin.
E faecalis is a human intestinal pathobiont with intrinsic and acquired resistance to many antibiotics, including vancomycin. Despite gaining phage resistance, mutant strains exhibited a loss of resistance to cell wall–targeting antibiotics in vitro.
Identifying evolutionary trade-offs is an emerging strategy for combating antibiotic resistance, such as prescribing sequences of synergistic antimicrobials wherein the evolution of resistance to the first induces susceptibility to the second.
Treating biofilms with phage has produced promising results in a handful of experimental and case studies. The unique action that phages exert on bacteria offers the potential for the 2 agents to act synergistically; their total efficacy is much greater than each individual action. Most antibiotics alone were ineffective at disrupting low concentrations of S aureus biofilms in vitro. However, the addition of phages led to substantial improvements in efficacy.
Thus, combining phage therapy with traditional antibiotics could help better manage antibiotic-resistant bacterial biofilms. In some cases, even though no synergism in antimicrobial activity is observed, the combined use of phages and antibiotics significantly reduces or even prevents the development of antibiotic- and phage-resistant bacteria.
Effect of bacteriophage infection in combination with tobramycin on the emergence of resistance in Escherichia coli and Pseudomonas aeruginosa biofilms.
From a clinical standpoint, phage-antibiotic combination therapy can improve or prolong the lifespan of the available antibiotic arsenal, and the increasing pressure to develop phage therapy can be somewhat alleviated. The principal disadvantage of their use is that more complex studies are required to establish effective codosing regimens because compatible pharmacokinetic and pharmacodynamic properties between the antibiotic and phages are required. Unfortunately, in most cases, the mechanism underlying potential phage-antibiotic interactions is unknown. In addition, although in vitro assessments of synergy justify combination therapy, these studies are rarely further pursued within animal models.
Conclusions
Antibiotic resistant bacteria threaten the extraordinary health benefits achieved with antibiotics. As we face the current antibiotic crisis, phage therapy has the potential to alleviate the ever-increasing problem of infectious diseases, either as an alternative to antibiotics or in combination with antibiotic therapies. Although clinical successes suggest the tolerability and, in some cases, efficacy of phage therapy, the clinical functionality still requires careful definition. The lack of well-controlled clinical trial data and complex regulatory frameworks have driven most recent human data generation on a single patient compassionate use basis. Most data include the concomitant use of antibiotics, which makes it difficult to draw solid conclusions as to the effectiveness of phages alone. However, compassionate use human data support the exploration of the combination of phages and antibiotics, which is a promising avenue for near-term clinical development.
Recent improvements in phage genomics, purification, and formulation have greatly contributed to improving the efficacy and reliability of phage therapy. Current knowledge gaps exist on the appropriate routes of administration, phage selection, frequency of administration, dosage, phage resistance, and pharmacokinetic and pharmacodynamic properties of phage. In addition, phages require thorough investigation into the immunologic response they may elicit. Advancement of other technologies that support phage therapy will have to follow suit and evolve. These technologies includes (1) rapid and accurate phage assessment methods and criteria, (2) standardization of phage manufacturing, (3) phage banking, (4) phage product stability during storage and transport, and (5) new quantitative methods that allow for precise monitoring of pharmacologic parameters of phages.
Some may decide, of course, that the transition to phage therapy cannot be done, perhaps because of the lack of necessary capabilities or financial resources or because of the belief that chemical antibiotics are superior and can defeat the resistance problem. The redoubling efforts to enhance ineffective antibiotics has in many cases succeeded in improving their performance.
However, this belief may only be postponing the day of reckoning for a postantibiotic era. Thus, development of alternative antimicrobial therapies is critical. Although more translational research is needed before the clinical implementation of phage therapy is feasible, phages may be pivotal in safeguarding the overall health of humans in the near future.
Disclosures
The authors have indicated that they have no conflicts of interest regarding the content of this article.
Acknowledgments
All authors conceptualized, designed, wrote, and reviewed the manuscript.
Appendix A. Supplementary data
The following are the Supplementary data to this article:
Development and use of personalized bacteriophage-based therapeutic cocktails to treat a patient with a disseminated resistant Acinetobacter baumannii infection.
Eradication of a multidrug-resistant, carbapenemase-producing Klebsiella pneumoniae isolate following oral and intra-rectal therapy with a custom made, lytic bacteriophage preparation.
Salvage debridement, antibiotics and implant retention (“DAIR”) with local injection of a selected cocktail of bacteriophages: is it an option for an elderly patient with relapsing Staphylococcus aureus prosthetic-joint infection?.
Innovations for the treatment of a complex bone and joint infection due to XDR Pseudomonas aeruginosa including local application of a selected cocktail of bacteriophages.
Phage therapy for limb-threatening prosthetic knee Klebsiella pneumoniae infection: case report and in vitro characterization of anti-biofilm activity.
Clin Infect Dis.Jul 2020; 23 ([Epub ahead of print])
Efficacy and tolerability of a cocktail of bacteriophages to treat burn wounds infected by Pseudomonas aeruginosa (PhagoBurn): a randomised, controlled, double-blind phase 1/2 trial.
A controlled clinical trial of a therapeutic bacteriophage preparation in chronic otitis due to antibiotic-resistant Pseudomonas aeruginosa; a preliminary report of efficacy.
Comparative analysis of different preservation techniques for the storage of Staphylococcus phages aimed for the industrial development of phage-based antimicrobial products.
Efficiency of single phage suspensions and phage cocktail in the inactivation of Escherichia coli and Salmonella typhimurium: an in vitro preliminary study.