Topic Analysis: Phage Therapy

Among the many harms inflicted upon the continent of Australia by European migrants was the introduction of rabbits to the island nation. There are multiple documented introduction events, including usage as food and targets for hunting. By 1920, it was thought Australia may be home to more than 10 billion rabbits, [1] each outcompeting local fauna for food and wrecking havoc on both crops and native vegetation. This was an unsustainable population, one that threatened the entire continent, and thus aggressive culling attempts were undertaken. These included the release of a rabbit-specific virus, myxoma, in 1950 that resulted in the death of 99% of the problematic lagomorphs. [2] While reducing the population from 10 billion to 10 million may seem an incredible achievement, it came with a hefty price, namely the surviving rabbits had a high likelihood to carry a genetic mutation that conveyed resistance to myxoma. Today the population is thought to be over 200 million rabbits, all seemingly descended from those resistant ancestors that survived.

Rabbits can reach sexual maturity between three and six months of age, meaning in the 70 years since the myxoma culling event, there have been somewhere between 140 and 280 generations of rabbits (for comparison: humans have had approximately three generations during the same period).

What does all this have to the with the topic of the blog, Phage Therapy? Consider this, if myxoma resistant rabbits have had 140-280 generations of offspring to build upon their resistance genes, what could happen if they reproduced exponentially faster? Bacteria reproduce extremely, in as little as twenty minutes, leading to much more rapid mutation and potential for resistances to be introduced. In fact, under optimal conditions, bacteria could have nearly 2 million generations in the same 70-year period since the myxoma event of 1950.

Enter MRSA (methicillin-resistant Staphylococcus aureus), colloquially considered a 'Super Bug', MRSA is the most widely known antibiotic resistant bacteria species plaguing humankind. A distinct strain of S. aureus, MRSA infections are indistinguishable from common staph infections aside from their unwillingness to respond to antibiotic treatment. According to the CDC, both S. aureus (30% of people) and MRSA (5% of people) are common on skin [3] and generally harmless, however if an infection occurs, doctors need powerful tools to fight back. Currently the available tools are becoming less efficient at fighting infection and may soon be insufficient to meet the challenges of a growing population of antibiotic resistant pathogens.

In 2019, the CDC observed 2.8 million cases of antibiotic resistant infections in the United States (from various infectious agents, both bacterial and fungal), with more than 35,000 deaths attributable to these infections. [4] Prior to the discovery of penicillin and subsequent antibiotics, infections was a leading cause of death, and without sweeping changes to antibiotic usage and new treatment developments, may yet be again. Amongst the most grim predictive models, has annual deaths attributable to antibiotic resistant bacteria exceeded 10 million by 2050.[5]

Number factors have contributed to this growing problem, including:
1. Overprescription of antibiotics by doctors, particularly as a calmative to patients with viral infections
2. Administration of antibiotics to livestock
3. Lack of interest in novel drug development because the return on investment for antibiotics is lower than other pharmaceuticals

With an increasing number of antibiotic resistanc pathogens, a rising number of cases and deaths, and a dearth of new antibiotics being brought to market, how can science hope to counteract a pending health crisis? The answer could come from the single coolest-looking organism on planet Earth, the bacteriophage.

Bacteriophages are omnipresent viruses (estimated to exist in unimaginable quantities, >10^31) that target specific bacteria species for infection.[6] Many bacteriophages accomplish this through a process called the lytic cycle (see diagram below). In the lytic cycle, a bacteriophage attaches to a bacterium, injects its DNA, and hijacks the host's cellular functions to replicate. When the amount of virus in the host cell is to great, the cell lyses (bursts) and the virus is released into the environment. This process allows for both the destruction of the target cell and the creation of more bacteriophage, resulting in high volumes of bacteriophage from a smaller initial population.

All this background information finally brings us to the main topic of this blog: Phage Therapy and Personalized Medicine. Scientists have long studied the mechanisms of how phages infect bacteria, replicate, and lyse cells but have recently refocused attention on the mechanisms as potential treatments for antibiotic resistant bacteria.

Utilizing bacteriophages for personalized medicine could give doctors highly precise weaponry to respond to antibiotic resistant bacterial infections, but additional research and robust clinical trials are needed.

In an idyllic world, doctors would obtain a sample from an infection, sequence the DNA to determine the infectious agent, choose the appropriate bacteriophage(s) and administer them to the patient. This process would allow doctors to administer small doses of a targeted treatment directly to the site of infection and use the replication methods of bacteria as a factory to generate additional bacteriophage. In some previously conducted clinical trials, a single treatment of bacteriophage was sufficient to treat an infection.

Based on this information, phage therapy may sound like a homerun, however there are numerous important barriers preventing wide-scale adoption. The biggest hurdles include:
1. Generation of a phage library: As mentioned previously, there are a lot of bacteriophages in the world and each targets different bacteria. To effectively use phages as treatment methods, scientists need to document the known phages, discover novel phages, and test and categorize each's target bacteria and efficacy. This is a challenge, not only due to the logistics of conducting the research but because unmodified phages are subject to patent law, making a cohesive library nearly impossible.
2. Treatment plans: As seen in the following diagram, antibiotic resistant infections are not limited to a patient's skin. Any body part can be a host for an infection and the route of phage administration becomes very important. These routes include oral, topical, inhalation, intravenous, and intrarectal modalities, with each requiring medications containing different properties. Determining route of administration is just one part of a treatment plan however, as dosage, frequency, phage cocktail composition, and other factors must also be considered when formulating a plan.

3. Phage resistant bacteria: Yes, bacteria can become resistant to phages, however the frequency and likelihood is substantially lower than antibiotic resistance. The reason for this is the much narrower range of targets when phages are administered when compared to antibiotics. In a way, a bacteriophage is a precise cut made with a scalpel, while chemical antibiotics are napalm and take the scorched-earth approach to infection treatment. This indiscriminate attack by antibiotics harms all bacteria in the host, including those that may play a beneficial roll.
4. Phage cocktail development: The promise of uniquely personalized phages selected and administered to patients based upon their infection is powerful, but unlikely. The much more likely solution are cocktails of phages selected to target a range bacteria that cause similar infections. This method would allow for a wider range of infections to be treated by a smaller number of medications, doctors to potentially eliminate the need for DNA sequencing, and a more rapid response to patients antibiotic resistant infections. To generate these cocktails, researchers need to understand each phage, how they may interact, how the combinations may impact patients based on their health profile or medication usage, and more, before "off-the-shelf" cocktails are a reality.
5. Patient acceptance: As the pushback to vaccinations has shown, a subset of people are unwilling to take direction from the medical community, even when the recommended treatment is in their best interests. Phage therapy expands upon these pitfalls because it involves the administration of a mutable organism into the patient. While bacteriophages and other viruses are not technically considered 'living organisms' as they cannot reproduce on their own, they do have DNA that is subject to random mutations. In fact, bacteriophage DNA mutates at a rate approximately 100x faster than their target bacteria. This means random errors are introduced in viral DNA replication approximately 1 time for each 10^8 DNA nucleotides replicated. This has less to do with any differences between bacteria and viruses and is directly proportional to the size of the organism's genome. More genetically complex organisms have larger genomes and more mechanisms in place to prevent or correct errors. Thankfully, the higher mutation rate in bacteriophages is beneficial in nearly every case, as it allows the viruses to rapidly change and keep pace with mutations in their target bacteria.

With such major roadblocks to overcome before phage therapy could become a viable strategy for combating antibiotic resistant infections, why should researchers devote time and effort towards its development?

There are numerous reasons, some of which this blog has already touched upon that make phage therapy a true potential game changer, including:
1. Low dosages: Owing to the bacteriophage's ability to utilize the bacteria's own replication mechanisms, a small initial dose of a phage cocktail can be sufficient as it will proliferate as long as the bacterial infection is present.
2. Minimal impact on normal flora[7]: Despite the occasional infection, the vast majority of bacteria in/on the human body are mundane and sometimes beneficial. Antibiotics attack these bacteria just as readily as the infectious agents, leading to destruction of beneficial bacteria and more rapid mutation towards resistance. Phage therapy would all but eliminate the stress put on non-target bacteria.
3. Low toxicity[7]: Aside from extremely rare instances of immune response triggered by phage therapy, the results of previous patient tests indicate that phages have very little chance to cause harmful side effects.
4. Resistance: As mentioned, bacteria can develop resistance towards phages, but this is extremely uncommon and would occur much less frequently than with antibiotics. Additionally, bacteriophages would not be administered in a similar fashion to antibiotics that have hastened resistance, namely they would not be given to livestock or prescribed for non-bacterial infection.
5. Effective against biofilms[7]: So far, much of the discussion of bacteria in this blog has assumed they are free-floating or otherwise unencumbered in the host organism. This is not common, as many infections form a bacterial biofilm, essentially a matrix of interwoven bacteria that has adhered to a surface of some sort. Phage therapy has shown more effectiveness at targeted and destroying these 'protected' bacterial cells compared to antibiotics.
6. Administered with antibiotics: Antibiotics, despite their decreased effectiveness, are still science's best weapon against infection. Because of their different methods of attack and lack of interactivity, antibiotics can be administered in tandem with phages for a more robust treatment plan.
7. Properties of phages: Bacteriophages exist everywhere and identifying new candidate phages can be as simple as scooping soil from your garden. Identifying and developing new phage treatments is substantially faster and less resource intensive than antibiotics and project to have a better financial return on investment. Bacteriophages are also very robust, easy to store (surviving for years at 4C with minimal degradation) and can thus be quickly and safely transported as needed.

Antibiotics can no longer continue to be humanity's sole treatment option against infections. The rapid increases in cases and species of antibiotic resistant bacterial has hastened the need for additional treatments. Phage therapy has the potential to be a second weapon in the the battle against rapidly evolving bacterial infection, a weapon with more precise targeting and fewer harmful side effects for patients and society. The days of personalized phage therapy are still in the future, but the research being done today highlight the potential for a lower cost, safer, and more robust method for treating infections.

References:
1. Rabbit Free Australia
2. University of Oxford
3. CDC MRSA Information
4. CDC Antibiotic Resistant Infection Threat Report 2019
5. Georgetown Law Review
6. Clinical Therapeutics
7. Bacteriophage