[Cause Exploration Prizes] Antimicrobial Resistance

By Open Philanthropy @ 2022-08-24T10:34 (+9)

This anonymous essay was submitted to Open Philanthropy's Cause Exploration Prizes contest and published with the author's permission.

If you're seeing this in summer 2022, we'll be posting many submissions in a short period. If you want to stop seeing them so often, apply a filter for the appropriate tag!

Overview/Importance

The rise of antimicrobial resistance (AMR) is turning into one of humanity’s most severe problems. Both direct and indirect consequences of AMR have lasting impacts on people’s health. Short- and long-term physical health is greatly affected by AMR. A resistant bacterial infection will double the chance of contracting a serious health issue and triple the chance of death. AMR also impacts individual economic health. From the initial infection and resultant care to the opportunity cost of wages not gained because of the sickness, money is lost. Multiply that by thousands of people and AMR related costs become increasingly high for country level governments and directly impact their GDP.

AMR has long been known to the scientific and medical communities to be a significant risk to health. The World Health Organization (WHO) developed a global containment strategy for AMR in 2001. Ever since then, other initiatives like, the Global Action Plan (GAP) on AMR and The Global Antimicrobial Resistance and Use Surveillance System (GLASS) were created. These programs have been fruitful with surveillance and data collection in which 66 countries participated. Routine data surveillance is done on AMR and antimicrobial consumption (AMC). GLASS also conducted focused surveillance on emerging AMR. Along with surveillance, scientists around the world have been working towards effective solutions. There have been developments in synthetic antimicrobials, silver nanobodies, and other therapeutics. However, WHO indicates that AMR is on track to cause 10 million deaths by 2050. The regions of Africa and Asia are projected to account for around 90% of the estimated casualties.

A re-emerging technology can be a major part in the fight against AMR. Bacteriophages were first discovered in 1910 and were used to treat various illnesses until the rise of antibiotics around 1940. Recently, there has been a resurgence in research attempts to use bacteriophages to fight AMR. A large part of the slow advancement of bacteriophage usage is cost. Phages are extremely specific to a certain bacterium. Unless the exact phage is found to fight that exact bacterium, scientists have to investigate new methods. Some potential paths they have followed include making a phage cocktail and re-engineering the bacteriophage. Both methods have proved effective, but not yet used in widespread application. A long-term commitment to researching the value of bacteriophage therapy increases the likelihood of future patient use. As the potential of bacteriophage therapy grows, the world needs an organization that will strategically fund phage research.

We hope to further the research in using bacteriophages to fight AMR. Our research will consist of using a T4 phage to introduce CRISPR-Cas proteins into bacteria. The CRISPR-Cas system will then edit the DNA of the bacteria causing it to go through apoptosis. This accomplishes the goal of killing off antimicrobial resistant bacteria (AMRB). A problem we have encountered is the selectivity of phages. A single type of bacteriophage will prey only on certain bacteria. We are hoping to remedy this problem by using a sortase-mediated reaction to alter the binding receptors allowing the bacteriophage to adhere to any bacteria instead of only a certain type. Using the sortase will allow for an external modification that can easily alter the bacteriophage as opposed to reengineering its genetic makeup. Additionally, the CRISPR-Cas system will be effective in almost all bacteria and therefore can be utilized multiple times with only slight modification. This design aims to simply reduce the number of virulent bacteria allowing for the immune system to fight off the remaining bacteria. As of right now, there has been no testing done on its effectiveness treating infection with or without antibacterial medication. However, using a combination of phages and medication is believed to lead to a more complete treatment because a lesser dose of antibiotics would be required if the bacteriophage knocks out a majority of the bacteria. We have no reason to think our design would deviate from that belief.

The pursuit of an internal usage of bacteriophages will be the focus of the research, as most AMRB are internal. Thus, they could be treated by internalizing the bacteriophage. There have been multiple instances of phage research against outer infections before and during World War II. Although a necessary pursuit, there are currently many treatments to fight surface level infections. The main problem the world is facing now is internal antibiotic resistance. Another reason this pursuit is of great importance is because the cause of antibiotic resistance is that the bacteria are constantly mutating and causing the antibiotics to be ineffective. Since our research hopes to allow for binding to any bacteria, it would be almost impossible for the bacteria to mutate in a way that scientists could not engineer a solution. As the bacteria evolve to become resistant to the phages, the phages can be engineered to better infect the bacteria. Having said that, diminishing the spread of AMR will still require major interventions. A grantmaking body focused on decreasing AMR worldwide could be a significant part of the overall solution.

Once bacteriophage research is underway, the application of it can be greatly expanded. Although this research focuses on AMR, bacteriophages could be applied to diseases such as cancer or cystic fibrosis. The application of bacteriophages will lead to many advancements in science; it just needs a financial jumpstart. Many other projects like new antibiotic research have immense costs and frequently receive funding. Yet, bacteriophage research, with all its potential, is not seeing the same amount of attention. 

One of the big questions bacteriophage research raises is: why pursue this form of treatment? There is still the possibility of finding or manufacturing new antibiotics in order to cure infections or bypass antimicrobial resistance. A main reason why bacteriophage research is a worthwhile pursuit is that it is better for the human body than antibiotics. When ingesting antibiotics, they are not always able to differentiate between normal bacteria and bacteria that are harmful to the human body. By using bacteriophages, their base nature and specific design will ensure normal microbiota will remain strong and only the pathogen will be destroyed. Furthermore, our world is changing, most predictions indicate that AMR will only grow in the coming years and decades. As a society, we must expand out into new healthcare territories to resolve current and future ailments. Granted, phages are not a new technology, yet we must seek out any area in which we can improve. Bacteriophages are of said area, we have not yet discovered their full potential. A full-time staff dedicated to making educated decisions on phage research and allocating funding would help uncover all that bacteriophages can do for us.

Tractability

Multiple research initiatives have explored possible alternatives to traditional antibiotics. Unfortunately, such processes take many years and require a massive number of resources. With direct support towards the most promising projects, many aspects of drug development can be streamlined, much like recently with the COVID-19 vaccine. 

It is also important to consider that with new research techniques and approaches, it is difficult to predict whether the results will finally point us in our desired direction. A major driving principle of science is that there is much we still do not understand and even unexpected results might be useful. Still, we believe that bacteriophages are the future.

A success for phage treatment against AMR is the story of one Tom Patterson. Patterson, a professor of Psychology at UC San Diego, was infected by a multi drug resistant strain of Acinetobacter baumannii while in Egypt. After being relocated to UC San Diego Health, Patterson received a novel treatment. With Food and Drug Administration (FDA) approval, Patterson was given a phage cocktail that was selective towards A. baumannii. Soon after the treatment started, Patterson showed significant signs of improvement. Since then, five other patients at UC San Diego Health were administered with an experimental phage treatment.

With the success of phage treatments at UC San Diego Health, the Center for Innovative Phage Applications and Therapeutics (IPATH) was established in 2018. It is one of a few dedicated bacteriophage research centers in North America. As such, IPATH will be a key resource for grantmakers dealing with phage technology. Another similar research center, The Center for Phage Technology (CPT) at Texas A&M University was founded even earlier. These two institutions are both located in the U.S., a place where phage treatment is only allowed in emergency situations and after federal approval. We propose that a collaboration should be formed between these centers and philanthropic organizations in order to lobby for the acceptance of phage treatment into more clinical trials and thus, mainstream patient care.

An example of bacteriophage-centered quality patient care can be found at the Eliava Phage Therapy Center (EPTC). Located in Tbilisi, Georgia, a former member of the Soviet Union, the EPTC does both local and distance phage therapies. The local therapy package offered by the EPTC is the focal point of its healing capabilities. For 3,900 euros (~$3,965 USD), a patient will get tested to determine if custom phages are needed, continuous phage treatments (if needed), return investigations on effectiveness of treatment(s), and many support services. Although, on the EPTC website, under “FAQ”, the response to the success rate question is ambiguous and does not give a clear answer. However, a study of the phage therapy experience at the EPTC can be found online and available to the public. It is worth noting that the study was authored by members of the Eliava Institute of Bacteriophages, Microbiology, and Virology and the EPTC. The contents of the study cover the treatment of three patients. All three of the patients took previously prepared phage concoctions and at least ordered one custom phage treatment, with five being the most custom phages ordered. In the end, none of the patients were fully cured of their bacterial infection. Nonetheless, two of the patients “accomplished their goals of switching from antibiotics to phages with no adverse effects and with subjective alleviation of their symptoms” (Zaldastanishvili et al.). In the case of decreasing AMR, I find this study to accomplish that. Above all, the use of less antimicrobials will at least prevent more resistance from occurring.

With this theme in mind, it is likely that alternative approaches may be the most efficient research projects to support, especially considering that decades of research and countless dollars still haven’t produced a solution towards antibiotic resistance. Novel creative approaches directed by a new generation of scientists, therefore, may provide the different perspective and insight necessary to finally build a better future for medicine.

In fact, along with bacteriophage engineering, multiple other exciting methods such as enzyme inhibitors, plant-derived phytochemicals, antimicrobial peptides, RNA silencing, CRISPR-Cas, nanoparticles, and a physicochemical approach using non-thermal atmospheric pressure plasmid are in the early stages of development. Many scientific limitations however still exist in these methods regarding specificity and delivery among others and it may still be years before solutions are discovered. Since they are newer ideas that may not work, we are hoping to take advantage of an older idea by enhancing it. This will save a lot of money and allow for the research to make the most of its money because we will not be starting from the ground and building up. We already have the building blocks; we just need the funding to create the whole picture of an antibiotic resistance free world. 

It is important to mention as well how impactful the iGEM organization is for inspiring our project. They encourage college students worldwide to solve real world problems and build a better understanding of both the scientific and societal aspects of research. A few projects from previous competitions have even led towards new technologies. In addition, for many individuals, the experience helped guide them towards their future careers. Supporting Miami University’s iGEM team (us, the authors), therefore, means not only encouraging novel studies on combating antibiotic resistance. It also means providing opportunities for a future generation of researchers.

Neglectedness

Currently there are numerous initiatives that exist to combat antibiotic resistance. These range from Antibiotic Stewardship programs to government and company sponsorships such as the Bill and Melinda Gates Foundation. For instance, in 2016, former U.S. President Barack Obama proposed to double the budget for antibiotic resistance research to $1.2 billion. Other funding opportunities have come from the Agency for Healthcare Research and Quality (AHRQ), the AMR Action Fund, and the National Institute of Allergy and Infectious Diseases (NIAID).

However, there are still several limitations that have slowed progress in current research. More informed and purposeful allocation of funding as well as campaigns to raise awareness amongst the general public are both important topics to address if we hope to improve current circumstances. For instance, numerous studies within the past two decades suggest that excessive use of antibiotics in the agriculture/food production industries, imprecise diagnosis/prescription by physicians, and improper use by patients have exacerbated the problem of antibiotic resistance. Misuse by patients and individuals in general refers to behaviors such as not finishing the treatment after symptoms lessen and storing leftover antibiotics for future use. One goal of iGEM is to open avenues of communication with non-scientific audiences. 

Our Miami team, in fact, has led and presented at two separate education events this summer. We worked with groups of elementary and middle school aged children to guide them through discussion about bacteria and antibiotic resistance as well as several engaging STEM related activities. We view these efforts and those of iGEM in general as a critical step to improving communication between scientific communities and the general public. The pandemic itself has served as a reminder about the dangers of miscommunication and if we are to successfully face future threats to global health, educating citizens worldwide is necessary. 

Antibiotic resistance is particularly overwhelming to study due to variability amongst pathogenic bacteria in both the mechanism and extent of resistance. This suggests that despite efforts to combat antibiotic resistance, it is difficult to gauge whether the topic is being addressed efficiently or even understood to its full extent. Phage therapy itself, in fact, has been ignored in western medicine for decades- partially as a result of overconfidence in antibiotics (which were seen as a “miracle drug”). The Miami iGEM team hopes to be part of the movement to amend the limited knowledge in this topic and compensate for the lost years of potential discoveries. Programs such as iGEM allow our team at Miami University to potentially present a new perspective and solution, which is likely to stimulate the innovation to resolve global issues such as antibiotic resistance.

Solutions/Money

Researching multiple modified phage concepts and production processes from scratch would be costly at first. Especially as a group of young scientists/lab, receiving funding can be difficult. Furthermore, when developing antibiotics is more prevalent and has been effective for the past few decades; why change it? The chance at a more cost effective, healthy, and dynamic solution is why. Producing modified phages will be that solution. However, that is usually expensive work, but a study has created a relatively cheaper phage genome synthesis production process. The study utilizes the Sniper assembly, named after the Sniper cloning method, the assembly uses. The scientists succeeded in synthesizing the Acinetobacter phage AP205 genome at about $0.015 per base pair (bp). The genome for AP205 is 4268 bp long; thus, it costs $64.02 per phage. Of course, that is still expensive overall. Even so, it is much less costly than other methods for gene assembly (figure 7). As well as, partial bacteriophage modification production may cost even less. In that, only part of the genome needs to be synthesized, rather than all of it. The two main areas that are foreseen to cost the most are clinical trials and initial production. Although costly, an initial investment is needed in all aspects of science. 

As mentioned above, once the initial research is done, the few modifications needed over the years will be greatly cheaper than the money used to create a whole new antibiotic. More so, at the current rate of AMR growth, said new antibiotics might become obsolete in a few years or earlier. By just editing the binding receptors of the bacteriophage or other minor changes, money will be saved. Additionally, strategic grant giving will optimize money spent on AMR research.

Even though more research needs to be done, we hope that the development of novel phage technologies will allow for better quality of life in all regions of the world. Currently antibiotics are hard to get in developing/Global South nations and disease is still extremely prevalent. An inexpensive bacteriophage drug could alleviate those problems and help those people live a healthier life.

Major Counter Arguments/ Uncertainty

One of the biggest problems scientists face with using bacteriophages is the lack of public knowledge. Since bacteriophages are classified as viruses, many people will shy away from their usage due to the recent COVID-19 virus outbreak. Viruses have always had a negative connotation and by saying we will introduce a virus to fight the bacteria, we foresee people focusing on the virus instead of the health benefit. Additionally, since bacteriophages can be classified as living (this is still a debate but for the purposes of this article we will classify it as living) they are temperamental. As with all living things, they cannot always be controlled which has been a red flag raised by many people. Another major obstacle this research has faced is the argument surrounding genetic modification. This has been a large argument in the science community. How people stand on these issues can make or break their acceptance of phage therapy. In some cases, components involved in phage research will cause people to be wary and fully against it. The principal way of winning these people over towards phage acceptance is educational pursuits. For the most part, once people realize the benefits of phage therapy, they should see its value. This argument is one of the reasons we choose to work with CRISPR-Cas13A because it targets the transcriptome instead of the genome. This key piece of information should be publicized to show that the bacteriophage will not alter a human's DNA which is a concern raised by many anti-GMO people. Overall, the main issues foreseen in regards to the project have been addressed and we therefore hope that we can gain support in pursuing this line of research. 

Sources

Singh, S., Sharma, A., Sharma, R. P., Kaur, R., & Sharma, R. (2021). “A comprehensive insight on the COVID-19 vaccine candidates.” Journal of Family Medicine and Primary Care, 10(7), 2457. https://doi.org/10.4103/jfmpc.jfmpc_1570_20 

Murugaiyan, J., Kumar, P. A., Rao, G. S., Iskandar, K., Hawser, S., Hays, J. P., Mohsen, Y., Adukkadukkam, S., Awuah, W. A., Jose, R. A., Sylvia, N., Nansubuga, E. P., Tilocca, B., Roncada, P., Roson-Calero, N., Moreno-Morales, J., Amin, R., Kumar, B. K., Kumar, A., van Dongen, M. B. (2022). “Progress in alternative strategies to combat antimicrobial resistance: Focus on antibiotics.” Antibiotics, 11(2), 200. https://doi.org/10.3390/antibiotics11020200 

White House plans big 2016 budget ask to fight antibiotic resistance. Science. (n.d.). Retrieved August 1, 2022, from https://www.science.org/content/article/white-house-plans-big-2016-budget-ask-fight-antibiotic-resistance

Kortright, K. E., Chan, B. K., Koff, J. L., & Turner, P. E. (2019). “Phage therapy: A renewed approach to combat antibiotic-resistant bacteria.” Cell Host & Microbe, 25(2), 219–232. https://doi.org/10.1016/j.chom.2019.01.014

Mallah, N., Orsini, N., Figueiras, A., & Takkouche, B. (2022). “Education level and misuse of antibiotics in the general population: A systematic review and dose–response meta-analysis.” Antimicrobial Resistance & Infection Control, 11(1). https://doi.org/10.1186/s13756-022-01063-5

Dadgostar, Porooshat. “Antimicrobial Resistance: Implications and Costs.” Infection and drug resistance vol. 12 3903-3910. 20 Dec. 2019, doi:10.2147/IDR.S234610

HIV drug resistance report 2017. Geneva: World Health Organization; 2017. License: CC BY-NC-SA 3.0 IGO

Azam, Aa Haeruman et al. “Bacteriophage Technology and Modern Medicine.” Antibiotics (Basel, Switzerland) vol. 10,8 999. 18 Aug. 2021, doi:10.3390/antibiotics10080999

Yuan Ding, He Chen, Jiao Li, Lianrun Huang, Guangyue Song, Zhenfeng Li, Xiude Hua, Gualberto Gonzalez-Sapienza, Bruce D. Hammock, and Minghua Wang “Sortase-Mediated Phage Decoration for Analytical Applications.” Analytical Chemistry 2021 93 (34), 11800-11808, doi: 10.1021/acs.analchem.1c02322

Guimaraes, C., Witte, M., Theile, C. et al. “Site-specific C-terminal and internal loop labeling of proteins using sortase-mediated reactions.” Nat Protoc 8, 1787–1799 (2013). https://doi.org/10.1038/nprot.2013.101

Zaldastanishvili, Elisabed et al. “Phage Therapy Experience at the Eliava Phage Therapy Center: Three Cases of Bacterial Persistence.” Viruses vol. 13,10 1901. 23 Sep. 2021, doi:10.3390/v13101901

Huiran Yeom, Taehoon Ryu, Amos Chungwon Lee, Jinsung Noh, Hansaem Lee, Yeongjae Choi, Namphil Kim, and Sunghoon Kwon “Cell-Free Bacteriophage Genome Synthesis Using Low-Cost Sequence-Verified Array-Synthesized Oligonucleotides.” ACS Synthetic Biology 2020 9 (6), 1376-1384, doi: 10.1021/acssynbio.0c00051

Gandra, C., Barter, D.M., Laxminarayan, R. “Economic burden of antibiotic resistance: how much do we really know?” Clinical Microbiology and Infection, ISSN: 1198-743X, Vol: 20, Issue: 10, Page: 973-980, doi: https://doi.org/10.1111/1469-0691.12798