Antibiotic Resistance: Challenges and CRISPR’s Promise

Mansi Joshi

One day at St. Mary’s Hospital, Alexander Fleming was observing Staphylococcus aureus bacteria colonies and noticed they were reduced or killed by the mold festering in the petri dishes. What was a ruined experiment turned out to be one of the best accidents for the world, when Fleming discovered the mold that was reducing the ability of the bacteria to grow significantly. This is known today as penicillin, which sparked an interest in years of research and experiments that have provided us with the most effective treatments today. 

However, as Marian Wright Edelman once stated, “In every seed of good there is always a piece of bad.” With antibiotics came a new era of medicine, but antibiotic resistance remains a common problem today that only seems to grow with abuse of prescription antibiotics. The CDC itself and numerous other health organizations say that 20 to 50 percent of all antibiotics prescribed in U.S. acute care hospitals are either unnecessary or inappropriate. It is important to note that antibiotics are not effective treatments for viral infections , which are far more common than bacterial infections, such as coughs and colds. Organizations such as private practices, hospitals, and in-store clinics such as CVS Health have become more careful in the way they prescribe antibiotics to prevent further antibiotic resistance and keep antibiotics as powerful treatments for generations to come. 

Antibiotic resistance arises from spontaneous mutations, or changes in DNA sequences, that allow the bacteria to develop mechanisms and evade antibiotics. The bacteria with the best mutations suited for the environment will survive antibiotic treatments, an idea known as “survival of the fittest.” Bacteria evade the antibiotics by the following mechanisms

  1. The bacteria do not allow antibiotics into the cell by destroying entryways and creating a highly selective membrane.
  2. The bacteria evades antibiotics by using efflux pumps in their membrane to remove antibiotics that enter the cell, thereby preventing the antibiotic from exerting its effects on the bacteria. Efflux pumps remove toxic substances from the bacterial cell and shuttle them into the extracellular environment. 
  3. The bacteria changes or inactivates antibiotics with mutations that allow proteins to digest the drug.
  4. The bacteria change the receptor that antibiotics would bind to so that the drug can no longer exert its effects.
  5. The bacteria develop new cellular mechanisms that can bypass the antibiotic drug.

Mutations that confer resistance through these properties make it difficult or impossible to treat certain infections. Although it seems simple to say that people can reduce the use of antibiotics to reduce antibiotic resistance, doing so will not completely eradicate the problem due to antibiotic drug abuse from previous decades. However, scientists are developing methods to help mitigate the effects of antibiotic resistance in the human population.

The first of these methods is to utilize antibiotic “drug cocktails”, a combination of multiple antibiotics that do not confer cross-resistance to treat bacterial infections. Cross-resistance is the phenomenon where the effects from one antibiotic drug increase the resistance of the bacteria to another antibiotic drug, thereby decreasing the effectiveness of a treatment which is not ideal to the patient. Cocktails, when used correctly, are an effective method in treating bacterial infections. This is because bacteria would require all the mutations associated with the drug’s targets to be resistant to the drug cocktail. Therefore, it is unlikely that the bacteria will have multiple mutations of drug resistance. 

Another method of reducing antibiotic resistance is to alternate and fluctuate different antibiotic medications. Once the bacteria gain resistance to one medication, they are less resistant to the second antibiotic used as an alternative. Studies show that this allows the bacteria to be more susceptible to death and thereby slows the spread of antibiotic resistance. 

Finally, phage therapy can also prove to be beneficial. Phages are viruses that kill bacteria and have been able to effectively fight resistant bacteria. Training the phages to predict bacterial resistance methods under multiple generations and multiple mutations allows the phages to better fight off primary infections. In fact, phage therapy proved  to be an effective treatment in infectious disease epidemiologist Steffanie Strathdee’s life when her husband was infected with a superbug, a bacterial strain that is highly resistant. The infection was so deadly that the doctors told Strathdee that her husband would not make it. However, Strathdee learned of phage therapy and watched as the doctors injected the treatment into her husband. Her husband survived the infection through this therapy and Steffanie Strathdee and her husband released a book regarding the experience. 

However, the most promising is a new method of antibiotic resistance that is in trial but is said to reverse the effects of antibiotic resistance and sensitize bacteria to antibiotics again. Through using CRISPR-Cas9, which is a technique to cut DNA at specific locations, researchers found that they can cut antibiotic resistance genes in bacteria to reverse the prior effects of antibiotic resistance. CRISPR-Cas9 is a natural system used in bacteria that provides defense against viruses by cutting their DNA, and researchers have been utilizing this system to selectively destroy plasmid genes that confer antibiotic resistance in bacteria. Plasmids are small, circular pieces of DNA that can replicate between bacteria through sexual reproduction between bacteria known as conjugation. By removing these plasmids, CRISPR-Cas9 prevents the spread of these plasmids and reduces the ability of the bacteria to spread resistance within the population. Researchers have shown that this method could have promising results and eradicate antibiotic resistance from populations in future generations. 

However, there were some challenges within the research itself. The first challenge is that the CRISPR-Cas9 system must be able to target multiple DNA sequences as different bacterial strains may have varying plasmid sequences, thereby conferring resistance through different mechanisms of antibiotic resistance. Therefore, it is difficult and costly to design a unique CRISPR-Cas9 system for multiple bacterial strains. Additionally, it takes time to create these systems and effectively test them for approval in the larger population. Another challenge is the potential of creating highly resistant strains if bacteria evolve resistance to the CRISPR-Cas9 system. It seems hard to believe that bacteria can evade this effective cutting machinery; however, just as bacteria have found ways to evade current systems there is no telling if they can find ways to evade newer technologies. 

Regardless, CRISPR-Cas9 could be the world’s saving grace with regards to the issue of antibiotic resistance. A highly specific mechanism, this could reduce the effects of resistance and cause less harm to the beneficial bacteria in the body. Furthermore, it provides another opportunity for increasing effectiveness of current treatments in the form of combination therapies. With this powerful tool, continuing the development of this technology could lead to better ways of treating antibiotic resistance and keep antibiotics as effective treatments for generations to come. We hope to continue thanking Alexander Fleming for providing the world with antibiotics!