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The Rise of Antibiotic Resistance

Antibiotics have been used to treat bacterial infections since the mid-1900s, with the discovery of penicillin occurring in 1928. Yet soon after the use of these drugs became ubiquitous with bacterial infections, antibiotic resistance appeared. The 21st century has seen a disturbing rise in what are known as “superbugs”—bacteria strains that have developed multidrug resistance (MDR) and have high rates of mortality. To make matters worse, many of these superbugs have adapted within hospital settings, making them particularly dangerous for the already vulnerable population that resides there. One such strain, Pseudomonas aeruginosa, or P. aeruginosa, “is of considerable concern for patients with cystic fibrosis” according to Julian and Dorothy Davies of the Department of Microbiology and Immunology at the University of British Colombia (2010, p. 417-420). While antimicrobial agents have saved countless lives since their advent, the use of antibiotic drugs has directly led to the increase in antibiotic resistance in a wide range of bacteria strains through the selective survival of cells with resistance genes.

How Antibiotics Work

There are a variety of ways that different antimicrobial agents work to destroy bacterial cells; according to Dr Fred C. Tenover of the Division of the Healthcare Quality Promotion at the Center for Disease Control, there are four main mechanisms typically employed by antibiotics to clear an infection. To understand how these drugs work, it is important to first understand the structural differences between bacteria and mammalian cells; bacteria are known as prokaryotic cells, while mammalian cells are known as eukaryotes. Most importantly regarding the functions of antibiotics, prokaryotic cells have a cell membrane in addition to a rigid cell wall, while eukaryotes lack this protective outer wall. Antibiotics such as cephalosporins and penicillins—also known as beta-lactam antibiotics—interfere with specific enzymes necessary for cell wall synthesis: therefore, preventing the replication of bacteria cells (Tenover, 2006, p. 3-4). By targeting cell wall synthesis, these antibiotics selectively destroy bacteria and ignore healthy mammalian tissue.

Figure 1: Structure of a Bacteria Cell. (©Encyclopædia Britannica, Inc. 2012).

Other antibiotics, such as tetracyclines and streptogramins, work by targeting bacteria protein synthesis. Once again, these antibiotics take advantage of the differences between mammalian and bacterial cells, as prokaryotic protein synthesis differs from that of eukaryotes. As bacterial ribosomes—the site inside of a cell where proteins are created from amino acids—are structurally different from eukaryotic ribosomes, this class of antibiotics functions by targeting certain areas of bacterial ribosomes. This prevents protein synthesis and therefore prevents further bacterial growth (Tenover, 2006, p. 3-4).

The third common mechanism utilized by antibiotics is to interfere with DNA production. Fluoroquinolones such as ciprofloxacin (Cipro) and levofloxacin (Levaquin) target two enzymes that are specific to and necessary for successful bacterial DNA synthesis: DNA gyrase and DNA topoisomerase IV (Drlica & Zhao, 1997, p. 377). Due to the double-stranded nature of DNA, when these two enzymes are inactivated by antibacterial drugs, a “lethal” break occurs across both strands of DNA during replication (Tenover, 2006, p. 3-4).

Finally, antimicrobials such as sulfonamides in combination with trimethoprim (TMP) function through a disruption in folic acid creation. These two drugs, working together, inhibit “the enzymatic pathway for bacterial folate synthesis” (Tenover, 2006, p. 3-4). In bacteria cells, folic acid is essential for DNA synthesis—without it, the cells are unable to replicate and eventually die.

Figure 2: Tounge Bacteria. (Steve Gschmeissner. 2019).

Acquiring Resistance: Mutations and Horizontal Gene Transfer

How bacteria cells acquire antibiotic resistance is a complex process and began long before humans began to use antibiotics; however, these genetic factors are selected for by the widespread use of antimicrobial agents in medical settings. There are two main ways that bacteria can develop resistance that are explained by Jose Munita and Cesar Arias of the International Center for Microbial Genomics: genetic mutations and horizontal gene transfer. “Mutations in genes are often associated with the mechanism of action” needed to inactivate or destroy a specific antibiotic agent (Munita and Arias, 2016, p. 2). Meaning, that when a mutation occurs in the genome of a bacteria cell that allows it to survive despite the presence of antimicrobial substances, that cell will go on to replicate. Thus, passing the genetic mutation needed for resistance on to its progeny cells, resulting in a population of bacteria cells all containing the specific mutation needed for resistance to a specific antibiotic.

Surprisingly, despite being single-cell organisms, bacteria can exchange genetic material with other bacteria cells, as well as with other organisms in their environment. This is known as horizontal gene transfer. There are many different ways that bacteria can acquire new DNA, including transduction, transformation, and conjugation (Munita and Arias, 2016, p. 3). In short, transduction occurs when an organism, such as a virus known as a phage, injects its DNA into a bacteria cell, and the foreign DNA is integrated into the bacterial host’s DNA. While transformation happens when bacteria uptake DNA from organisms in their surrounding environment. Finally, conjugation occurs when a bacteria cell comes in contact with another bacteria cell, and an exchange of DNA takes place (Soucy and Huang, et al., 2015, p. 473). Transformation and conjugation often involve the uptake of a plasmid—a circular strand of DNA that can replicate independently of the bacteria’s genome (see Figures 1 and 3); plasmids are typically involved in both transformation and conjugation and will often contain resistance genes. In each of these processes, once the bacteria acquire the foreign DNA, the cells can pass it on to new cells during the replication process, creating more cells with the resistance genes.

Figure 3: Transformation of a Bacteria Cell with a Plasmid. (©Khan Academy. 2016).

Mechanisms of Antibiotic Resistance

When exposed to specific antibiotics, bacteria with these acquired genes express mechanisms of resistance and survive to replicate once again, while bacteria without these genes die in the face of these antimicrobials. This creates a population of bacteria cells that can colonize an area and are resistant to specific antibiotics, which presents a potentially large problem in the case of an infection. These resistance mechanisms include the inactivation of antibiotics through enzymes, removal of antimicrobials through efflux pumps, and modification to specific binding sites.

Mutations in certain classes of genes that confer antibiotic resistance may give rise to certain enzymes, or overexpression of certain enzymes, which can inactivate antimicrobials. Beta-lactam antibiotics, such as penicillins, are often inactivated by a class of enzymes in bacteria cells known as beta-lactamases (Wright, G. D., 2011, p. 4058). This class of enzymes functions, in short, by binding to, modifying, and ultimately inactivating the antimicrobial molecules. Beta-lactamases are one of the most common types of enzymes that contribute to antibiotic resistance with more than 1,000 types documented since their discovery in the 1940s, shortly after penicillin itself began to be used (Munita and Arias, 2016, p. 5).

Figure 4: Mechanisms of Antibiotic Resistance. (©Encyclopædia Britannica, Inc. 2012).

Additionally, efflux pumps are an essential part of cell biology that are embedded in a cell membrane and control which substances enter and exit the cell. In a bacterium that has an extra membrane outside of the cell wall (also known as Gram-negative bacteria), specific efflux pumps can prevent antibiotics from entering the cell or remove the antimicrobial substances that have already entered the cell, contributing to high levels of resistance. E. coli and P. aeruginosa are two examples of bacteria that exhibit MDR through overexpression of efflux pumps (Blair, J. M. A., Webber, M. A, et al., 2014, p. 43-44).

Antibiotics typically bind to a specific target site or target protein within a bacteria cell to carry out a distinct mechanism. For example, ciprofloxacin targets and inactivates an enzyme needed for bacterial DNA replication, and a mutation in the shape or conformation of this enzyme prevents Cipro from binding to—and therefore inactivating—this essential enzyme (Wright, 2011, p. 4056). As shown in Figure 4, the modified drug target has a triangular target site, and because the antibiotic has a circular conformation, it does not adhere to the target. This simplified model details what occurs when this type of mutation happens, the key (the antibiotic) no longer fits in the lock (the target enzyme).

The threat of antibiotic-resistant bacteria continues to rise every day despite growing efforts to dampen this risk; an estimated 1.27 million people died from antimicrobial-resistant infections in 2019, according to a comprehensive study conducted by Dr Mohsen Naghavi at The Institute for Health Metrics and Evaluation, and these numbers are likely to grow. A seeming conundrum takes shape, as the use of antibiotics creates the very strains of bacteria they intend to destroy; the selective pressure that causes antibiotic-resistant bacteria to colonize an infection or an ecosystem is only present with the introduction of antimicrobial substances. However, with organizations such as the Global Antimicrobial Resistance Surveillance System (GLASS) and Global Antibiotic Research and Development Partnership (GARDP) working to monitor and solve this crisis, new treatments for antimicrobial-resistant bacteria are being researched and developed each year to hopefully reduce the number of deaths attributed to these types of infections (GARDP, 2021); hopefully, a future without antibiotic-resistant bacteria is on the rise despite the seeming evolutionary arms race that bacteria appear intent on winning.

Bibliographical References

Blair, J. M. A., Webber, M. A., Baylay, A. J., Ogbolu, D. O., & Piddock, L. J. V. (2014). Molecular Mechanisms of Antibiotic Resistance. Nature Reviews Microbiology, 13 (1), 42–51.

Drlica, K., & Zhao, X. (1997). DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiology and Molecular Biology Reviews: MMBR, 61(3), 377–392.

Davies, J., & Davies, D. (2010). Origins and Evolution of Antibiotic Resistance. Microbiology and Molecular Biology Reviews, 74(3), 417–433.

GARDP. (2021, December 2). Research & Development.

McFarland, A. G., Bertucci, H. K., Littman, E., Shen, J., Huttenhower, C., & Hartmann, E. M. (2021). Triclosan Tolerance Is Driven by a Conserved Mechanism in Diverse Pseudomonas Species. Applied and Environmental Microbiology, 87 (7).

Tenover, F. C. (2006). Mechanisms of Antimicrobial Resistance in Bacteria. The American Journal of Medicine, 119(6), S3–S10.

McManus, M. C. (1997). Mechanisms of Bacterial Resistance to Antimicrobial Agents. American Journal of Health-System Pharmacy, 54(12), 1420–1433.

Munita, J. M., & Arias, C. A. (2016). Mechanisms of Antibiotic Resistance. Microbiology Spectrum, 4(2).

Murray, C. J., Ikuta, K. S., Sharara, F., Swetschinski, L., Robles Aguilar, G., Gray, A., Han, C., Bisignano, C., Rao, P., Wool, E., Johnson, S. C., Browne, A. J., Chipeta, M. G., Fell, F., Hackett, S., Haines-Woodhouse, G., Kashef Hamadani, B. H., Kumaran, E. A. P., McManigal, B., . . . Naghavi, M. (2022). Global Burden of Bacterial Antimicrobial Resistance in 2019: a Systematic Analysis. The Lancet, 399(10325), 629–655.

Soucy, S. M., Huang, J., & Gogarten, J. P. (2015). Horizontal Gene Transfer: Building the Web of Life. Nature Reviews Genetics, 16(8), 472–482.

Thomas, C. M., & Nielsen, K. M. (2005). Mechanisms of, and Barriers to, Horizontal Gene Transfer Between Bacteria. Nature Reviews Microbiology, 3(9), 711–721.

Wright, G. D. (2011). Molecular Mechanisms of Antibiotic Resistance. Chemical Communications, 47 (14), 4055.

Figures References:

Cover Image: Jeffery, S. (2011). The Rise of Superbugs. © The Economist Newspaper Limited. [Illustration]. Image retrieved from

Figure 1: Bacterial Cell Structure. ©Encyclopædia Britannica, Inc. (2012). [Illustration]. Image retrieved from

Figure 2: Gschmeissner, S. (2019). Tounge Bacteria. [Photograph]. Getty Images, Image retrieved from

Figure 3: Bacterial Transformation. ©Khan Academy. (2016). [Illustration]. Image retrieved from

Figure 4: Examples of Mechanisms of Antibiotic-resistance. ©Encyclopædia Britannica, Inc. (2012). [Illustration]. Image retrieved from


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Erica Littman

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