Antibiotic-resistant Bacteria: Our Self-inflicted Undoing?

Penicillin, the First Modern Antibiotic Drug

The discovery of penicillin's antibiotic properties was one of the greatest findings in recent history. In 1928, Alexander Fleming observed that a petri dish contaminated with a fungus (Penicillium notatum) had a zone where the bacteria could not grow (Lobanovska & Pilla, 2017). After Fleming extracted the antibacterial substance (Penicillin), he, along with Ernest Chain and Howard Florey, injected eight mice with lethal doses of the bacteria Group A Streptococcus. The four that received penicillin as treatment survived while the other 4 that did not receive penicillin all died (Lobanovska & Pilla, 2017).

What's more impressive? Its mechanism; one that bypasses human's eukaryotic cells and specifically targets bacteria. Eukaryotic cells in animals lack cell walls, whereas bacteria (both Gram-positive and Gram-negative) possess cell walls because they are prokaryotes. The peptidoglycan (PGN) layer (Figure 1) protects the bacteria from lysis (bursting from osmotic pressure) and is therefore essential to their survival. This tough PGN relies on enzymes known as transpeptidases to form peptide/protein cross-linkages of the polysaccharide chains (Lobanovska & Pilla, 2017).

Figure 1: Cell Wall Composition of Gram-positive and Gram-negative Bacteria (Khan Academy)

The penicillin molecule acts as an irreversible competitive inhibitor. Penicillin inhibits the transpeptidases by permanently binding to their active sites, meaning the substrates can no longer bind (Lobanovska & Pilla, 2017). With the enzymes inhibited, the bacteria cannot produce this key protective layer for themselves nor for binary fission, leading to their decimation. The antibiotic property relies on the bacteria's PGN and transpeptidase which are absent in humans, thus targeting only bacterial cells for lysis! Undoubtedly, this drug has saved countless lives.

Emergence of Resistance

It seemed like deadly bacterial infections were to become a thing of the past. However, bacteria had an indiscriminate ally: natural selection. The first sign of antibiotic-resistant bacteria appeared in Staphylococcus aureus in 1942–just one year after human clinical trials and before Fleming et al. even received their Nobel Prize (Lobanovska & Pilla, 2017). In two decades, this strain, S. aureus, became 80% resistant in hospital and widespread community settings (Lowy, 2003). The beta-lactam rings present in the penicillin structure were being inactivated by the enzyme beta-lactamase that the bacteria, S. aureus, now produced (Lowy, 2003). With repeated binary fission, the gene that codes for this anti-penicillin enzyme became prominent in the population of its evolutionarily advantageous characteristics.

Figure 2 fom Davies & Davies, 2010: Numbers of unique β-lactamase enzymes identified since the introduction of the first β-lactam antibiotics.

In 1961, as penicillin's efficacy declined, a variation of the drug, methicillin, was introduced which bypassed bacteria's new defensive enzyme (Lowy, 2003). However, the outcome was a strain even harder to treat and more deadly: Methicillin-Resistant S. aureus (MRSA), which has a significantly higher mortality rate than Methicillin-Susceptible S. aureus (MSSA) (Cosgrove et al., 2003).

Worst, many bacteria, including S. aureus, can transfer their genetic code to other populations or other species, via conjugation or bacteriophage transduction, which uses bacterial viruses as seen in the figure below (Haaber et al., 2017).

Figure 3: Gene-transfer methods (University of Leicester)

Various strains of antibiotic-resistant bacteria can share their advantageous genes and result in "superbugs'' or multidrug-resistant (MDR) pathogens. Some of these superbugs have been shown to have "increased virulence and enhanced transmissibility" in addition to their resistance (Davies & Davies, 2010). We seem to be playing a dangerous game with the future.

Perhaps the developed world can keep up with the superbugs, but the interconnectedness of the world means they are more likely to spread to places that lack the medicinal firepower to combat these pathogens, especially those more virulent. Even one of our strongest antibiotics, colistin, now has fallen to the force of evolution as well (Aghapour et al., 2019).

An Evolutionary Tangent

Although more antibiotics have been and are being discovered, natural selection quickly catches up. The widespread use of antibiotics increases the exposure of certain bacterial strains which means there is an increased selective pressure for these bacteria to become resistant. In a population of bacteria, which can form quickly due to their short generations, there are variations in their genetic material (variations via mutations or acquired from other bacteria). Those with any resistance will survive and repopulate, increasing the prevalence of their resistance. This is made worse with the misuse of antibiotics where an incomplete course of antibiotic only kills the weak but leaves the fittest bacteria alive to replicate: for example, taking antibiotics only until the infection dissipates instead of taking them for the whole duration as prescribed. Another source of the "constant selection pressure" is the use of antibiotics in the environment, such as for aquaculture, animal farms, and cleaning products; millions of metric tons "antibiotic compounds have been released into the biosphere over the last half-century" (Davies & Davies, 2010). We are inviting future epidemics with our careless use of medicinal powers.

It is interesting to note the biological origins and the force of evolution. Studying the force of nature can reveal profound insights into the natural world and enable us to predict or extrapolate causations. Darwin's theory of Survival of the Fittest can explain the spread of resistant superbugs but did these mechanisms really just come from random mutations?

"Resistance in bacteria can be intrinsic or acquired. Intrinsic resistance is a naturally occurring trait arising from the biology of the organism—for example, vancomycin resistance in Escherichia coli. Acquired resistance occurs when a bacterium that has been sensitive to antibiotics develops resistance—this may happen by mutation or by acquisition of new DNA” ( Davies & Davies, 2010).

I was incredulous to the idea that random mutations can only arise from something as complex as an enzyme capable of disabling antibiotics, like beta-lactamase. How do mutations engender complex changes? An explanation could be the bacteria already has resistance genes or resistant determinants in their gene pool – fungi and bacteria that produce antibiotics themselves must have their own defences, and these genes can then be acquired through the exchange methods mentioned overtime (Hawkey, 1998). They may not need to develop new weapons for antibiotics and instead, they just need to find the right tool buried somewhere in their gene pool. Zaman et al. summarizes this additional ally of the pathogens: "antimicrobials possessed resistance genes that defend their antimicrobial products and these genes developed antibiotic resistance even long ago before the antibiotic started working for treatment purpose." Still, this mainly just shifted the mystery to the origins of natural antibiotics. The world of evolution must be so much more complicated than what it is often reduced to.

Diagnosis: Emerged Superbugs, Treatment: ?

Figure 4: Statistics Poster from FAIRR's Responding to Resistance

Various strains of antibiotic-resistant bacteria can share their advantageous genes and result in "superbugs'' or multidrug-resistant (MDR) pathogens. Some of these superbugs have been shown to have "increased virulence and enhanced transmissibility" in addition to their resistance (Davies & Davies, 2010). We seem to be playing a dangerous game with the future.

A future where a small infection is deadly due to their resistance is scary to imagine. Their presence, though invisible, should be a concern for everyone. In the United States, MRSA is responsible for more deaths each year than "HIV/AIDS, Parkinson’s disease, emphysema, and homicide combined" (Ventola, 2015). Especially considering our era of antibiotics, this 11, 285 deaths is terrible. Furthermore, the difficulty in treatment means financial burdens, both of the state and the patients, producing "$20 billion in health care costs and $35 billion a year in lost productivity" (Ventola, 2015).

Many have suggested cycling the use of antibiotics to eliminate a constant selection pressure but this assumes the resistant genes would be absent afterwards, which may not be the case as, once "antibiotics are reintroduced, the problem strains (or r genes) are quickly reselected" (Davies & Davies, 2010). There was the optimistic belief that these acquired resistant genes are costly to their energy expenditure and that it would therefore be unwise to keep them when no longer necessary. The hope is that these advantageous genes will be lost without the constant selection pressure and that the bacteria will revert back to a form prior to antibiotics. However, it seems that "reversibility [of resistance] in clinical settings is expected to be slow or non-existent:" the microbes rather undergo "compensatory evolution" than to simply regress and to forget their learned traits, and if the assumption that these traits are costly is invalid, then the "driving force for reversibility" would be weak (Andersson & Hughes, 2010). Some traits happened to be beneficial without any trade-offs––ergo, there is no motivation to discard such an evolutionary gift.

Despite the number of proposed solutions, the issue of these superbugs persists. Some are clearly beneficial but hard to fully implement, such as prescribing only when necessary, completion of antibiotics treatments, and preventing infections in the first place (via proper hygiene, for example). Some of the more innovative solutions include using bacteriophages as an alternative to antibiotics. These bacterial viruses hijack specific bacteria and cause their deaths through lysis, a method already approved by the Food and Drug Administration in the United States (Ghosh et al., 2019).

Another one is using predatory bacteria such as Bdellovibrio and like organisms (BALOs): these bacteria will only attach to certain bacteria and cause "minimum or no inflammatory response" in human cells (Ghosh et al., 2019).

Several more possible solutions are being researched concurrently. The treatment may not have been found but at least we are beginning to treat this diagnosis seriously. Human ingenuity and adaptiveness may come out on top in the war with evolving microbes.

References

Aghapour, Z., Gholizadeh, P., Ganbarov, K., Bialvaei, A. Z., Mahmood, S. S., Tanomand, A., Yousefi, M., Asgharzadeh, M., Yousefi, B., & Kafil, H. S. (2019). Molecular mechanisms related to colistin resistance in enterobacteriaceae. Infection and Drug Resistance, 12, 965–975. https://doi.org/10.2147/IDR.S199844

Andersson, D. I., & Hughes, D. (2010). Antibiotic resistance and its cost: Is it possible to reverse resistance? Nature Reviews Microbiology, 8(4), 260–271. https://doi.org/10.1038/nrmicro2319

Cosgrove, S. E., Sakoulas, G., Perencevich, E. N., Schwaber, M. J., Karchmer, A. W., & Carmeli, Y. (2003). Comparison of mortality associated with methicillin‐resistant and methicillin‐susceptible Staphylococcus aureus bacteremia: a meta‐analysis. Clinical Infectious Diseases, 36(1), 53–59. https://doi.org/10.1086/345476

Davies, J., & Davies, D. (2010). Origins and evolution of antibiotic resistance. Microbiology and Molecular Biology Reviews, 74(3), 417–433. https://doi.org/10.1128/mmbr.00016-10

Ghosh, C., Sarkar, P., Issa, R., & Haldar, J. (2019). Alternatives to conventional antibiotics in the era of antimicrobial resistance. Trends in Microbiology, 27(4), 323–338. https://doi.org/10.1016/j.tim.2018.12.010

Haaber, J., Penadés, J. R., & Ingmer, H. (2017). Transfer of antibiotic resistance in Staphylococcus aureus. Trends in Microbiology, 25(11), 893–905. https://doi.org/10.1016/j.tim.2017.05.011

Hawkey, P. M. (1998). The origins and molecular basis of antibiotic resistance. BMJ, 317(7159), 657–660. https://doi.org/10.1136/bmj.317.7159.657

Lobanovska, M., & Pilla, G. (2017). Penicillin’s discovery and antibiotic resistance: Lessons for the future? The Yale Journal of Biology and Medicine, 90(1), 135–145. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5369031/

Lowy, F. D. (2003). Antimicrobial resistance: The example of staphylococcus aureus. Journal of Clinical Investigation, 111(9), 1265–1273. https://doi.org/10.1172/jci200318535

Ventola, C. L. (2015). The antibiotic resistance crisis: Part 1: Causes and threats. P & T : A Peer-Reviewed Journal for Formulary Management, 40(4), 277–283.

Zaman, S. B., Hussain, M. A., Nye, R., Mehta, V., Mamun, K. T., & Hossain, N. (2017). A Review on Antibiotic Resistance: Alarm Bells are Ringing. Cureus, 9(6). https://doi.org/10.7759/cureus.1403