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Antimicrobial Resistance 101: Evolution As a Driver of Resistance

Foreword


Antimicrobials were a major breakthrough in science. Microorganisms that include viruses, bacteria, fungi and more can be killed by treatment with relatively simple molecules. Infections that would be a death sentence before could finally be treated, with incredible efficacy. Soon after the first antimicrobials were discovered, however, pathogens targeted started to become resistant. Antimicrobial resistance is a big problem in modern medicine. The first bacterial infections start to appear that have evolved to be resistant to the complete arsenal of antibiotics. As a result, more patients infected with resistant pathogens cannot be treated. Because the situation is likely to become worse in the coming decades, it is time to think about alternatives.


This 101 series is divided into six articles including:


1. Antimicrobial Resistance 101: Evolution As a Driver of Resistance

2. Antimicrobial Resistance 101: Resistance Mechanisms

3. Antimicrobial Resistance 101: The Global Problem of Antimicrobial Resistance

4. Antimicrobial Resistance 101: The Clinical Burden of Resistant Microorganisms

5. Antimicrobial Resistance 101: Solutions to Antimicrobial Resistance

6. Antimicrobial Resistance 101: Antimicrobial Resistance in the Future


Antimicrobial Resistance 101: Evolution As a Driver of Resistance


The spectrum of size in the universe is an enormous one. The largest “thing” to exist, the universe, is so large that it is hard to put it in numbers. Besides, not nearly all of it has been mapped, nor observed. The order of magnitude is estimated to be tens of billions of light years in diameter (Tillman & Gordon, 2022). The fundamental element on which everything is built, the atom, is somewhere between a few picometers and a nanometer (Angelo, n.d.). In the context of very large, fast and heavy things, like massive stars or black holes, relativity theory, proposed by Einstein, has proven immensely accurate. At the smallest scale, however, physics seems to be defied by the infamous realm of quantum theory. This weird universe seems highly counterintuitive, and one of the basic laws says that every particle in the universe is both a particle and a wave. Even more, every “quantum” has this particle-wave duality, even light. Yes, light is both a particle and a wave.


At each of these vastly different size scales, the universe works very differently and is governed by different laws. Laws that seem relevant to understand one of such contexts, do not mean they are relevant to others. Humans, and things in their environment, mostly live under the pressure of gravity. Given that humans are big and strong enough to swim, thereby pushing water aside, viscous forces are not very impactful on them, nor on any other animal of this size. However, when looking through a microscope, and studying bacteria, the world is very different. The objects are not very heavy, and consequently not so strong. Rather than gravity, viscous forces seem to govern this small world (Dufrêne & Persat, 2020). Any living thing at this scale works very differently from animals that we see in daily life. There is one rule, however, that dictates life at this scale, just as it does at the larger scale of what humans observe: evolution.

Figure 1: An overview of the scale of things in the universe (Math’s Fun, n.d.).

Evolution dictates how organisms progressively become more diverse, leading to new species that are better adapted to their environment. The fundament of evolution is called “natural selection”. Through it, individuals with the best genes are selected to reproduce, allowing a selective penetrance of these features into new generations. Through this mechanism, in combination with human neglect and arrogance, microorganisms have become better adapted to the weapons against them, deployed in human and animal medicine, with disastrous consequences. Say that a certain bacterial strain is being treated with antibiotics that kill 99% of the population. The remaining 1% tolerates the drug better, and is therefore said to be resistant. The remaining population will reproduce and therefore spread its genetic information over the next generations, which will become more resistant as well.


In 2016, scientists at the Harvard Medical School developed the largest petri dish on the planet to simulate how the best-studied bacterium, Escherichia Coli evolves to become resistant to a certain antibiotic. On the left and right side of the petri dish, the researchers let some E. coli grow, and towards the middle, the concentration of the antibiotic increased until it was 1000 times the original concentration. This showed that at every point at which the concentration becomes larger, bacteria will die. As a result, the individuals that are able to survive in these elevated concentrations are selected to produce progeny, which, in turn, will have the same ability to stand higher concentrations. This led to the development of Figure 2A towards 2B (Pesheva, 2016).

Figure 2: The development of antibiotic resistance of E. coli in real-time. A: at the start of the experiment. B: after 10 days (modified from Pesheva, 2016).
The History of Antimicrobials

When analysing this study, it does not take much imagination to realise that spilling antibiotics into the environment can have disastrous consequences, as the bacteria that are exposed to these chemicals will likely grow resistant. This is exactly what has been happening since the first antibiotics were found in 1918, by Alexander Fleming (Jhora, 2021). This medical doctor actually discovered antibiotics by accident: by not taking very good care of hygiene and cleaning protocols, the medical doctor had made fungus grow in his bacterial culture, which had produced penicillin, a molecule that kills bacteria; or an antibiotic (Jhora, 2021).


Immediately, the implications of penicillin were recognised. Infections caused by bacteria, killing many people at the time, could now be fought by molecules to which bacteria were highly susceptible. In 1944, penicillin was used in the clinic for the first time with miraculous results. The scientific community was astounded at the ability to kill bacteria, without severe side effects to the patient. A year later, in 1945, Fleming received the Nobel Prize for Medicine. In his acceptance speech, he said: “The time may come when penicillin can be bought by anyone in the shops. Then there is the danger that the ignorant man may easily underdose himself and, by exposing his microbes to non-lethal quantities of the drug, make them resistant” (Fleming, 1945). As penicillin was used in an increasing amount of cases, more research was done on this, but also other new antibiotics. These treatments were very effective in the Second World War, curing many soldiers suffering from infections. Eventually, many new antibiotics were discovered, mostly in the 1950s, the golden age of antibiotics (Jhora, 2021). However, in 1947, a few years before the start of this age, the first cases of penicillin-resistant infections were observed. This proved to be more of a rule rather than an exception, as shortly after the discovery and the use of a new antibiotic, more resistant bacteria were found.

Figure 3: A timeline of antibiotic resistance. Below the black bar, the antibiotics are protrayed. Above the black bar, species identified are shown, that are resistant to the antibiotic that is reflected by the colour (LGC, n.d.).

Fleming had realised that his discovery would save millions of lives in the decades, if not centuries to come. He had also realised, however, that antibiotics misuse could result in disastrous scenarios in which treatments by antibiotics would become less efficacious over time. Fleming’s argument is one that many people know nowadays: patients should finish antibiotic treatment according to the doctor’s instructions, rather than stop taking the medication as soon as they feel better. The idea is that the treatment kills bacteria progressively over time; once the patient feels better, the majority of bacteria have been killed though likely not all. If treatment is stopped at this point, the bacteria can still survive in the body with some leftover concentration of the antibiotics, much like how E. coli grows resistant in the experiment above. However, if the patient is continuously flushed with a high concentration of the right antibiotic, it is likely that the pathogen will not have the chance to survive, and will die quickly instead (Llewelyn et al, 2017).


Recent research has shown that this thinking may not be the full picture. This form of resistance is called “target selection”, by which a specific strain grows resistant. Although the argument is not necessarily wrong, it seems that globally “collateral selection” has a much larger influence: instead of describing the process of becoming resistant in a given species, this concept says that any opportunistic pathogen that comes into contact with an antibiotic can become resistant to it (Llewelyn et al, 2017). In other words, the number of antimicrobials used should be limited overall. Therefore, perhaps patients should take as little antibiotic as possible (Llewelyn et al, 2017).

Figure 4: A schematic overview of the combination of target selection (red) and collateral selection (orange) (FOPH, 2019).
What Are Microorganisms?

Microorganisms are a very large group of microscopic organisms that comprise bacteria, viruses, fungi, archaea, algae and protozoa. Although species in all these groups can cause disease, generally when talking about microbes, scientists talk about bacteria, viruses and fungi. This is also where the distinction between antimicrobials and antibiotics comes in: antimicrobials are drugs that kill microorganisms, while antibiotics solely affect bacteria; antifungals and antivirals target fungi and viruses, respectively. Although these groups of organisms are similar in size, they work vastly differently, which is why this distinction is very important to make (Mahnert et al, 2019).


The focus of the next article in this series will be on resistance mechanisms of all these pathogenic microorganisms, or microbes. Broadly speaking, these all acquire resistance in the same way, that is, by being exposed to the drug. Evolution pushes for genetic variability, causing some individuals to be slightly more resistant to the drug. This feature is selected for, leading to a more resistant next generation. This finally results in the behaviour observed in the Harvard study reported above. Although bacteria, fungi and viruses are very different in every aspect, resistance is seen in species of these three groups of microbes altogether. The problem of antimicrobial resistance is therefore more widespread than just bacteria.

Figure 5: Microorganisms contain bacteria, viruses, fungi, protozoa, archaea and algae (Health Europa, 2019).

Not all microorganisms are bad for complex beings like humans. In fact, humans rely on bacteria. The microbiota is the collection of all bacteria found in the digestive tract (Koutoukidis, 2022). This community is immensely diverse and is not even close to being fully understood because of the complexity of the network. Many of these bacteria digest molecules that humans cannot process, which therefore causes a relationship that offers advantages to both humans and the bacteria. Such a relationship is called “symbiotic” (Koutoukidis, 2022). In return for shelter inside the body, bacteria process things that humans cannot. Of the massive amounts of bacteria on the planet, only a small portion causes human disease, which is estimated at about 1 in a billion. Often, research is focused on antibiotics, while less so on antivirals or antifungals. However, the number of studies on antiviral and antifungal resistance is growing as well. Concerning fungi, there is a general lack of scientific knowledge. The therapeutic arsenal is small, and so is the amount of research on them. An additional issue with fungi is that they are eukaryotic, while bacteria are prokaryotic. This means that their cellular structure is incredibly different. As animals are eukaryotic, fungi are much closer to humans than bacteria; therefore, antifungals tend to have much more severe side effects than antibiotics or antivirals (Fisher, 2022).


Recent Insights in Antimicrobial Resistance – One Health

The concept of “One Health” was coined in 1984 by Calvin Schwabe (Schwabe, 1984). One Health, or One Medicine, as he actually called it, is an interdisciplinary field that studies the interactions between humans, animals and the environment. Take malaria, for example, caused by the parasite Plasmodium (Castillo, 2021). This parasite survives in mosquitoes, which can transmit the organism to humans and other animals. Only certain mosquitoes can transmit Plasmodium in only a certain part of the world. To fully understand the disease, and to come up with strategies for wiping out malaria for good, not only the parasite and its clinical implications should be studied; instead, research should also focus on the mosquito, and the environment (Castillo, 2021). Given that antimicrobials are used in the bioindustry even more than in human medicine, resistance truly is a One Health problem (Emes, 2022). Wasted water from farms, with leftovers of antibiotics, comes in contact with the environment, where bacteria now meet substances they never would in a natural setting, creating resistance. Only for about a decade, scientists realise that, through complex interactions between industries, microbes all over the world indeed come in contact with such antimicrobials and therefore become resistant to these drugs (Collignon, 2019).

Figure 6: The concept of One Health (isglobal, 2021).

Legislation concerning antimicrobial use is vastly different across the world. Although there are not many rules in Asian countries, the European Union has restricted many antimicrobials from being used in animal health at all, and there are even stricter measures on the way. Drugs that are not allowed to be used in animal health include the last-resort drug “carbapenem” (Temkin, 2014). The classification of last resort means that it may be tried in the clinical setting when alternatives have failed. In other words, there is no real alternative to the drug itself. Although carbapenem may not be used in European bioindustry, researchers in Italy recently found that bacterial infections resistant to carbapenem are common on pig farms (Bonardi, 2022). Bacteria in pig farms, which should never have been exposed to a drug that is only used when all other options have failed in human medicine, have become resistant to that very drug. This dystopian truth shows the necessity of a One Health approach. Humans (and animals) shed a tiny portion of drugs in their urine and faeces, meaning that wastewater holds significant concentrations of drugs, including antibiotics, antivirals and antifungals (Collignon, 2018). The way that sewage water from cities, or even from animal farms comes in contact with the environment allows bacteria, viruses and fungi to grow resistant to fundamental drugs for both human and animal medicine.


This One Health perspective has only been adopted since the start of this century. For a long time, the risks and dangers of antimicrobial resistance were not recognised, and Fleming’s warning was (partly) ignored. Now that resistant bacteria, viruses and fungi prove to be great threats to human health, large, influential organisations including the WHO, and the centres for disease control and prevention of the US (CDC), the EU (ECDC) and Africa (Africa CDC) monitor such microbes intensely (WHO, n.d.; ECDC, n.d.; Africa CDC, n.d.). Although surveillance will be an important aspect of fighting antimicrobial resistance, much more needs to be done (Collignon, 2018). Internationally, legislation has to be updated to ensure global standards rather than enormous differences per country. The consequences of having such differences are becoming increasingly evident in the fight against climate change, which will not be any different from the battle with antimicrobial resistance. Perhaps the most important factor will be to heavily decrease the use of antimicrobials, and to educate the public on how to use these drugs properly. People should not take antibiotics when they have a common cold, a viral infection against which these drugs are not active, to begin with (Collignon, 2018).

Figure 7: The infographic by the ECDC on antibiotic resistance (ECDC, 2018).

The problem of antibiotic resistance is real, and it is now. Like climate change, this problem has been coming for a long time, and people warning about the problem have been met with scepticism in the past. Another aspect that both these enormous issues have in common is that they stem from human influence. Although evolution, and thereby resistance to antimicrobials, is a natural process, much like climate change, human actions have severely accelerated both (Christak, 2019). According to UNEP, the United Nations Environmental Programme, the threat of antimicrobial resistance is much larger than people realise. UNEP suggests that by 2050, 10 million deaths could occur annually as a consequence of resistant infections, which would cost over three trillion US Dollars (UNEP, n.d.).


Evolution will intrinsically drive microbes to become resistant to drugs. The only impact that humans may have is by influencing the rate at which this happens. In the final half of the last century, humans have practically treated infections without control, the consequence of which becomes increasingly evident. The problem of antimicrobial resistance knows many faces. For one, the science behind it is complex. Resistant mechanisms are difficult, and so is the identification of new drugs to fight microbes. The fact that, internationally, drugs are used very differently in human health and in the bioindustry makes this problem even more challenging to face. Luckily, there are quite a few possible treatments that may offer capable alternatives to antibiotics, antifungals or antivirals. These are being used more and more in clinical research in order to be perfected. All these elements will be the topic of the next articles in this series.

Bibliographical References

Africa Centre for Disease Control and Prevention (Africa CDC). (n.d.) Africa CDC Framework for Antimicrobial Resistance. https://africacdc.org/download/africa-cdc-framework-for-antimicrobial-resistance/


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Bonardi, S., Cabassi, C. S., Manfreda, G., Parisi, A., Fiaccadori, E., Sabatino, A., Cavirani, S., Bacci, C., Rega, M., Spadini, C., Iannarelli, M., Crippa, C., Ruocco, F., & Pasquali, F. (2022). Survey on Carbapenem-Resistant Bacteria in Pigs at Slaughter and Comparison with Human Clinical Isolates in Italy. Antibiotics, 11(6), 777. https://doi.org/10.3390/antibiotics11060777


Christaki, E., Marcou, M., & Tofarides, A. (2020). Antimicrobial Resistance in Bacteria: Mechanisms, Evolution, and Persistence. Journal of Molecular Evolution, 88(1), 26–40. https://doi.org/10.1007/s00239-019-09914-3


Collignon, P., & McEwen, S. (2019). One Health—Its Importance in Helping to Better Control Antimicrobial Resistance. Tropical Medicine and Infectious Disease, 4(1), 22. https://doi.org/10.3390/tropicalmed4010022


Dufrêne, Y. F., & Persat, A. (2020). Mechanomicrobiology: how bacteria sense and respond to forces. Nature Reviews Microbiology, 18(4), 227–240. https://doi.org/10.1038/s41579-019-0314-2


Emes, D., Naylor, N., Waage, J., & Knight, G. (2022). Quantifying the Relationship between Antibiotic Use in Food-Producing Animals and Antibiotic Resistance in Humans. Antibiotics, 11(1). https://doi.org/10.3390/antibiotics11010066


European Centre for Disease Prevention and Control (ECDC). (n.d.). Antimicrobial resistance. https://www.ecdc.europa.eu/en/antimicrobial-resistance


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Jhora, S. T. (2021). Fleming’s Warning and the future pandemic. Bangladesh Journal of Medical Microbiology, 15(2), 1–4. https://doi.org/10.3329/bjmm.v15i2.57811


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Mahnert, A., Moissl-Eichinger, C., Zojer, M., Bogumil, D., Mizrahi, I., Rattei, T., Martinez, J. L., & Berg, G. (2019). Man-made microbial resistances in built environments. Nature Communications, 10(1), 968. https://doi.org/10.1038/s41467-019-08864-0


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Ruiz-Castillo, P., Rist, C., Rabinovich, R., & Chaccour, C. (2022). Insecticide-treated livestock: a potential One Health approach to malaria control in Africa. Trends in Parasitology, 38(2), 112–123. https://doi.org/10.1016/j.pt.2021.09.006


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Temkin, E., Adler, A., Lerner, A., & Carmeli, Y. (2014). Carbapenem-resistant Enterobacteriaceae: biology, epidemiology, and management. Annals of the New York Academy of Sciences, 1323(1), 22–42. https://doi.org/10.1111/nyas.12537


Tillman, N., T., & Gordon, J. (2022). How big is the Universe. https://www.space.com/24073-how-big-is-the-universe.html


United Nations Environmental Programme (UNEP). (n.d.). Antimicrobial resistance: a global threat. https://www.unep.org/explore-topics/chemicals-waste/what-we-do/emerging-issues/antimicrobial-resistance-global-threat#:~:text=According%20to%20recent%20estimates%2C%20in,poverty%20in%20the%20next%20decade.


World Health Organization (WHO). (n.d.). Antimicrobial Resistance. https://www.who.int/health-topics/antimicrobial-resistance

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