What are Antibiotics?

In the late 1920’s, the Scottish microbiologist Alexander Fleming returned from a trip to find that one of his petri dishes containing the bacterium, Staphylococcus aureus, was contaminated with the mold, Penicillium notatum. Like a good scientist, he did not just throw it out and start over; rather, he made an observation: there were no bacterial staph colonies growing directly around the mold. There was a zone that was free of bacterial growth directly surrounding the mold. Upon closer inspection, he noticed that the mold was secreting a liquid (now called penicillin) that he later learned was the cause of death to the bacteria growing in close proximity to the mold.

What Fleming had discovered (actually, re-discovered) was an antibiotic: a chemical that inhibits the growth of or kills microorganisms (e.g. bacteria). Antibiotics have evolved in fungi and bacteria as defenses against other microbes. Microorganisms often compete with each other for the same resources. In response to competition, many fungal and bacterial species have evolved chemical weapons to inhibit other species. Antibiotics are the chemical weapons of fungi and bacteria.

What do antibiotics do? How do they kill bacteria? They work through several different means. Some inhibit the synthesis (or production) of bacterial cell walls; some inhibit the synthesis of proteins; still others inhibit the replication of bacterial DNA. All of these are, of course, detrimental to the bacteria that encounter the antibiotic. So detrimental, in fact, it often kills them.

We humans know a good thing when we see it. A chemical substance that kills bacteria: we could use this to our advantage! And did we ever. Within a few decades, both naturally occurring and synthetic antibiotics were produced in mass quantities and given to people who were sick with infectious diseases. And they worked. Antibiotics were the miracle cure to all kinds of infectious diseases that had been plaguing humans for hundreds of years. Antibiotics worked so well, in fact, that in 1969, the U.S. Surgeon General declared: “it is time to close the book on infectious disease.” The war against bacteria was over, and we had won!

Or had we?

Antibiotic¹ Resistance

In 1941, all strains of staphylococcal bacteria (common causes of wound and postoperative infection) were susceptible to (killed by) penicillin. Three years later, one strain of staph was no longer susceptible to penicillin; it was resistant to (not killed by) penicillin. Today, especially in hospitals, there are strains of staph bacteria that are resistant to, not just one, but nearly all known antibiotics. Although most of the multiple-drug resistant staph strains are only found in hospitals, recently, four children in North Dakota and Minnesota were killed by staph infections that they had acquired outside of a hospital.

Staphylococcus is not the only problem bacterium. More than two-dozen types of bacteria are now resistant to one or more types of antibiotics that had previously been effective against them. Certain strains of three bacterial species (Enterococcus, Pseudomonas, and Mycobacterium tuberculosis) are resistant to every antibiotic, including vancomycin, the antibiotic previously known as “the drug of last resort.” Multi-drug resistant tuberculosis (TB, caused by Mycobacterium tuberculosis) is nearly epidemic in some areas of the world (e.g. Russia)² .

Antibiotics are not as effective at killing bacteria as when they were first introduced. People are dying from infections that were easily treated just a few years ago. It has been estimated that infections caused by resistant bacteria kill as many as 77,000 people every year in the United States alone. Resistance to antibiotics costs dollars as well as lives: it costs the nation up to $30 billion every year.

What happened? Why can we no longer cure infections that were very easily treated just a few years ago?

What is Resistance to Antibiotics?

There are several ways to address this question. First of all, there is a prevalent misconception that antibiotics no longer work because the people who take the drugs have developed a tolerance for the drug. This is not the case. Humans do not develop a tolerance for antibiotics. Antibiotics work by inhibiting or killing the bacteria living inside of us. The reason they no longer work (i.e. we do not get better after taking the antibiotic) is that the bacteria are no longer inhibited/killed by the drug—they are resistant to the effects of the antibiotic.

So, back to our question, what is resistance to antibiotics? Let us first address this question physiologically. There are several ways that bacteria resist the effects of antibiotics. Some resistant bacteria inactivate the antibiotic by destroying or modifying the drug itself so that it is no longer toxic. Some resistant bacteria pump the drug out of the bacterial cell so that the concentration of the drug is too low to be effective. Still, other resistant species have an altered form of the target site of the drug (the place on the cell where the drug binds), so the antibiotic cannot “find” its target. These are examples of the types of resistance characters that bacteria use to fight antibiotics.

Now, let us address this question on a different level: evolutionarily. What has happened to make these bacteria resistant to antibiotics? Have individual bacteria developed a tolerance to the drug? Have they physiologically acclimated to the presence of the antibiotic so that it no longer affects them? No. What has happened is bacterial evolution. Mutations that allow the bacteria to resist the effects of the antibiotic occur and have a selective advantage. These mutations have the type of effects that were described in the previous paragraph (for example, there is a mutation that results in an altered form of the target site). These resistance characters are often simple mutations (i.e. changes in a single gene). The result is that resistant bacteria differ genetically from their susceptible ancestors.

So what happens if a bacterial cell has a mutation that allows it to resist the effect of an antibiotic? If that bacterium is in the presence of the antibiotic, then it will have an advantage: the drug will not kill it! It will be able to reproduce, while the susceptible bacteria (which are inhibited or killed by the antibiotic) will not. In the presence of the antibiotic, the resistant mutant has a selective (reproductive) advantage over normal cells³. Originally, most or all bacteria in the population were susceptible to the antibiotic⁴ . Over many generations, the resistant type will make up a greater and greater percentage of the population. Eventually, most or all of the individuals in the bacterial population will be resistant to the antibiotic. The population has evolved resistance due to natural selection by antibiotics: the genetic structure of the population has changed, from susceptible to the antibiotic to resistant to the antibiotic.

Why Does Resistance Evolve so Quickly?

Bacterial populations can evolve resistance very quickly. For example, in one hospital, initially 5% of the strains of staphylococcal bacteria were resistant to the antibiotic ciprofloxacin. Within one year, 80% of the bacterial strains were resistant. From 5% to 80% in one year! Why do bacterial populations evolve resistance so quickly? There are two basic reasons:

1) in general, bacteria have the capacity to evolve quickly
2) humans are helping them to evolve even faster

Bacteria Biology

There are several aspects of bacteria biology that contribute to their capacity for rapid evolution. Bacteria, relative to humans, have very short generation times. A generation time is the time it takes to go from one generation to the next. For example, in humans, it takes on average about 20 years to go from the birth of a child to the birth of that child’s child. Therefore, the generation time for humans is approximately 20 years. Contrast this with the average bacterial generation time of hours or even minutes! Under favorable conditions, a single bacterial cell will very quickly reproduce into a colony containing many generations of its offspring and their offspring. These colonies can have so many individual cells that, within hours or days, it will be large enough to see with the naked eye. Organisms with fast generation times, like bacteria, have the capacity for very rapid adaptation to a changing environment. Since evolutionary change occurs across generations, organisms with fast generation times (like bacteria) can evolve much faster than organisms with slow generation times (like humans). Some bacteria species can go through thousands of generations in a single year.

Bacterial populations are also very high in numbers and are quite genetically variable. Mutations are the primary source of genetic variation. Mutations (accidents in DNA replication) are rare events. In bacteria, a mutation at a particular gene occurs on average once in about every 10,000,000 cell divisions. Since bacteria are so numerous and divide so often, even these rare events actually occur quite often. As an example, E. coli cells in a human colon divide 2 x 1010 times every day. That means that every day in an E. coli population, approximately 2000 cells will have a mutation at a particular gene⁵ . So, even though mutations are rare events, they occur often enough in bacterial populations to create a lot of genetic variation within populations.

Mutation is not the only way that a bacterium can acquire a resistance gene. Bacteria have three other methods of acquiring genes that sexual organisms (like us) do not have. Bacteria can pick up pieces of DNA (containing genes) from their environment (transformation), they can obtain a gene from another bacterium (conjugation), and genes can also be transferred to a bacterium by a virus (transduction). So, even if a resistance gene does not occur through mutation, it can be acquired through one of these methods.

To summarize, bacterial populations evolve resistance to antibiotics so quickly because of their fast generation times, large population sizes, and unique methods of gene acquisition. These are some of the reasons that bacteria have been so evolutionarily successful.

Human Behavior

The second reason that bacterial populations evolve resistance to antibiotics so quickly is that several aspects of human behavior actually contribute to their capacity to evolve rapidly. Understandably, when antibiotics first became available, people started to use them. A lot. Today, antibiotics are overused, and unfortunately antibiotics are often misused.

Overuse:
• It has been estimated that nearly half of all medical prescriptions for antibiotics in the U.S. are unnecessary. Many doctors prescribe antibiotics under pressure from their patients, even if the antibiotic is not warranted (e.g. for a viral infection). Direct-to-consumer marketing by pharmaceutical companies can also lead to inappropriate demand for antibiotics by patients.

• Almost half of all antibiotics produced in North America and Europe are given to livestock; most are given not to fight infection, but prophylactically to promote growth in healthy animals. There is growing evidence that this use of antibiotics in livestock leads to resistance in human bacteria.

• It is currently trendy to include antibacterial agents in common household cleaning products (even hand lotion!). It is becoming more and more difficult to find cleaners without antibacterial agents.

Misuse:
• Medical doctors, including veterinarians and dentists, often incorrectly prescribe antibiotics: they prescribe the wrong antibiotics or the incorrect dosage of an antibiotic for a particular infection; they prescribe antibiotics for non-bacterial infections (e.g. colds, coughs, or influenza); they prescribe antibiotics prophylactically (in a low dosage for months at a time to prevent future infections; for example, for young children with a history of multiple ear infections).

• Many doctors also prescribe broad-spectrum antibiotics, which kill many different types of bacteria, rather than run a diagnostic lab test so they can prescribe a narrow-spectrum antibiotic that would specifically target the bacteria causing the infection.

• In many other countries, antibiotics are freely available over the counter, without a doctor’s prescription, leading to widespread misuse.

• Patients themselves also contribute to the problem when they feel better after a few days, and then stop taking the antibiotics, instead of continuing with the full cycle prescribed to them. In a 1995 Gallup poll, it was estimated that more than half of American adults taking antibiotics failed to complete their prescribed dosage.

Compounding all of these problems, the pharmaceutical industry (until very recently) had all but stopped research and development of new antibiotics.

Bacteria Biology + Current Human Behavior = Fast Evolution

How have these two factors helped speed up the evolution of resistance? In essence, we are exerting extremely strong selection pressures on these bacteria by our heavy use of antibiotics. Bacteria are continuously exposed to antibiotics, and this has created very strong selection on these populations to evolve resistance. The more exposure to antibiotics that bacterial populations have, the greater the selection pressure on these populations to evolve resistance. The rate that evolutionary change occurs depends directly upon the strength of natural selection imposed. Strong selection leads to rapid evolution.

Antibiotics do not just kill the bacteria species that we want them to act on (i.e. the bacteria causing the infection we are trying to get rid of). Antibiotics also affect a lot of bacteria that are beneficial to us, or that are commensal with us (neither harmful nor beneficial). This decreases the population sizes of these other bacteria, which reduces the competition for the harmful bacteria that survive. This lack of competition for resources allows the surviving resistant bacteria to do very well.

In addition, by using antibiotics incorrectly, we are giving the bacterial populations the opportunity to adapt quickly. For example, if you take an antibiotic correctly—in an adequately high dosage and for the entire cycle—most of the bacteria in your system will be killed. By greatly reducing the population size of the bacteria, you greatly decrease the chance that any one bacterium will mutate to a resistant form. However, if you incorrectly take the antibiotic—if you stop taking it after a few days or if the dosage is not high enough—more of the bacteria will survive⁶ . Higher numbers of bacteria means a greater chance that a resistance mutation will occur in any one of the bacterial cells. When these mutations do occur, they rapidly increase in the population, due to the very strong selection pressure exerted by the presence of the antibiotic.

In conclusion, the combination of several aspects of bacterial biology (fast generation time, high population sizes) and human behavior (heavy use of antibiotics, misuse of antibiotics) has led to an ever-increasing problem of bacteria resistant to our only means of controlling them.

What is the Future of Antibiotics?

Can we stop the evolution of resistance? Because of their quick generation times and high numbers, bacteria have a very high capacity to quickly adapt to changing environments. We cannot change the biology of the bacteria. As long as we expose bacteria to antibiotics, they will evolve resistance to them. However, we can slow down the evolution of resistance by modifying human behavior.

What can be done to slow down the evolution of resistance?

First, decrease the selection pressure on bacterial populations by decreasing the overall use of antibiotics. Researchers are recommending prudent use of antibiotics (see website of the Alliance for the Prudent Use of Antibiotics). Doctors and patients need to be educated about when and how to use antibiotics appropriately. Antibiotics should not be prescribed for viral infections, such as the common cold. For minor bacterial infections, a period of “watchful waiting” for a day or two to see if the infection will clear on its own has also been recommended.

Scientists are also recommending that the agricultural industry discontinue the use of antibiotics in livestock and on crops, especially those antibiotics that are used to treat disease in humans (see website of the Union of Concerned Scientists).

Second, stop giving bacteria extra opportunities for mutations (i.e. use antibiotics appropriately). When an antibiotic is necessary, the most appropriate antibiotic should be prescribed based on the results of laboratory tests to confirm the precise bacterium causing the infection. Often, a doctor will prescribe an antibiotic without conducting a laboratory test to determine the bacterial species causing the infection. If the antibiotic is not appropriate, and the patient does not get better, he/she then comes back for a different prescription. In this case, all of the bacteria in the patient were unnecessarily exposed to an inappropriate antibiotic. When possible, narrow-spectrum antibiotics should be used, rather than a broad-spectrum antibiotic, which affects many different types of bacteria.

Antibiotics need to be taken in strong enough dosages to kill all the bacteria causing the infection, and they need to be taken responsibly: each dose should be taken on time, and all doses (i.e. the full cycle) should be taken. Doctors and pharmacists should be educated about responsible usage, and they should actively encourage their patients to take antibiotics responsibly—exactly as prescribed, and for the entire course. Patients should not demand antibiotics from their doctors.

Third, reduce the spread of resistant bacteria from one person to another. This can be done with the same techniques used for controlling the spread of diseases themselves—better hygiene, clean water, vigorous hand washing, etc. The agricultural industry can also help to stop the spread of resistant bacteria by not using the same antibiotics in animals that are also used in humans (to avoid, for example, transferring resistant bacteria to humans in the food that we eat).

Finally, more research is needed. Research on the optimal use of antibiotics will be necessary. It is still unclear exactly how to decrease the selection pressure on bacterial populations. The above suggestions can only help, but more research about how bacterial populations respond to antibiotics is still needed. Also needed is basic research on microbial biology: physiology, genetics, ecology, and evolution. Understanding basic biological processes in these organisms will help to develop new drugs and treatment protocols.

Most “new” antibiotics these days are modified from older ones. Because these drugs are so similar to older varieties, resistance evolves very quickly. Research and development of completely new antibiotics will also become increasingly important. Pharmaceutical companies have started to respond to this need, but since it can take up to ten years for a new drug to be approved for use in the United States, there will be a lag time before new drugs will become available.

Summary and Conclusions

To summarize, antibiotics have been miracle drugs, curing all sorts of formerly incurable infectious diseases. Unfortunately, humans have used these drugs unwisely, allowing the bacteria to quickly evolve ways to get around them. If we had been aware of the principles of evolutionary biology, if we had understood that the heavy use of antibiotics applies enormous selection pressure on bacterial populations to evolve resistance, and that incorrect usage of antibiotics gives the bacterial populations the opportunity to quickly evolve resistance, then we may not have found ourselves in the situation that we are today. Granted, even if antibiotics had been used wisely from the very beginning, bacterial populations would still have evolved resistance eventually; however, it would have taken much longer, we would have known it would happen, and would have been better prepared to manage the evolution of resistance. Unfortunately, because we ignored evolution for so long, we are in a crisis of antibiotic resistance.

References and Web Resources

References Used:

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Levin, B.R. & R.M. Anderson. 1999. The population biology of anti-infective chemotherapy and the evolution of drug resistance: more questions than answers, in S.C. Stearns (ed.) Evolution in Health & Disease. Oxford University Press, Oxford.
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Web resources on antibiotic resistance:

Alliance for the Prudent Use of Antibiotics
Centers for Disease Control and Prevention
National Institutes of Health
Union of Concerned Scientists
U.S. Food and Drug Administration
World Health Organization