Microbial Ecology

Antimicrobial resistance to drugs

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Escherichia coli. Source: USDA; Credit: Eric Erbe.

Antimicrobial resistance is the ability of microbes, such as bacteria, viruses, parasites, or fungi, to grow in the presence of a chemical (drug) that would normally kill it or limit its growth.

Antimicrobial (Drug) Resistance

  • Increasing use of antimicrobials in humans, animals, and agriculture has resulted in many microbes developing resistance to these powerful drugs.
  • Many infectious diseases are increasingly difficult to treat because of antimicrobial-resistant organisms, including HIV infection, staphylococcal infection, tuberculosis, influenza, gonorrhea, candida infection, and malaria.
  • Between 5 and 10 percent of all hospital patients develop an infection, leading to an increase of about $5 billion in annual U.S. healthcare costs.
  • About 90,000 of these patients die each year as a result of their infection, up from 13,300 patient deaths in 1992.
  • People infected with antimicrobial-resistant organisms are more likely to have longer hospital stays and may require more complicated treatment.
The difference between non-resistant bacteria and drug resistant bacteria. Non-resistant bacteria multiply, and upon drug treatment, the bacteria die. Drug resistant bacteria multiply as well, but upon drug treatment, the bacteria continue to spread. Credit: NIAID.

Definition of Terms


Antimicrobial is a general term given to substances including medicines that kill or slow the growth of microbes.

Microbe is a collective name given to bacteria (e.g., Staphylococcus aureus, which causes some staph infections), viruses (e.g., influenza, which causes the flu), fungi (e.g., Candida albicans, which causes some yeast infections), and parasites (e.g., Plasmodium falciparum, which causes malaria).

Examples of antimicrobial agents are:

  • Tetracycline (one antibiotic used to treat urinary tract infections)
  • Oseltamivir or Tamiflu (antiviral that treats the flu)
  • Terbinafine or Lamisil (antifungal that treats athlete’s foot)


An antibiotic is a medicine designed to kill or slow the growth of bacteria and some fungi. Antibiotics are commonly used to fight bacterial infections, but cannot fight against infections caused by viruses.

Examples of antibiotic are:

  • Azithromycin or Zithromax (Z-Pak)
  • Vancomycin—the last line of defense for certain methicillin-resistant Staphylococcus aureus (MRSA) infections.


Antibacterial is the term given to substances that kill or slow the growth of bacteria when treating human and environmental surfaces. These include substances that aid in proper hygiene.

Examples of antibacterial-containing commercial products are:

  • Hand soaps, gels, foams
  • Dishwashing detergents
  • Mattresses


Examples of antimicrobial (drug) resistance are:

The History of Antimicrobial (Drug) Resistance


Microbes are living organisms that reproduce, thrive, and spread quickly and efficiently, increasing their numbers. Microbes include bacteria (e.g., Staphylococcus aureus, which causes some staph infections), viruses (e.g., influenza, which causes the flu), fungi (e.g., Candida albicans, which causes some yeast infections), and parasites (e.g., Plasmodium falciparum, which causes malaria).

Antimicrobial is a general term given to medicines that kill or slow the growth of microbes.

Antimicrobial drug resistance is the ability of a microbe to grow in the presence of a chemical that would normally kill it or limit its growth.


In 1928 while working with Staphylococcus bacteria, Scottish scientist Alexander Fleming noticed that a type of mold growing by accident on a laboratory plate was protected from, and even repelled, the bacteria. The active substance, which Fleming called penicillin, was literally an antibiotic—it killed living organisms.

Thus began the age of using natural and, later, synthetic drugs to treat people with bacterial infections. Though not widely popular until the 1940s, antibiotics and other antimicrobials have saved countless lives and blunted serious complications of many feared diseases and infections. The success of antimicrobials against disease-causing microbes is among modern medicine's great achievements.

The Problem

After more than 50 years of widespread use, evolution of disease-causing microbes also has resulted in many antimicrobials losing their effectiveness.

As microbes evolve, they adapt to their environments. If something stops them from growing and spreading—such as an antimicrobial—they evolve new mechanisms to resist the antimicrobials by changing their genetic structure. Changing the genetic structure ensures that the offspring of the resistant microbes also are resistant.

Antimicrobial resistance makes it harder to eliminate infections from the body. As a result of a microbe’s ability to survive in spite of antimicrobials, some infectious diseases are now more difficult to treat than they were just a few decades ago. In fact, antimicrobials have helped people so effectively that humans are hurting the protective value of medicines through overuse and misuse.

More prudent use of antimicrobials will help to slow the development of resistance.


Microbes, such as bacteria, viruses, fungi, and parasites, are living organisms that evolve over time. Their primary function is to reproduce, thrive, and spread quickly and efficiently. Therefore, microbes adapt to their environments and change in ways that ensure their survival. If something stops their ability to spread, such as an antimicrobial, genetic changes can occur that enable the microbe to survive. There are several ways this happens.

Natural (Biological) Causes

Selective Pressure

In the presence of an antimicrobial, microbes are either killed or, if they carry resistance genes, survive. These survivors will replicate, and their progeny will quickly become the dominant type throughout the microbial population.


Microbes reproduce by dividing every few hours, allowing them to evolve rapidly and adapt quickly to new environmental conditions. With each replication, mutations arise and some of these mutations may help an individual microbe survive exposure to an antimicrobial.

Gene Transfer

Microbes also may get genes from each other, including genes that make the microbe drug resistant. 

Societal Pressures

The use of antibiotics, even when used appropriately, creates a selective pressure for resistant organisms. However, there are additional societal pressures that act to accelerate the increase of antimicrobial resistance.

Inappropriate Use

Selection of resistant microorganisms is exacerbated by inappropriate use of antimicrobials. Sometimes healthcare providers will prescribe inappropriate antimicrobials, wishing to placate an insistent patient who has a viral infection or an as-yet undiagnosed condition.

Inadequate Diagnostics

More often, healthcare providers must use incomplete or imperfect information to diagnose an infection and thus prescribe an antimicrobial just-in-case or prescribe a broad-spectrum antimicrobial when a specific antibiotic might be better. These situations contribute to selective pressure and accelerate antimicrobial resistance.

Hospital Use

Critically ill patients are more susceptible to infections and, thus, often require the aid of antimicrobials. However, the heavier use of antimicrobials in these patients can worsen the problem by selecting for antimicrobial-resistant microorganisms. The extensive use of antimicrobials and close contact among sick patients creates a fertile environment for the spread of antimicrobial-resistant germs.

Agricultural Use

Scientists also believe that the practice of adding antibiotics to agricultural feed promotes drug resistance. More than half of the antibiotics produced in the United States are used for agricultural purposes.1, 2 However, there is still much debate about whether drug-resistant microbes in animals pose a significant public health burden.


  1. National Research Council, Committee on Drug Use in Food Animals. The use of drugs in food animals: benefits and risks. Washington (DC): National Academy Press; 1999.
  2. Mellon M, Benbrook C, Benbrook KL. Hogging it: Estimates of antimicrobial abuse in livestock. Cambridge (MA): Union of Concerned Scientists; 2001.


Diagnostic tests are designed to determine which microbe is causing infection and to which antimicrobials the microbe might be resistant. This information would be used by a healthcare provider to choose an appropriate antimicrobial. However, current diagnostic tests often take a few days to give results.

Oftentimes, healthcare providers need to make treatment decisions before the results are known. While waiting for test results, healthcare providers may prescribe a broad-spectrum antimicrobial when a more specific treatment might be better. The common practice of treating unknown infections with broad-spectrum antimicrobials is another factor in the emergence of antimicrobial resistance.


If you think you have an infection of any type—bacterial, viral, or fungal—talk with your healthcare provider. Some infections will go away without medical intervention. Others will not and can become extremely serious. Ear infections are a good example: Some middle ear infections are caused by a virus and will get better without treatment. However, other middle ear infections caused by bacteria can cause perforated eardrums, or worse, if left untreated.

The decision to use antimicrobials should be left to your healthcare provider. In some cases, antimicrobials will not shorten the course of the disease, but they might reduce your chance of transmitting it to others, as is the case with pertussis (whooping cough).

Antibiotics cannot fight against infections caused by viruses.

Antibiotics are appropriate to use when

  • There is a known bacterial infection
  • The cause of the infection is unknown. In that case, the consequences of not treating a condition could be devastating (e.g., in early meningitis).

Of note, the color of your sputum (saliva) does not indicate whether you  need antibiotics. For example, most cases of bronchitis are caused by viruses. Therefore, a change in sputum color does not indicate a bacterial infection.


To prevent antimicrobial resistance, you and your healthcare provider should discuss the appropriate medicine for your illness to avoid overusing or misusing medicines. Strictly follow prescription medicine directions, and never share or take medicine that was prescribed for someone else. Talk with your healthcare provider so that he or she has a clear understanding of your symptoms and can decide whether an antimicrobial drug, such as an antibiotic, is appropriate. 

Do not save your antibiotic for the next time you get sick. Take all of the medicine as prescribed by your healthcare provider. If your healthcare provider has prescribed more than the required dose, discard leftover medicines once you have completed the prescribed course of treatment.

Healthy lifestyle habits always go far in preventing illness, including proper diet, exercise, and sleeping patterns as well as good hygiene, such as frequent hand washing.

A Growing Health Issue

The emergence of drug-resistant microbes is not new or unexpected. Both natural causes and societal pressures drive bacteria, viruses, parasites, and other microbes to continually change in an effort to evade the drugs developed to kill them.

Natural causes

Like all organisms, microbes undergo random genetic mutations, and these changes can enhance drug resistance. Resistance to a drug arising by chance in just a few organisms can quickly spread through rapid reproduction to entire populations of a microbe.

Societal pressures

Antimicrobial resistance is fostered by the overuse and misuse of antimicrobial drugs in people as well as animals; a lack of diagnostic tests to rapidly identify infectious agents; and poor hand hygiene and infection control in healthcare and community settings.

Together, these forces contribute to the problem of drug-resistant infections that are increasingly difficult and costly to treat.

Drug-Resistant Microbes of Concern Today

Methicillin-Resistant Staphylococcus aureus (MRSA)

Methicillin-resistant Staphylococcus aureus (MRSA) bacteria, increasingly seen not only in hospitals and healthcare settings (hospital acquired or HA-MRSA) but also in the wider community, especially among people in close contact such as athletes (community associated or CA-MRSA). More about MRSA.

Vancomycin-Resistant Enterococci (VRE)

Vancomycin-resistant Enterococci (VRE) bacteria are resistant to vancomycin, an antibiotic regarded as a drug of last resort. More about VRE.

Microbes Increasingly Resistant to Drugs










(2011). Antimicrobial resistance to drugs. Retrieved from http://www.eoearth.org/view/article/51cbf1e97896bb431f6a72c0


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