What are antibiotics?

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The use of drugs that are selectively toxic to microorganisms
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Indications and Procedures

Humans live in the midst of a microbial world of bacteria, fungi, and protozoa. Microorganisms were the first inhabitants of the earth. When multicellular animals arose, some microbes adapted to use them as a source of nutrients. Most of these microorganisms did no harm to their hosts. In fact, humans carry around bacteria numbering in the trillions. Some were not harmless and possessed the means to penetrate tissues and invade internal organs. As a result, animals evolved a variety of defensive strategies, referred to as immune responses, to resist such invasion. Infections develop when these responses fail to repel the invading bacteria. To combat such infections, humans can turn to antibiotics for help.

Antibiotics are drugs that kill, or inhibit the reproduction of, bacteria. In the strict use of the term as defined by Selman Waksman, the discoverer of streptomycin, an antibiotic is “a chemical substance produced by microorganisms which has the capacity to inhibit the growth of bacteria and even destroy bacteria and other microorganisms in dilute solution.”

The effectiveness of antibiotics arises from their selective toxicity, which relies on differences between the fundamental biology of pathogenic bacteria and that of an infected person. The sulfonamides, or sulfa drugs, the first class of antibiotic compounds to achieve widespread use, are chemically similar to molecules used by bacteria for the synthesis of folic acid, an essential vitamin. When sulfonamides are present, they interfere with folic acid synthesis, preventing growth of the bacteria. Because humans lack the ability to synthesize folic acid (which is obtained from food), their cells are unaffected by sulfonamides. The beta-lactams, a class of antimicrobial chemicals that includes the penicillins and cephalosporins, interfere with the synthesis of peptidoglycan, an essential component of bacterial cell walls that is totally lacking in human cells. Other antibiotics target unique aspects of microbial protein synthesis and nucleic acid metabolism. Antibiotics are sometimes used in combination; for example, beta-lactams may be used to weaken bacterial cell walls, promoting access of a second antibiotic directed against an internal target.

The clinical microbiology laboratory can assist physicians in determining appropriate antibiotic therapy by identifying infectious agents and determining the susceptibility or resistance of the agent to a range of potential antibiotics. In the early days of antimicrobial chemotherapy, it was often sufficient to diagnose an infection from its symptoms, from which one could infer the type of microorganism causing the infection (for example, gram-positive or gram-negative bacteria) and prescribe one of a limited number of broad-spectrum agents with confidence that it would be effective. Today, while immediate application of broad-spectrum antibiotics may be called for to contain a serious infection, concern over creating resistant pathogens leads more physicians to request the identification and testing of microorganisms. Furthermore, the extensive resistance encountered among pathogens suggests that a broad-spectrum agent may be ineffective.

Advances in clinical microbiology are directed toward increasing the speed and accuracy of the identification of infectious agents, with a primary goal of providing information useful in prescribing antimicrobial chemotherapy. Clinical samples (infected fluids, biopsy samples, or tissue swabs) are used to inoculate selective and differential media that favor the growth of a suspected pathogen. Material from isolated colonies is then subjected to a variety of tests designed to characterize aspects of the microorganism’s physiology and metabolic biochemistry, which provide criteria for the taxonomic identification of the organism. While some smaller laboratories rely on the manual inoculation of test media and reference to printed diagnostic tables for identification, the trend is toward greater automation to allow more rapid processing of multiple samples. Panels of test media prepared in multiwell plates can be simultaneously inoculated, and because many of the tests are evaluated by color changes, test results can be read with spectrophotometers designed to scan the individual tests. Test data are entered into computer programs that match the test results with probability matrices to provide a probable identification of the organism used to inoculate the tests. In the largest laboratories, efficiency can be enhanced by using robotics to conduct many of the steps, from inoculation to the reporting of test results and probable identification.

While automation can help to speed up the rate at which test information is obtained, classic identification tests are limited by the need for the incubation and growth of the test organism; this limitation can be particularly burdensome in the case of microorganisms that are especially slow-growing, among which are the mycobacteria that cause tuberculosis. In response, laboratories increasingly rely on identification methods that allow direct examination of the microorganism. Serological tests, which use antibodies directed against antigens specific to a particular microbe, and DNA probes, targeted to species-specific genes, are being applied to an increasing range of pathogenic microorganisms. Some of these tests have advanced to the point that infectious agents can be identified directly in clinical samples, circumventing the need for isolation in the laboratory. In 2013, a research team from the University of Toronto announced the creation of an electronic chip that can analyze blood for pathogens in a matter of minutes, far more quickly than previous methods. The chip can simultaneously test for multiple viruses and bacteria, which will facilitate rapid detection and more targeted treatment of the infectious agent.

In evaluating the susceptibility of a microorganism to an antibiotic, microbiologists seek to determine the minimal inhibitory concentration (MIC) at which an antibiotic will inhibit the growth of the microbe in a standard growth medium; the MIC can be correlated with an effective dose of the antibiotic. In broth dilution tests, a defined number of microbial cells is inoculated into a series of broth tubes containing different concentrations of an antibiotic; the MIC is reported as the lowest concentration of the antibiotic that prevents growth of the organism in the broth. The same technologies used to automate identification can be used to allow a large number of broth dilution tests to be carried out in multiwell plates, so that susceptibility to a range of antibiotics can be determined simultaneously.

Where automation is unavailable, broth dilution testing is impractical because of the labor involved, and laboratories may rely on an indirect method called a disk diffusion test, or Kirby-Bauer assay. In this method, disks of filter paper impregnated with a defined amount of antibiotic are placed on a plate of solid growth medium that has been seeded with cells of the microorganism being tested. During incubation, the antibiotic diffuses from the disk, leading to a gradient of antibiotic concentration extending in all directions from the disk. If the microbe is susceptible to the antibiotic, its growth will be inhibited in a circular zone surrounding the disk; the diameter of the zone of inhibition varies directly with the MIC for that antibiotic. As with traditional identification methods, tests for antibiotic susceptibility are limited by the requirement that the test organism be allowed time to grow in the laboratory. It is likely that commercial DNA probes will be developed to allow the direct detection of genes that encode resistance to individual antibiotics.

Uses and Complications

Given the importance of differences between the biology of infectious microorganisms and the biology of the infected host to the effectiveness of antibiotics, it is not surprising that antibiotics have been used most successfully to control infections caused by bacteria, whose molecular and cellular biology differs vastly from that of humans. Consequently, most antibiotics directed against bacteria show a favorable chemotherapeutic index, which is the ratio of the maximum dose that can be administered without causing serious harm to the recipient of the drug to the minimum dose that will be effective in controlling the infection.

Infections caused by eukaryotic fungi and protozoa are particularly difficult to treat because of the similarities between the cell structure and function of these organisms and those of human cells. While the topical application of antifungal agents such as miconazole is very effective in the treatment of fungal skin infections and vaginal candidiasis, the treatment of systemic fungal infections (usually with amphotericin B) is much more difficult to perform and is more likely to cause serious side effects. Amphotericin B, the mainstay of antifungal therapy for decades, was particularly toxic. Newer antifungal agents, such as the azoles and echinocandins, are better tolerated and sometimes more effective, but antifungal therapy remains a challenge. Similar complications accompany efforts to treat protozoal infections with antimicrobial agents; this situation is especially frustrating, since parasitic infections such as malaria and schistosomiasis pose a major worldwide health problem. The number of methods available for the chemical treatment of viral infections is extremely limited, in view of the fact that viruses rely on the molecular machinery of the infected host for their reproduction. One antiviral strategy that has met with limited success is to design nucleotide analogues that interfere with viral nucleic acid synthesis; both acyclovir, used for infections caused by the herpes simplex virus, and azidothymidine, the first agent shown to affect the course of human immunodeficiency virus (HIV) infection, belong to this class of drugs.

In addition to potential toxicity, other factors need to be considered when choosing an antibiotic for treatment of a particular infection. Attention must be given to the course of treatment when an antibiotic is administered, so that a sufficient concentration is maintained at the site of infection. If an antibiotic is administered orally, then it must be able to survive the environment of the gastrointestinal tract in order to reach the targeted tissues. Only certain antibiotics are able to cross the blood-brain barrier for effective treatment of infections of the central nervous system.

Antibiotics can be classified according to their spectrum of activity (the range of pathogenic organisms that they effectively kill or inhibit); broad-spectrum antibiotics are effective against many species, while narrow-spectrum antibiotics target a specific group. A broad-spectrum antibiotic can be prescribed upon diagnosis of an infection, without identification of the particular pathogen responsible; this trait can be important when immediate containment of the infection is essential to the health of the patient. Yet the indiscriminate use of broad-spectrum antibiotics can harm microorganisms other than those causing an infection. External surfaces, including the skin, gastrointestinal tract, upper respiratory tract, and vagina, are inhabited by large numbers of microorganisms, collectively referred to as the normal microbiota. While this relationship is hardly a symbiotic one, such organisms do help to maintain environments that inhibit the growth of pathogenic microbes. Administration of broad-spectrum antibiotics can cause the depletion of normal microbiota organisms, leading to conditions favoring superinfection by a pathogen other than the one targeted by the antibiotic. For example, vaginal candidiasis (often called a yeast infection) can develop with the administration of antibacterial drugs. The bacteria that normally inhabit the vagina maintain an acidic environment that inhibits the growth of the pathogenic fungus Candida albicans, which may nevertheless persist in low numbers. If these bacteria are adversely affected by antibiotic treatment, then the vagina may become less acidic, allowing C. albicans to grow and cause tissue damage. Other superinfections can lead to serious damage to the gastrointestinal tract. There is also concern that the use of broad-spectrum antibiotics may encourage the growth of antibiotic-resistant strains among the microorganisms that constitute the normal microbiota. Because antibiotic resistance can be transferred from one bacterial species to another, conditions that favor the growth of any antibiotic-resistant microbes can contribute to the development of antibiotic-resistant pathogens.

Specific resistance to the action of antibiotics is a matter of great concern to medical personnel who deal with infectious diseases. In the early 1940s, when the first antibiotics came into widespread use, virtually all strains of Staphylococcus aureus (a bacterium that causes a variety of infections) were susceptible to penicillin G, a beta-lactam that can be administered orally. By the 1990s, it was rare to isolate a strain of S. aureus from an infection that was not resistant to multiple beta-lactams. Similar situations prevail with other pathogenic microorganisms, seriously impairing the ability to control many infections. Antibiotic resistance usually develops when a pathogen possesses specific genes encoding proteins that allow the organism to avoid the action of the antibiotic. Such proteins may inactivate the antibiotic molecule, interfere with the uptake of the antibiotic, or modify the target of the antibiotic so that it is no longer affected by the antibiotic. In bacteria, the genes encoding antibiotic resistance (called resistance determinants, or R-factors) are usually found on plasmids, small circular deoxyribonucleic acid (DNA) molecules that are separate from the bacterial chromosome. A single plasmid may contain genes for resistance to several antibiotics. Many plasmids also contain genes that allow them to be transferred from one cell to another, even if the cells are of different species. These genes can cause antibiotic resistance to spread rapidly among microorganisms.

Because the presence of an antibiotic in an animal’s tissues favors the survival of bacteria carrying resistance determinants for that antibiotic, continued application of an antibiotic tends to increase the incidence of resistance to that antibiotic. Overcoming this dilemma is difficult. Narrow-spectrum antibiotics should be used whenever practical, since they limit the range of species subject to selection for antibiotic resistance. Some microbiologists have urged that the nontherapeutic application of antibiotics, such as the use of tetracycline as a growth-promoting factor in animal feeds, be discontinued because it can contribute to the spread of resistance determinants. The identification of new natural and synthetic compounds for which resistance has not yet been encountered can help to defeat pathogens that have developed resistance to the current repertoire of antibiotics, but experience teaches one to expect that such victories will be temporary; the implementation of each new antibiotic will lead to the discovery of new resistance determinants.

Perspective and Prospects

The latter decades of the nineteenth century are often referred to as the golden age of microbiology, because it was during this time that microbiologists identified many of the pathogenic microorganisms responsible for infectious diseases. Although such knowledge was useful in helping to control the transmission of infectious diseases in populations through public health measures and vaccination programs, it did little to alleviate the suffering of the individual already infected with now-identifiable pathogens. Actual treatment of infections required the identification of chemical compounds that would be selectively toxic to the microorganisms, and such compounds were unknown at that time. Nevertheless, the potential value of such compounds motivated many scientists to devote their research to the search for chemicals that would destroy microorganisms without damaging an infected person.

The few compounds used at this time (mostly heavy metal salts) tended to exhibit a very low chemotherapeutic index, and some scientists despaired of finding poisons that were poisonous for only some forms of life. Then, in 1910, Paul Ehrlich demonstrated that Salvarsan (arsphenamine), an arsenical compound, was selectively toxic to the bacterial agent of syphilis. Although Salvarsan was useless for other infections, it provided evidence that selective toxicity was possible and encouraged the medical community to find other selective toxins. Extensive chemical screening programs led, in 1935, to the commercial production of the sulfanilamides, which are active against multiple species of bacteria.

The greatest conceptual advance in the development of antimicrobial drugs was made by those bacteriologists who concentrated on the phenomenon of antagonism, whereby certain microorganisms produce compounds that inhibit others. Study of these compounds eventually led to the practical application of gramicidin (described by René Dubos in 1939), penicillin (described by Alexander Fleming in 1928), and streptomycin (described by Selman Waksman in 1943). Penicillin receives special attention in the history of antibiotics because the industrial processes developed to allow production of massive quantities of the drug proved valuable in the commercial exploitation of other antibiotics. With the goal of increasing the yield of penicillin, motivated in part by a desire to have an alternative to the sulfonamides for the treatment of infections attending World War II, industrial microbiologists optimized the composition and aeration of the growth media and selected mutant strains of the penicillin-producing fungus that secreted the drug in amounts far greater than those seen by Fleming. In doing so, they established some of the engineering principles that allowed for the growth of biotechnology.

Eventually, major pharmaceutical companies committed themselves to extensive screening programs to identify additional natural antibiotics. Microorganisms isolated from soil were tested for their ability to inhibit the growth of pathogens. Eventually it was realized that although a diverse range of organic molecules possess antibiotic properties, such compounds are produced by a limited range of microorganisms. More than half of the natural antibiotics currently in use are produced by mycelial bacteria called actinomycetes. One approach that has complemented the identification of new natural antibiotics is the chemical modification of such drugs through the addition or removal of groups of atoms. Compared to natural antibiotics, such semisynthetic derivatives may have properties that promote accumulation at high levels in the target tissue or prevent recognition of the antibiotic molecule by products of resistance determinants. All the beta-lactams in common use today are semisynthetic molecules.

While microbiologists have been discovering further natural antibiotics and synthesizing others, they have also been learning more about the molecular biology of infectious pathogens. Research is also progressing on ways to decrease the unnecessary use of antibiotics. Rapid flu tests can now be used by doctors to determine whether patients need antibiotics at all. New uses for antibiotics are also being discovered every day. For instance, researchers have begun to explore ways to attach powerful implants to medical devices in order to decrease infection postoperatively. Together, all these types of knowledge will allow antibiotic development to become increasingly useful.


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