Pharmaceutical Microbiology


Written by MicroDok


There is no consensus to the definition of antibiotics. But it is very important that we do not displace the key points (“Killing and Inhibition”) that must be contained in any definition of an antibiotic. Abinitio, an antibiotic was originally defined as a substance produced by one microorganism, which inhibits the growth of other microorganisms. But due to the development of other synthetic or chemical methods by which drugs can be produced, there has been a modification to this definition.

Today, an “antibiotic” can be defined as a substance produced by a microorganism (wholly or partly by chemical synthesis), which in low concentrations kill or inhibit the growth of other microorganisms in vivo. The discovery of antibiotics and their subsequent application to clinical medicine is one of the outstanding scientific achievements of the twentieth century. Antibiotics – “Magic Bullets” as fondly called by many have been used for about 6 decades now to treat and cure variable series of diseases including tuberculosis (TB), pneumonia, gonorrhea, urinary tract infections (UTI’s), respiratory infections, syphilis, et cetera and they have been found to be very efficacious in this aspect. Antibacterial drugs (antibiotics) has been the most effective of all medicines and their success is reflected by their continued use in clinical medicine and the decrease in morbidity and mortality from bacterial infections over the past 50 years.

Today, it is very difficult to imagine a society without antibiotic despite the emergence of antibiotic resistant strains of bacteria that is gradually eroding the efficacy of our therapeutic regimens. Antibiotics cure disease by killing or injuring bacteria. Some antibiotics are ‘Bactericidal’, meaning that they work by killing bacteria. Other antibiotics are ‘Bacteriostatic’, meaning that they work by stopping bacteria multiplication. Each different type of antibiotic affects different bacteria in many different ways, thus stopping their deleterious effect to the host. Some antibiotics can be used to treat a wide range of infections and are known as ‘broad-spectrum’ antibiotics. Others are only effective against a few types of bacteria and are called ‘narrow-spectrum’ antibiotics.


Antibiotic history dates back to 1928 when Sir Alexander Fleming discovered the antibacterial effects of the yeast, Penicillium notatum, a Fungus in his laboratory. The “antibiotic era” was ushered in through the work of several pioneering scientists including Sir Alexander Fleming, Howard Florey, Ernest chain, Selman Waksman, Albert Schatz, Paul Ehrlich to mention but a few. Sir Alexander Fleming astutely recognized that a contaminated Petri dish of Staphylococcus aureus actually contained a bacterium – killing mould, which was later deciphered to be P. notatum. His work together with that of Ernest Chain and Howard Florey in 1939 lead to the isolation, purification, and commercial production of penicillin (a beta – lactam drug widely used in clinical medicine today) in 1940.

Penicillin, a beta – lactam antibiotic is a cell wall inhibitor. Unlike other antibiotics, the penicillin does specifically affect the synthesis of peptidoglycan – which is very crucial in the synthesis of cell wall in bacterial cell. This jeopardizes the integrity and structure of bacterial cells, thereby exposing them to external pressure or harmful chemicals that finally destroy the bacterial cell. Just a few years later after the discovery of the antibacterial properties of the penicillins, the antibacterial properties of “Sulphonamides” were also noted by Paul Ehrlich in 1932. Since then, a plethora of other antibiotics were also discovered and produced synthetically and semi – synthetically, thus giving hope to clinical medicine in the treatment of bacterial related infections.

Antibiotics target different features of bacterial physiology, thus expanding the range of bacterial species that can be successfully treated with them. In the early 1940’s, the industrialization of penicillin production was quickly followed by the successful isolation and development of a large number of antibiotics that has led to most of the major classes of antibiotics in use even today, namely: Tetracycline, Chloramphenicol, Glycopeptides, Aminoglycosides, Cephalosporins, and Rifamycins. It is no doubt that the discovery and development of antibiotics and their introduction into clinical medicine, together with the introduction of such infection control measures like vaccination, use of clean water, and personal hygiene brought infectious diseases caused by bacterial species under control.


Before the advent of conventional medicine used in clinical medicine today for the treatment of infectious diseases, people in ancient times and even now have been using some herbal plants traditionally for centuries to combat microbes that cause diseases in man. Recently, scientists have studied and reported results that support the use of these herbal plants (Carson et al., 2006). Herbal antibiotics have been found to be milder than pharmaceutical antibiotics, and according to the Center for Disease Control and Prevention (CDC), the overuse of pharmaceutical antibiotics cause pathogens to mutate and grow stronger, giving them the chance to mount resistance to antibiotics. Some of the herbal plants used for the treatment of infectious diseases include: The Neem Tree/plant (Azadirachta indica), Ginger, Garlic, Tea Tree Plant et cetera. Antibiotics are obtained or sourced from one of the following means:

  1. MICROORGANISMS: Microorganisms are the primary source of antibiotics. Though not all antibiotics used today in clinical medicine are produced completely (wholly) from microorganisms, microorganisms still provide the parent root from which antibiotics are developed. Bacitracin and polymyxins are obtained from Bacillus species; streptomycin and tetracycline are obtained from Streptomyces species; gentamicin from Micromonospora purpurea; penicillins and cephalosporins are obtained from Penicillium and Cephalosporium species respectively.
  2. SYNTHESIS: Synthetic antibiotics are antibiotics produced from natural drugs by making a prototype (model) of the natural drug in the laboratory through chemical reactions without having to do anything with the original source of the drug. Example of a synthetic antibiotic is chloramphenicol.
  3. SEMI – SYNTHESIS: Semi – synthetic antibiotics are natural antibiotics that are modified by the removal or addition of a particular chemical group in order to increase the therapeutic effect of the drug. Here, compounds isolated from natural sources (e.g. plants or microorganisms) are used as starting materials and a fermentation process is involved in the production of such antibiotics. After which, the antibiotic is further modified by a chemical process in the laboratory. Examples of drugs produced this way include: penicillins, cephalosporins, and the antimalarial drug artemether.


There are several classification/types of antibiotics today, which is based on bacterial spectrum of activity (whether broad or narrow) or type of activity exhibited by the agent (whether bactericidal or bacteriostatic). Some antibiotics are also classified based on their chemical structure. And this leaves antibiotics within a particular structural class to have similar patterns of effectiveness, toxicity, and allergic potential. The types of antibiotics expanded here are not exhaustive of the different classes or types of antibiotics and they include:

BETA – LACTAM ANTIBIOTICS: The beta – lactam antibiotics are a broad class of antibiotics that consist of all antibiotic agents that contains a beta – lactam ring/nucleus in its molecular structure (Figure 1). They are the oldest class of antibiotics especially the penicillins and they are produced from Penicillium and Cephalosporium bacteria. Examples of antibiotics in this class include: penicillins, cephalosporins, monobactams and carbapenems. The beta – lactam antibiotics work by inhibiting the synthesis of cell wall in bacteria. They are the most widely used group of antibiotics in clinical medicine, and they are active on both Gram positive and Gram negative bacteria. Beta – lactam antibiotics have no antibacterial activity on bacterial cells that lack cell wall e.g. Mycoplasmas. They are only effective on bacterial species that have cell wall.

Figure 1: General Structure of Penicillins (Beta – Lactam Antibiotics)

MACROLIDES: The macrolides are a group of antibiotics that are characterized by possessing molecular structures that contain large (12-16 membered) lactone rings linked through glycosidic bonds with amino sugars (Figure 2). They are derived from Streptomyces bacteria, and they are bacteriostatic, binding with bacterial ribosomes to inhibit protein synthesis. Macrolides are active against most Gram positive bacteria but not against the Enterobacteriaceae. Examples of antibiotics in this category include: erythromycin, azithromycin, and clarithromycin.

Figure 2: Structure of Erythromycin, a Macrolide

FLUOROQUINOLONES: The fluoroquinolones (fluorinated – quinolones) are second – generation quinolones that are produced by the addition of a fluorine atom (molecule) on the carbon-6 (C-6) of quinolones (Figure 3).  They are synthetic antibiotics and are not sourced from microorganisms. Nalidixic acid is the first quinolone while ciprofloxacin, ofloxacin and norfloxacin are examples of fluoroquinolones. They are active on both Gram positive and Gram negative bacteria, and they are mostly used in the treatment of urinary tract infections (UTI’s). The fluoroquinolones target the DNA gyrase and topoisomerase IV enzymes of bacterial cell, leading to the inhibition of DNA synthesis or replication in them. Thus, the fluoroquinolones inhibit bacteria by interfering with their ability to make DNA. This activity makes it difficult for bacteria to multiply and cause havoc in vivo. They are used to treat most UTI’s, skin infections, and respiratory infections because of their excellent absorption in vivo.

Figure 3: General Structure of Quinolones, progenitor of Fluoroquinolones

TETRACYCLINES: The tetracyclines are a group of antibiotics that is characterized by a four cyclic ring (Figure 4). They are derived from a group of Streptomyces bacteria and they inhibit bacterial protein synthesis. Examples include oxytetracycline, doxycycline and chlorotetracycline. Tetracyclines have a wide range of activity on both Gram positive and Gram negative bacteria, thus they are broad spectrum bacteriostatic agent.

Figure 4: General Structure of Tetracyclines

AMINOGLYCOSIDES: Aminoglycoside antibiotics contain amino sugars in their structures and they possess a cyclohexane ring (Figure 5). They are derived from Streptomyces bacteria, and they are bactericidal in action, and they inhibit the synthesis of protein in bacterial cell. Examples of antibiotic in this category include gentamicin, kanamycin, tobramycin and streptomycin.

Figure 5: Structure of Streptomycin, an Aminoglycoside


The antibiotics described above including those not described in this work are used to treat infections caused by disease causing microorganisms (bacteria). Majority of them exert a highly selective toxic action upon their target microbial cells but have little or no toxicity towards mammalian cells. These antibiotics can therefore be administered at concentrations sufficient enough to kill or inhibit the growth of infecting organisms without damaging mammalian cells. The ways by which these antibiotics exert their antibacterial activities on microbes in vivo without necessarily harming the host (patient) taking the drug is called the “Mechanism of Action of Antibiotics”. It reveals and explains the rationale behind the selective toxicity of antibiotics and how they stop the venomous effects of bacteria. Below are some of the major mechanisms of action of antibiotics:

  1. INHIBITION OF MICROBIAL CELL WALL SYNTHESIS: Peptidoglycan is a vital component of the cell wall of virtually all bacteria. But it is more pronounced in Gram positive bacteria than in Gram negative bacteria. The peptidoglycan is responsible for maintaining the shape and mechanical strength of the bacterial cell wall. If it is damaged in anyway, or its synthesis is inhibited (e.g. by antibiotics), then the shape of the bacterial cells becomes distorted and they will eventually burst (lyse) due to the high internal osmotic pressure following the influx of fluids or substances like drugs from the outside into the bacterial cell. Mammalian cell is devoid of peptidoglycan, thus antibiotics which inhibit microbial cell wall synthesis show outstanding selective toxicity. Examples of antibiotics that inhibit bacterial cell wall synthesis include: Penicillins, Bacitracin, Glycopeptides (e.g. Vancomycin), and Cephalosporins. These antibiotics stop the cross – linking of N-acetyl-glucosamine and N-acetyl-muramic acid (transpeptidation reaction) which is supposed to lead to the formation of peptidoglycan, an important component of bacterial cell wall.
  2. INHIBITION OF DNA SYNTHESIS FUNCTION: Deoxyribonucleic acid (DNA) is a vital component of the chromosome of bacterial cells as they are known to direct the activity of the cells. Antibiotics that inhibit the synthesis of DNA in bacterial cell work by interfering with the transcription stages which are very vital to the final and complete formation of bacterial DNA. These antibiotics block the DNA gyrase enzyme (Topoisomerase II) which is important to the complete synthesis of DNA in bacteria. Examples of antibiotics that inhibit bacterial DNA synthesis function include: Sulfonamides, Trimethoprim, Rifampicin, Quinolones, and Fluoroquinolones.
  3. DESTRUCTION OF MICROBIAL CELL MEMBRANE: The integrity of the cytoplasmic membrane in bacterial cell is very important for the normal functioning of all cells. Bacterial cell membranes do not contain sterols. This differentiates them from fungal and mammalian cells which do contain sterols, thus giving such antibiotics a highly selective toxicity on bacteria. Antibiotics that destroy the cytoplasmic membrane of bacterial cells cause irreversible leakage of cytoplasmic components by disturbing the integrity of the membrane. This can also impair other metabolic functions associated with the membrane. Examples of antibiotics that destroy microbial cell membrane include: Polymyxins.
  4. INHIBITION OF PROTEIN SYNTHESIS: Bacterial ribosomes are smaller than their mammalian counterparts. The ribosomes in bacterial cells are vital for the synthesis of proteins. Antibiotics that inhibit the synthesis of protein in bacterial cells act by binding to a receptor on either the 30S or 50S subunit ribosomes. This action prevents the complete reaction of translocation, thereby inhibiting the synthesis of protein in bacterial cells. Antibiotics that are protein synthesis inhibitors include: Tetracyclines, Chloramphenicol, Macrolides, and Streptomycin.


Antibiotics have some specific characteristics that distinguish them from other agents that are used for the treatment of microbial infections. Some of these features are as stated below:

  1. Selective Toxicity: Antibiotics must be selectively toxic as they dissipate their antibacterial properties in vivo. This means that antibiotics should kill or inhibit pathogens without causing any harm or damage to the host (patient) in anyway.
  2. Spectrum of Activity: Antibiotics should have a reasonable spectrum of activity (broad or narrow), showing efficacy over a given or wide variety of bacteria.
  3. Antibiotics should not eliminate the normal microbial flora of the body as they exert their antibacterial properties in vivo.
  4. They should be specific in their action. Thus, antibiotics should be readily directed to the site of infection where their effect is highly needed in the body.
  5. Antibiotics should not be too costly so that their prescription should not be biased or based on their price or cost.
  6. Antibiotics should not be easily neutralized or excreted from the body until it has performed its function. Thus, they should be chemically stable in vivo.
  7. Microorganisms should not become easily resistant to them.


Antibiotic resistance is a phenomenon that occurs when bacteria are not killed or inhibited by usually achievable systemic concentration of an antibiotic (drug) with normal dosage schedule and/or fall in the minimum inhibitory concentration ranges of the drug in question. It occurs when bacteria change in some way that reduces or eliminates the effectiveness of drugs or other agents designed to cure or prevent the infection. Thus the bacteria survive and continue to multiply causing more harm in the host taking the drug. Antibiotic resistance is a natural phenomenon and it is exacerbated following the prior administration of an antibiotic.

According to the World Health Organization (WHO) the introduction of every antimicrobial agent into clinical practice has been followed by the detection in the laboratory of strains of microorganisms that are resistant, i.e. able to multiply in the presence of drug concentrations higher than the concentrations in humans receiving therapeutic doses. Microorganisms harbor resistance genes which encode various mechanisms that allow them to resist the killing or inhibitory effects of specific antibiotics directed towards them. These mechanisms also offer resistance to other antibiotics or antimicrobial agents of the same class and sometimes to several different antimicrobial classes.

The problem of antibiotic resistance is a vital topic and a global health problem that has received increasing attention over the last two decades. It is certainly not a new topic neither was it unpredictable. When antibiotic resistance occurs, it is the microbe (bacterium) that is resistant, not the antibiotic nor the patient or host taking it. Species of bacteria that are normally resistant to penicillin for example, can develop resistance to these drugs either through mutation (vertical transmission) or through acquisition from other bacteria of resistance genes (horizontal transmission). This dual means of acquiring resistance explains why the resistance trait can spread rapidly and replace a previously drug – susceptible population of bacteria. Antibiotic resistance is on the rise threatening our ability to treat infectious diseases and even some of those that cause most deaths in the past (e.g. tuberculosis).

Diseases such as tuberculosis, which once thought to be under control, are becoming increasingly difficult to treat as medicines become less effective – steadily depleting the arsenal of drugs available for their treatment. Antibiotic resistant bacteria were first discovered soon after the medicinal use of penicillin began. The first signs of antibiotic resistance were actually observed in 1940, five years before penicillin became commercially available to the public. In that year, the first observed bacterial enzyme (beta-lactamase) that destroyed penicillin was described. This was the first observed evidence of bacterial resistance to an antibiotic action. Therefore, the history of antibiotic resistance coincided with the history of antibiotics themselves.

The number of antibiotics belonging to various families, their varied mode of action and the number of bacteria in which antibiotic resistance has been documented suggests that, in principle, any microbe could develop resistance to any antibiotic. Antibiotic resistance is one of the biggest challenges that bedevil our health sector worldwide. Resistance of microbes to antibiotics has been documented not only against antibiotics of natural and semi – synthetic origin, but also against purely synthetic compounds (such as the fluoroquinolones) or those which do not even enter the cells (such as vancomycin). And unfortunately, the discovery and development of newer antibiotics have not kept pace with the emergence and rate at which bacteria develops and mount resistance to antibiotics. Thus, the rate at which microbes are developing resistance to antibiotics is much faster than the rate at which the drugs are developed to curb the problem.


Bacteria have evolved to survive in diverse environments. They survive exposure to harsh chemicals including antibiotics, and they also survive difficult growth conditions. They have learned to “detoxify” harmful substances e.g. antibiotics. Antibiotic resistance can either be intrinsic or acquired.

INTRINSIC (INNATE) RESISTANCE: Some bacteria are said to possess innate/intrinsic resistance against antibacterial action put forward by antibiotics. They mount a great ingenuity in devising means or ways of neutralizing the killing or inhibiting action of antibiotics directed towards them. This innate form of antibiotic resistance in bacteria shows the different variations in the structure of the cell envelope of the organism, which allows them to mount resistance against drugs. It is a vertical means by which bacteria acquire resistance. Intrinsic or innate form of antibiotic resistance can occur by any one of the following route:

  • Spontaneous mutation in the chromosomal DNA of bacteria.
  • Accumulation of several point mutations in bacteria.
  • An evolutionary process occurring only under selective pressure e.g. prior exposure of bacteria to antibiotics.

ACQUIRED (PHENOTYPIC) RESISTANCE: This type of antibiotic resistance is acquired by bacteria from the environment or other microorganisms by one of the means of genetic transfer (conjugation, transformation, and transduction). In acquired/phenotypic resistance, the bacteria acquire reduced susceptibility to antibiotics through adaptation to growth within a specific environment. Acquired resistance is a horizontal means by which bacteria become resistant to antibacterial properties of antibiotics. This form of antibiotic resistance can be achieved in bacteria by one of the following route:

  • Resistance can be maintained on horizontal mobile elements like plasmids, integrons and transposons.
  • Resistant genes can be transferred among bacteria through means of genetic transfer.
  • Resistance genes can be integrated into the bacterial chromosome or can be maintained in an extra chromosomal state (e.g. plasmids).


Antibiotic – resistant bacteria owe their drug insensitivity and ingenuity in developing resistance against our therapeutic regimens to resistance genes which they harbor or possess. It is these genes that resistant bacteria transfer to non – resistant susceptible strains, thus compounding the problem of antibiotic resistance. Below are some of the major ways through which bacteria pass on their antibiotic resistance genes to susceptible non – resistant bacteria:

1. CONJUGATION: Conjugation is the form of gene transfer and recombination in bacteria through which genetic materials are transferred from one bacterium to another through a direct cell – to – cell contact. It is the most important genetic transfer mechanism by which bacteria transfer their antibiotic resistance genes to susceptible bacteria. Conjugation is mediated by a particular kind of circular DNA called a plasmid, which replicates independently of the chromosome. Many plasmids carry genes that confer resistance to antibiotics. When two bacterial cells are in close proximity to each other, a hollow bridge like structure known as the “pilus” forms between the two cells. This allows a copy of the plasmid as it is duplicated (in the donor cell known as the F+ cell) to be transferred from the donor bacterium or F+ bacterium to the recipient bacterial cell known as the F- bacterium. After successful conjugation and transfer of genetic material, the F- bacteria becomes F+ bacteria. This process called conjugation enables a susceptible bacterium to acquire resistance genes to a particular antibiotic.

Illustration of conjugation.

2. TRANSDUCTION: Transduction is the transfer of genetic material between bacteria by bacteriophages (bacterial viruses). Here, antibiotic resistance genes are incorporated into a phage capsule which is later injected into another bacterium. In the process of transduction, bacterial DNA is transferred from one bacterium to another inside a virus that infects bacteria. These viruses are called bacteriophages or phage. When a phage infects a bacterium, it essentially takes over the genetic process of the bacteria to produce more phage. During this process, bacterial DNA may inadvertently be incorporated into the new phage DNA. Upon bacterial death and lyses or breaking apart, these new phage goes on to infect other bacteria. This brings along genes from previously infected bacterium into the recipient bacterium. These genes might contain advantageous genes such as antibiotic resistance genes, which will leave the recipient bacterium resistant to a particular antimicrobial agent (e.g. antibiotics).

Illustration of transduction, showing the lytic and lysogenic cycles of viruses or phages.

3. TRANSFORMATION: Transformation is a mode of genetic transfer in bacteria in which a piece of free DNA (genetic materials) is taken up by a bacterium and integrated into the recipient genome. During this process, genes are transferred from one bacterium to another as “naked” DNA. When bacterial cells die and break apart, DNA can be released into the surrounding environment. Other bacteria in close proximity can scavenge this free floating DNA and incorporate them into their own DNA. This incorporated DNA can contain advantageous genes such as antibiotic resistance genes and benefit recipient bacterial cells.


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