Pharmaceutical Microbiology


Written by MicroDok

An antibiotic has to go through a number of steps in order to exert its antibacterial action in vivo. They have to come into contact with the host taking them before ever their antibacterial properties can be dissipated. First, the antibiotic has to enter the host cell, and once inside the cell, the antibiotic has to remain stable and accumulate to killing or inhibitory concentrations enough to deactivate invading microorganisms (or bacteria). In some cases, the antibiotic need to be activated to an active form and finally it has to locate and interact with its target (s) in order to exert its action. Any alteration in any one or more of these processes can render the cells of the bacteria resistant to the antibiotic directed against it.

This is what happens whenever a bacterium mounts resistance to antibiotics which was supposed to inactivate their degrading effects to the host, hence the need for the mechanism of acquiring resistance by bacteria. In addition to this, the increased dissemination and prevalence of resistance is an outcome of natural selection and should be viewed as an expected phenomenon of the “Darwinian” biological principle of “survival of the fittest”. In any large population of bacteria, a few cells will be present which posses traits that enable them to survive in the presence of harmful substances (e.g. antibiotics), in this case the ability of the bacteria to fade off or evade the action of the antibiotic directed against them.

Susceptible organisms (i.e. those lacking the advantageous traits like antibiotic resistance genes) will be eliminated, leaving behind the remaining resistant population of bacteria. With long time antibiotic in use in a given environment, the bacteria communities will change dramatically, with more resistant organisms increasing in proportion. This can result in a situation where the antibiotic is needed; it may not be effective to treat what was once and easily treatable infection. In this scenario, bacteria are now unaffected by the antibiotic because of selective pressure posed on them by initial, “unnecessary”, and long time antibiotic usage in a particular population. Below are some of the mechanisms employed by bacteria to mount resistance against antimicrobial agents (antibiotics):

1. Antibiotics resistance by influx-efflux systems: Certain bacteria can often become resistant to antimicrobial agents through a mechanism known as “efflux”. Efflux pumps are pumps found in bacteria cells, which help them to export antimicrobial agents (e.g. antibiotics) and other compounds out of the bacterial cell. The antibiotics enter the bacteria through chemical channels called “porins”, and then it is pumped out again by the efflux pumps. By actively pumping out the antibiotic and other harmful substances out of the cell, the efflux pumps prevents the intracellular accumulation of the antimicrobial agent that is necessary to exert optimal antibacterial activity inside the bacterial cell.

Bacterial cells have an inherent (natural) capacity to restrict the entry of small molecules (e.g. antibiotics) that destabilizes its internal metabolism. This is what the cell wall and outer cell membranes in both Gram positive and Gram negative bacteria respectively do. The ability of bacteria to restrict the entry of material into its internal environment is more pronounced in Gram negative bacteria unlike in Gram positive bacteria which are devoid of “outer membrane” that the former possess. The “outer membrane” is a first – line defense (protection) mechanism in Gram negative bacteria, and its absence in Gram positive bacteria is the reason why Gram positive bacteria is highly sensitive to antibiotics.

This is because there is no form of security to protect its peptidoglycan. The “influx – efflux” system in bacteria has to do with the entry and partial accumulation of harmful substances like antibiotics within the cytoplasm of a bacterium and the subsequent exit or removal of these harmful substances from the bacterial cell through efflux pumps. The “efflux system” in bacterial cell pumps out the antibiotics that finally made their way into the cytoplasm of the bacterium, thereby preventing their intracellular accumulation. The most well studied efflux system is in Escherichia coli and with this mechanism in place; bacteria can easily mount resistance to antibiotics directed against them.

2. Antibiotic resistance by chemical alteration of antibiotics in vivo: Some antibiotics (e.g. the Nutrofuran family used to treat UTI’s) need to be activated in vivo before ever they can reduce (bring out) their antibacterial activity against a given pathogen to which they were meant to attack and deactivate. Such antibiotics are activated in vivo by being reduced by a specific enzyme (gene). Only then can they be able to elicit their biological properties in vivo. For example, antibiotics in the Nitrofuran family like nutrafurantoin are reduced by cellular reductase enzymes encoded by nfsA and nfsB Any mutation in these genes can eventually lead to a nitrofuran resistance. In contrast to this, the chemical alterations of some antibiotics (e.g. Beta – lactams) in vivo by enzymes (e.g. Beta – lactamases) can inactivate the biological activity of these antibiotics, thereby leading to resistance.

3. Antibiotic Resistance due to Target Alterations: Most pathogens have the ability to alter target (s) of antibiotics in their cell. These alterations in the target of the drugs occur in such a way that the toxic effect of the antibiotic on the target pathogen is countered. A typical example is the alteration that occurs in penicillin – binding – proteins (PBPs) in bacteria. The PBPs are transpeptidases which catalyze the cross-linking reaction between two stem peptides, each linked to adjacent N-acetyl-muramic acid residues of the peptidoglycan backbone. This reaction confirms and gives rigidity to the bacterial cell wall. Penicillin exerts its antibacterial activity by binding to the PBPs, thereby preventing the cross-linking of N-acetyl-muramic acid and N-acetyl-glucosamine that will eventually lead to the formation of a very rigid bacterial cell wall. But alterations in this target (PBPs) due to a mutational change in the organism can mount antibiotic resistance on the bacterial cell.

4. Antibiotic resistance due to non – heritable states of bacteria: The non – heritable form of antibiotic resistance posed by bacteria to antibiotics has to do with some physiological states in which bacteria exist in, and which are not heritable or transferred by other organisms. These non – heritable physiological states of bacteria includes: Persistence State, Swarming State, and Biofilm State; and they are known to render bacteria insensitive to antibiotics. Such physiological states are expressed by bacteria in a transient state, and they are reversible and non – heritable. In such states, bacteria are said to be antibiotic tolerant. These non – heritable states of bacteria are as follows:

A. PERSISTENCE STATE: In this state, bacteria exist in a small fraction of slow or non – growing, antibiotic tolerant cells called persisters. They exist in this form and remain insensitive to harmful substances like antibiotics.

B. BIOFILM STATE: Biofilms are organized structures in which many bacterial species exist in. In biofilms, bacterial cells of several species are embedded in a self – produced exo – polysaccharide matrix. These structures are highly organized and they permit the transport of nutrients and metabolic wastes in and out of the matrix structure. Biofilms have a very high tolerance to high concentrations of antibiotics.

C. SWARMING STATE: Swarming is a form of multicellularity in many bacterial species, and it is characterized by the migration of highly differentiated bacterial cells (swarm cells) on semi – solid surfaces. This gives them some form of protection from antibiotics as, they are known to remain in close contact with one another and they also migrate as a group in this form.

Diagram showing the mechanisms by which bacteria evade (dodge) antibacterial activities of antibiotics. From:


Genetic resistance of microbes to antibiotics is due to a chromosomal mutation in the bacterial DNA or acquisition of antibiotic resistance genes on plasmids or transposons from other bacteria. Bacteria are extremely ingenious in becoming resistant to antibiotics directed towards them because they are able to regulate their drug resistance genes over time. This is often exacerbated by prior antibiotic usage especially irrational drug use. In this case where bacteria regulate their drug resistance genes, antibiotics used against them for treatment is inadvertently rendered useless in vivo. The genetic basis for antibiotic resistance may include: the acquisition and further expression of new DNA by horizontal gene transfer or mutations in cellular genes or acquired genes that alter antibiotic target sites on the bacteria. The genetic alterations (mutation) mediate a diversity of biochemical mechanisms of resistance that benefits the bacteria, and in turn makes the antibiotic less efficacious in vivo. These mechanisms may include:

  1. Enzymatic inactivation of the antibiotic.
  2. Target substitutions, amplification or modifications bypassing the binding of the antibiotic, or reducing the affinity of the bacteria for the drug.
  3. Barriers such as efflux pumps which reduce the access of the antibiotic to the target site of the bacteria.


A great many factors contribute to the antibiotic resistance that we now face in both the community and in the hospital. Most of these factors have to do with both human behavior and activities while the other factors are contributed by the microbes themselves. The first among these factors that contribute to the development of antibiotic resistance is “Natural selection”. Microbes, over time, are capable of adapting in ways which increases their ability to survive in a changing environment. Bacterial genomes represent a large natural pool of diverse genetic information that can be accessed under appropriate selection pressures, using a variety of gene acquisition and dissemination mechanisms“. Human application of toxic agents on massive scale activates these genetic systems to promote survival of the microbial population.

As a result, each and every antibiotic will have a finite lifetime depending on the magnitude and nature of its use; thus the development of antibiotic resistance is inevitable. The basic idea here is that, as pathogens encounter large amounts of antibiotics, those that have little or no resistance to the antimicrobial agent are killed off en masse, while on the other hand, those that already possess some measure of resistance due to previous encounters with the drug or random mutation in their genome, have a much higher likelihood of survival. Once the weaker bacteria have been destroyed by the antibiotics, the remaining resistant organisms will continue to thrive. Though the process of natural selection takes generations to occur, but in bacteria, those generations are produced in a matter of hours or days rather than years or decades in other organisms. In addition to the above factors, other contributing factors to the development of antibiotic resistance in bacteria include:

  • Overuse of antimicrobial agents especially unwisely.
  • Excessive use of antibiotics in livestock and animal feeds.
  • Poor patient compliance towards drug regimens.
  • Self medication that defies a doctor’s prescription.


The impact and cost of antibiotic resistance on the public health and economy of a nation are enormous. It is therefore imperative that we optimize the use of antibiotics in both our communities and hospitals in order to curtail or abate the development of bacterial resistance which is gradually eroding our therapeutic armamentarium. Due to the selection pressure caused by antibiotic use, a large pool of resistant genes has been created and this resistance places an increased burden on the society in terms of high mortality, morbidity, and cost of treating infections that they cause.

Patients infected with drug resistant organisms are more likely to have ineffective therapy, longer duration of hospital stay, need of treatment with broad spectrum antibiotics that are most toxic and more expensive than their counterparts. All these factors increases the cost of treatment for an individual patient; and on a national or global scale, its effect on the economy can be colossal. Antibiotic resistance drives up health care cost, thereby increasing the severity of disease and death rates of some infections since not all patients can afford the hospital bill due to the economic situation around. Ineffective treatment due to antimicrobial resistance will eventually culminate to increased human suffering, lost productivity, and often death.


Antibiotic resistance can be controlled by one of the following methods:

  • Hand washing as a measure of infection control.
  • Review of antibiotic use in hospitals.
  • Updating of clinicians, nurses, pharmacists, and even patients on rationale antibiotic use.
  • Good personal hygiene in both the hospital and in the community.
  • Restriction of human medicine in livestock and animal feeds.
  • Patronage of over – the – counter (OTC) drugs by patients for self medication without doctor’s prescription should be discouraged.
  • Patients should always endeavour to take full course of their drugs when under any medication.


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