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Dr Alvin Fox
Emeritus Professor
University of South Carolina School of Medicine





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Logo image Jeffrey Nelson, Rush University, Chicago, Illinois  and The MicrobeLibrary

A severe rash


Sterilization/disinfection/ antisepsis

Selective toxicity
Minimal inhibitory concentration (MIC)
Susceptibility testing
Penicillin binding proteins (PBP)
Beta lactam
Clavulinic acid
Penicillinase/beta lactamase
Polymyxin B


Sterilization refers to killing (or removal) of ALL bacteria in a non-selective fashion. For example, autoclaving involves heating liquids (e.g. media) or solids to 121oC under steam pressure. The materials must be heat resistant. Ethylene oxide is sometimes used in hospitals for equipment that cannot be heated. Membrane filters have pores that trap bacteria, but allow drugs and small chemicals to pass through; thus pre-sterilized filters can be used to sterilize delicate solutions. UV light is used for decreasing bacterial levels on surfaces such as in operating rooms; however it is not totally effective. Ionizing radiation is more efficient and can be used for sterilizing instruments and food.

Disinfectants (e.g. phenol-based) can be useful in killing many bacteria on certain instruments, but cannot be used for internal consumption or on skin. Antiseptics (e.g. iodine or 70% alcohol) are used topically (e.g. on skin surfaces) to reduce bacterial load.


In contrast, antibiotics are agents that are "selectively" toxic for bacteria (either killing them [bactericidal] or inhibiting their growth [bacteriostatic]) without harm to the patient. They can thus be ingested. By definition, these compounds must act on structures found in bacteria, but not in the host. Antibiotics work most efficiently in conjunction with an active immune system to kill infecting bacteria in the host. After isolation of pure colonies (see Bacteriology lecture 2), the susceptibility of bacterial isolates can be tested to a variety of antibiotics. The minimal inhibitory concentration (MIC) refers to the lowest concentration of an antibiotic that stops visible growth. More simply, the zone of inhibition around a disk impregnated with antibiotic (Kirby-Bauer) is another measure of antibiotic activity.


One major class of antibiotics inhibits the synthesis of peptidoglycan (figure 1). Once cell wall synthesis (involving penicillin binding proteins) is inhibited, enzymatic autolysis of the cell wall can occur. Without the restraining influence of the cell wall the high osmotic pressure inside the cell bursts the inner and/or outer membranes of bacteria. Thus, these antibiotics are generally bactericidal. Several mechanisms are involved in inhibition of peptidoglycan synthesis:

(1) The terminal two amino acids of a peptide side chain of peptidoglycan are unusual amino acids (D-alanine as opposed to its isomer L-alanine). The antibiotic cycloserine is an analog of D-alanine and interferes with enzymatic conversion of L-alanine to D-alanine in the cytoplasm. Thus, subsequent synthesis of peptidoglycan cannot occur.

(2) The peptidoglycan subunit (containing one side-chain and an attached peptide to be used in cross-bridge formation) is passed across the cytoplasmic membrane attached to undecaprenol diphosphate. After the nascent peptidoglycan monomer leaves the carrier on reaching the cell wall, the undecaprenol diphosphate is dephosphorylated to its monophosphate form. Bacitracin  inhibits the dephosphorylation reaction and in the absence of monophosphorylated carrier peptidoglycan subunit synthesis stops. 

Antibiotic Attack
Requires Flash

cross-link.jpg (68065 bytes) Figure 1 Cross-linking of peptidoglycan

penicill.jpg (28597 bytes) Figure 2 Structure of penicillin

(3) The final step in peptidoglycan synthesis involves linking the sugar portion of the peptidoglycan subunit to the glycan backbone of the existing cell wall polymer. Cross-linking of the peptide portion of the subunit to a peptide in the cell wall then occurs. During this process D-alanine is enzymatically excised from the end of a pre-existing peptide side chain allowing it to be cross-linked (by a new peptide bond) to the recently synthesized peptidoglycan subunit. Vancomycin  binds to D-alanine-D-alanine thus sterically inhibits transpeptidation (cross-linking).

(4) The beta lactam antibiotics include penicillins (e.g. ampicillin), cephalosporins and monobactams. They bind to and inhibit enzymes (penicillin binding proteins) involved in the transpeptidation (cross-linking) of peptidoglycan. These antibiotics have in common the four membered lactam ring. Attached to the lactam, penicillins have an additional five membered ring and cephalosporins a six membered ring. Monobactams consist of the lactam ring alone and display antibiotic activity.


penicil2.jpg (133882 bytes) Figure 3 Resistance to beta lactams - Gram-negative bacteria

penicil3.jpg (143037 bytes) Figure 4  Resistance to beta lactams  - Gram-positive bacteria


Penicillin is made by the mold Penicillium chrysogenum. During fermentation the mold forms 6-aminopenicillanic acid which has a thiazolidine ring and a beta-lactam ring fused together (figure 2). This, however, is acid labile and subject to degradation by bacterial enzymes. More stable derivatives are made biochemically so that in addition to increased stability, they are better absorbed from the gastro-intestinal tract and have a wider spectrum of bactericidal effects.

Various chemical side chains have been synthetically linked to the ring structures producing a host of antibiotics with different properties in the host. Many penicillins (figure 2) display little activity against Gram negative bacteria, since they do not penetrate the outer membrane. Cephalosporins and other newer penicillins are active against Gram negative bacteria, since they can penetrate the outer membrane. Other chemically modified penicillins have lower elimination rates from the patient; decreasing the frequency of administration of these drugs.

Penicillins can be destroyed by beta lactamase (penicillinase) produced by resistant bacterial strains (figure 3). Clavulinic acid, also has a beta lactam component which binds strongly to beta lactamases inhibiting their activity. It is used in conjunction with certain penicillins allowing their use against otherwise resistant bacteria. Another form of resistance involves a change in the structure of penicillin binding proteins such that the antibiotic does not bind efficiently (figure 4). In the case of Gram negative bacteria, penicillins pass across the outer membrane using porins. Resistance may develop from mutation leading to modified porins.


polymyx2.jpg (53919 bytes)

Figure 5 Structure of polymyxin


Polymyxin B (figure 5) binds to the lipid A portion of lipopolysaccharide and also to phospholipids. However, it binds preferentially to lipid A. This disrupts the outer membrane of Gram negative bacteria. Since the cell membrane is not exposed in Gram positive bacteria polymyxin has little activity against them. This drug is toxic to human cells, since it can also lyze eukaryotic membranes; this explains its limited clinical use.

Figure 5A

Vancomycin is a drug of last resort against Gram-positive bacteria. It is a glycopeptide (figure 5A) made by an Acinobacter species. Vancomycin-resistance has arisen making this antibiotic less useful.

It is very hydrophilic and forms hydrogen binds with terminal D-alanyl-D-alanine moieties of the NAM/NAG-subunits and stops polymerization of the subunits to form long chains. It also prevents polymer cross-linking.

Vancomycin use is often replaced by Daptomycin.


Figure 6 Daptomycin (Cubicin) DAPTOMYCIN

Daptomycin (Cubicin - figure 6) is a natural lipopeptide that is used to treat multi-resistant Gram-positive bacterial infections. It is a natural product made by the soil fungus Streptomyces roseosporus. The lipid portion of the molecule binds to the cell membrane resulting in depolarization (loss of membrane potential). It can be used to treat:

  • Enterococci (including glycopeptide-resistant Enterococci (GRE))
  • Staphylococci (including methicillin-resistant Staphylococcus aureus)
  • Streptococci
  • Corynebacteria.

It is used in the United States against Gram-positive skin infections, Staphylococcus aureus bacteremia and right-sided Staphylococcus aureus endocarditis. Daptomycin cannot be used to treat pneumonia because it binds to pulmonary surfactant.

Daptomycin may cause life-threatening eosinophilic pneumonia in people over 60 years.

Figure 7

Bacitracin is a cyclic polypeptide produced by Bacillus subtilis var Tracy. It is used topically against Gram-positive bacterial eye and skin infections but is not used systemically. Bacitracin inhibits dephosphorylation of C55-isoprenyl pyrophosphate which transports peptidoglycan components bacterial cell walls outside the inner membrane


Transport of a peptidoglycan subunit across the cell membrane to the cell wall

Figure 8A
Undecaprenol phosphate and the peptidoglycan subunit are phosphorylated

Figure 8B
A pyrophosphate bond is formed between the undecaprenol and the subunit

Figure 8C
The subunit is transferred from the membrane to the cell wall

Figure 8D
The subunit is released and the pyrophosphate cleaved in the absence of bacitracin

Figure 8E
In the presence of bacitracin, the pyrophosphate is not cleaved




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