Antimicrobial agents — principles of action

Overview: The Conceptual Framework

Antimicrobial agents are best understood as ligands whose receptors are microbial proteins. The concept of the pharmacophore, the active chemical moiety of the drug that binds to its microbial target, was introduced by Ehrlich and remains foundational. The key principle underlying all antimicrobial therapy is selective toxicity: the drug must interfere with a biochemical target that is either unique to the microorganism or sufficiently different from the human homologue that therapeutic concentrations kill or inhibit the pathogen without causing unacceptable host toxicity.

Microorganisms of medical importance fall into four categories:

Classification of an antimicrobial can be performed across three dimensions:

1. Spectrum, the class and range of microorganisms affected
2. Biochemical target, the pathway the drug disrupts
3. Chemical structure, the pharmacophore class (e.g. β-lactam ring, fluoroquinolone scaffold)

Mechanisms of Action by Biochemical Target

1. Cell Wall Synthesis Inhibitors

Bacteria (but not human cells) rely on a rigid peptidoglycan cell wall to maintain structural integrity against osmotic pressure. This makes cell wall synthesis an ideal selective target.

β-Lactams (penicillins, cephalosporins, carbapenems, monobactams):

• Bind covalently to penicillin-binding proteins (PBPs), which are transpeptidase enzymes responsible for cross-linking peptidoglycan strands
• Inhibition of cross-linking leads to a structurally weakened wall; osmotic lysis follows in actively dividing bacteria
• Bactericidal against susceptible organisms
• Gram-positive bacteria have the peptidoglycan layer exposed; Gram-negative bacteria have an outer lipopolysaccharide membrane that limits access, relevant to spectrum selection in the ED

Glycopeptides (vancomycin, teicoplanin):

• Bind to the D-Ala-D-Ala terminus of peptidoglycan precursors, physically blocking transglycosylation and transpeptidation
• Too large to penetrate the Gram-negative outer membrane, hence active only against Gram-positive organisms
• This explains vancomycin's role in MRSA and Gram-positive sepsis in the ED

2. Cell Membrane Synthesis and Function Disruptors

Polymyxins (polymyxin B, colistin):

• Interact with the lipopolysaccharide of the Gram-negative outer membrane, disrupting membrane integrity, "detergent-like" mechanism
• Rapid bactericidal effect against Gram-negatives including Pseudomonas and Acinetobacter
• Nephrotoxicity and neurotoxicity limit use to multi-drug resistant (MDR) organisms, a last-resort agent the ED clinician may encounter in critically ill transferred patients

Daptomycin:

• Lipopeptide that inserts into the Gram-positive bacterial cell membrane, forming a pore, causing depolarisation and rapid cell death
• Active against MRSA and vancomycin-resistant Enterococcus (VRE)

Antifungals targeting ergosterol (azoles, polyenes):

• Fungal membranes use ergosterol rather than cholesterol, a key difference from human cell membranes
• Azoles (fluconazole, voriconazole) inhibit lanosterol 14α-demethylase (CYP51), blocking ergosterol synthesis → accumulation of toxic intermediates → membrane dysfunction
• Polyenes (amphotericin B) bind directly to ergosterol and form pores in the fungal membrane → ion leakage and cell death; significant nephrotoxicity reflects low-level binding to cholesterol in human cell membranes

3. Ribosomal Translation Inhibitors

Bacterial ribosomes are 70S (comprising 30S and 50S subunits), whereas human ribosomes are 80S. This structural difference underpins selective toxicity for this drug class.

ED relevance: Aminoglycosides are used in severe Gram-negative sepsis. Their concentration-dependent killing means once-daily dosing (gentamicin 4-7 mg/kg) achieves high peak:MIC ratios. Linezolid is used for MRSA pneumonia and VRE; it inhibits monoamine oxidase (MAO), serotonin syndrome is a real risk if co-prescribed with serotonergic agents such as tramadol or fentanyl.

4. Nucleic Acid Metabolism and Topoisomerase Inhibitors

Fluoroquinolones (ciprofloxacin, levofloxacin, moxifloxacin):

• Inhibit bacterial DNA gyrase (topoisomerase II) and topoisomerase IV, which are essential for DNA replication, transcription, and repair
• These prokaryotic enzymes differ structurally from human topoisomerases, providing selective toxicity
• The result is double-strand DNA breaks → rapid bactericidal effect
• Killing is concentration-dependent: the pharmacodynamic driver is the $AUC/MIC$ ratio
• Levofloxacin 500 mg orally achieves bactericidal urinary concentrations in a single dose, relevant to oral step-down in UTI/pyelonephritis

Rifamycins (rifampicin):

• Inhibit bacterial DNA-dependent RNA polymerase (encoded by rpoB gene), blocking transcription
• Never used as monotherapy (rapid resistance emerges); used in combination for MRSA device infections, TB, and meningococcal prophylaxis

Metronidazole:

• A prodrug activated by intracellular reduction in anaerobic/microaerophilic organisms → reactive intermediates that cause DNA strand breaks
• Selective for anaerobes and specific parasites (Trichomonas, Giardia, Entamoeba)
• Critical in ED management of intra-abdominal sepsis, aspiration pneumonia, C. difficile (oral route), and necrotising fasciitis

5. Antiviral Targets

Viruses exploit host cell machinery for replication, limiting selective toxicity options. However, several virus-specific enzymes and proteins serve as effective targets:

Interferons represent a distinct mechanism: rather than targeting the virus directly, they induce antiviral activities within the infected human cells, activating innate immune responses that limit viral replication.

6. Folate Synthesis Inhibitors

Human cells obtain folate from dietary sources; bacteria must synthesise their own folate, making folate synthesis a selectively exploitable pathway.

• Sulfonamides inhibit dihydropteroate synthase (DHPS), blocking the incorporation of PABA into dihydropteroic acid
• Trimethoprim inhibits dihydrofolate reductase (DHFR), blocking conversion of dihydrofolate to tetrahydrofolate
• Sequential blockade (trimethoprim-sulfamethoxazole / co-trimoxazole) produces synergistic bactericidal activity
• Co-trimoxazole is used in the ED for uncomplicated UTI, Pneumocystis jirovecii pneumonia (PCP) prophylaxis and treatment, and community-acquired MRSA soft tissue infection

Bactericidal vs. Bacteriostatic: Clinical Significance

In septic shock, the host immune response is overwhelmed, bactericidal agents are essential because the immune system cannot be relied upon to clear static organisms.

Types and Goals of Antimicrobial Therapy

Antimicrobial therapy can be classified in relation to the disease progression timeline:

In the ED, the vast majority of antibiotic decisions are empirical, made before microbiological confirmation is available.

Emerging Mechanisms: Antisense Antibiotics and Beyond

Antisense antibiotics represent a novel class that works by inhibiting gene expression in bacteria in a sequence-specific manner. By targeting the mRNA transcripts of essential bacterial genes, they can silence virulence factors or metabolic enzymes. This approach is in active development and addresses MDR organisms.

Principles of Selective Toxicity

The concept of selective toxicity rests on exploiting differences between the microorganism and the host cell:

1. Unique targets, structures present in microbes but not in human cells (e.g. peptidoglycan cell wall, 70S ribosome, ergosterol, viral integrase)
2. Structural differences in shared targets, human homologues exist but differ sufficiently (e.g. bacterial vs. human topoisomerases, bacterial vs. human DHFR)
3. Preferential intracellular activation, prodrugs activated selectively in microbial environments (e.g. metronidazole in anaerobes)

When selective toxicity is incomplete, drug toxicity results, a key consideration in sepsis management where the clinician must weigh efficacy against adverse effects (e.g. aminoglycoside nephrotoxicity, amphotericin B nephrotoxicity).

Emergency Medicine Relevance

Sepsis and Empirical Antibiotic Selection

Understanding mechanisms of action directly informs empirical antibiotic selection in the ED:

• Gram-positive coverage requires agents that penetrate or bypass the thick peptidoglycan wall: β-lactams for MSSA, vancomycin (glycopeptide) for MRSA, binding D-Ala-D-Ala terminus where β-lactams cannot
• Gram-negative sepsis requires agents that can traverse the outer LPS membrane, extended-spectrum β-lactams, carbapenems, aminoglycosides, fluoroquinolones
• Anaerobic coverage for intra-abdominal sepsis, aspiration, and necrotising fasciitis relies on metronidazole (DNA strand disruption in anaerobes) or β-lactam/β-lactamase inhibitor combinations

Septic Shock: Why Mechanism Matters

• Bactericidal agents are essential, static agents leave bacterial clearance to a failing immune system
• Time to first antibiotic dose matters: β-lactams and glycopeptides must be present at the site of infection at sufficient concentration to disrupt cell wall synthesis during active bacterial replication
• For concentration-dependent killers (aminoglycosides, fluoroquinolones), the pharmacodynamic target is a high peak:MIC ratio, supports bolus rather than prolonged infusion

Toxicology and Drug Interactions in the ED

• Metronidazole + alcohol → disulfiram-like reaction (inhibition of acetaldehyde dehydrogenase); warn patients being discharged
• Linezolid (MAO inhibitor) + serotonergic drugs → serotonin syndrome; relevant when prescribing opioids (particularly fentanyl, tramadol)
• Fluoroquinolones → QTc prolongation; check ECG in patients on other QT-prolonging agents; hypomagnesaemia and hypokalaemia (common in septic/malnourished patients) increase risk
• Azole antifungals are potent CYP3A4 inhibitors, significant drug-drug interactions with many ED-used medications

Antimicrobial Resistance: A Practical Framework

Resistance arises from the same target-based framework as efficacy:

• Target modification (e.g. altered PBPs in MRSA, mutated rpoB in rifampicin-resistant TB)
• Enzymatic inactivation (e.g. β-lactamases destroying the β-lactam ring)
• Efflux pumps (ABC transporters), expel the drug before it reaches its target
• Reduced permeability, loss of outer membrane porins in Gram-negatives

For the ED clinician, this translates to understanding why vancomycin fails for Gram-negatives (cannot penetrate outer membrane), why carbapenems are reserved for ESBL producers, and why combination therapy is mandatory for Mycobacterium tuberculosis (rapid single-step resistance via rpoB mutation).

Key Antimicrobial Classes: Rapid Reference for the ED

Sources

• Australian Medicines Handbook (AMH)
• Life in the Fast Lane CCC (open educational resource)
• Deranged Physiology (open educational resource)