CLASSIFICATION OF ANTIBIOTICS

Sources:
Microbiology Lippincott Williams & Wilkins
https://courses.lumenlearning.com/microbiology/chapter/drug-resistance/
https://www.encyclopedie-environnement.org/en/health/antibiotics-antibiotic-resistance-and-environment/

Gladwin / Sakurai / JC 2019

MECHANISMS OF ANTIBIOTIC RESISTANCE

• Mechanisms of Antibiotic Resistance can be classified broadly:
  • Efflux Pumps
  • Blocked Penetration / Alteration in access to target site
  • Target Modification
  • Modification of Drug or pathways
• There might be multiple resistance mechanisms at play in the same organism

Spread of Bacterial Resistance

• Selective pressure selects for favourable mutations of resistance
• mosaic genes (from other bacteria eg strep pneumo from strep mitus) or uptake of DNA from environment
• transfer of resistant bacteria from person to person
• horizontal gene transfer;
• transduction – acquisition of bacterial DNA from a phage (a virus that propagates in bacteria);
• transformation – uptake and incorporation of free DNA released into the environment by other bacterial cells;
• conjugation – gene transfer (usually on plasmids), by direct cell-to-cell contact through a bridge.

Sources:
Microbiology Lippincott Williams & Wilkins
https://courses.lumenlearning.com/microbiology/chapter/drug-resistance/
https://www.encyclopedie-environnement.org/en/health/antibiotics-antibiotic-resistance-and-environment/

Gladwin / Sakurai / JC 2019

2019A 09: 70% of candidates passed this question.
This question was well answered. Marks were awarded for correct pairing of mechanism of action and resistance with examples of drug class. Few mentioned the mechanisms by which resistance is present; acquired or generated.

Anti-staphylococcal antibiotics

Daptomycin, Rifampicin

2022B 09: 82% of candidates passed this question.
In general, the question was well answered. Better answers provided examples of antibiotics from different categories of mechanism of action and were able to describe specific side effects relevant or unique to that antibiotic. Mechanisms of action that were generic in terms of site of action attracted fewer marks. Some examples of antibiotics that candidates provided were not anti-staphylococcal antibiotics (eg; Benzyl Penicillin, Clavulanic acid). The examiners commented that the use of a tabular format as an answer template resulted in answers scoring marks in most time efficient manner. Frequent omissions or commissions resulting in lost marks noted by the examiners were as follows; many papers showed a lack of detail regarding the precise mechanism of action of penicillins particularly around inhibition of transpeptidases whilst the use of non-specific side effects such as nausea vomiting and diarrhoea did not attract marks.

GRAM POSITIVE BACTERIA

Gram Stain

Method of differentiated bacteria according to their cell wall characteristics, using
staining with crystal violet dye

• Gram positive bacteria have a thick outer cell wall composed of peptidoglycan,
  which stains positive with crystal violet dye
• Gram negative bacteria have an outer cell membrane enclosing a thinner
  peptidoglycan cell wall, which has decreased affinity to the crystal violet dye

Gladwin / Sakurai / JC 2020

PHARMACOLOGY OF VANCOMYCIN

2015A 05: 75 % of candidates passed this question.
The classification should have demonstrated a framework that covered relevant gram positive pathogens. Examples should have included both genus and species. More detail than “strep” or “Staph” was expected.
Knowledge of vancomycin was expected to include an outline of pharmaceutics, pharmacodynamics, pharmacokinetics, dosing and adverse effects. In particular, pharmacokinetics should be well understood as there are significant implications for dosing.
Common errors included incorrect examples such as “clostridium” or classifications lacking detail with respect to examples.

2013B 16: 16 candidates passed (59.3%).
A commonly used drug in intensive care practice, for which a high level of understanding is required (Level A). In general answers were sufficient for a pass, but there was still a lack of sufficient breadth of knowledge, in particular to pharmacokinetics and detailed mechanism of action.

2012A 12: 6 (60%) of candidates passed.
A basic and fundamental pharmacology question which required candidates to present their answer in a coherent fashion, as well as demonstrate sufficient knowledge. Candidates were expected to mention spectrum and mechanism of action, pharmacokinetics (including dose, distribution, elimination, etc) and adverse effects, activity profile e.g. time-dependent, antimicrobial activity depends on the duration that the serum drug concentration exceeds the minimum inhibitory concentration (MIC) of the target organism and not concentration dependence.

2018B 10: 49% of candidates passed this question.
Most candidates structured their answers well. Expected information included: the class of antibiotic of each agent, their respective pharmaceutics, pharmacodynamics, pharmacokinetics, indications and adverse effects. Better answers provided pharmacodynamic and pharmacokinetic information relevant to each drug rather than generic statements. Good answers also included the common resistance mechanisms for both agents.

2016A 22: 83% of candidates passed this question.
The structure required to score well was provide by the questions asked. Marks were lost by not mentioning that flucloxacillin is a beta lactam that it does not cover MRSA and that vancomycin covers enterococcus. Better answers could identify that vancomycin is slower at killing sensitive staph than flucloxacillin. Adverse effects were specifically asked for in the question so omitting facts such as associated nausea/ vomiting/ diarrhoea/ anaphylaxis etc. cost some candidates marks. If 25% of marks are allocated to side effects then it is expected more than one adverse effect would be mentioned. Some candidates had incorrect facts – Enterococcus is not a gram negative organism.

2023B 19: 39% of candidates passed this question.
A structured answer under the headings of mechanism of action, dose, pharmacokinetics and pharmacodynamics worked most effectively for this question. It was expected that candidates would link the mechanism of action of Ceftriaxone (binds to PBP and inhibits final step in peptidoglycan) to its spectrum of activity. Dosing would also include indications for higher dosing, and consideration of the fact that ceftriaxone is available as an IM administration. Details on hypersensitivity (fever, nephritis, haemolytic anaemia) and consideration of C.diff infection was a main part of its pharmacodynamics. For pharmacokinetics, a structural approach is recommended, important points included excretion through both kidneys and bile and absence of liver metabolism.

2021A 16: 62% of candidates passed this question.
Most candidates used a structured approach with the usual major pharmacology headings. Mechanism of action was well described by most, with better answers including mechanisms of resistance. Higher scoring candidates included an explanation as to the combination of the drugs. Likewise, better answers included detailed information on spectrum of activity beyond “gram positive and gram negative”, including relevant groups of organisms which are not covered. There also seemed to be some confusion about coverage for anaerobes, which piperacillin tazobactam covers well. Specific detail about adverse reactions, other than ‘allergy, rash, GI upset, phlebitis, etc’, is expected for commonly used antibiotics.

MECHANISMS OF ANTIBIOTIC RESISTANCE

• Mechanisms of Antibiotic Resistance can be classified broadly:
  • Efflux Pumps
  • Blocked Penetration / Alteration in access to target site
  • Target Modification
  • Modification of Drug or pathways
• There might be multiple resistance mechanisms at play in the same organism

Spread of Bacterial Resistance

• Selective pressure selects for favourable mutations of resistance
• mosaic genes (from other bacteria eg strep pneumo from strep mitus) or uptake of DNA from environment
• transfer of resistant bacteria from person to person
• horizontal gene transfer;
• transduction – acquisition of bacterial DNA from a phage (a virus that propagates in bacteria);
• transformation – uptake and incorporation of free DNA released into the environment by other bacterial cells;
• conjugation – gene transfer (usually on plasmids), by direct cell-to-cell contact through a bridge.

Sources:
Microbiology Lippincott Williams & Wilkins
https://courses.lumenlearning.com/microbiology/chapter/drug-resistance/
https://www.encyclopedie-environnement.org/en/health/antibiotics-antibiotic-resistance-and-environment/

Gladwin / Sakurai / JC 2019

PHARMACOLOGY OF CIPROFLOXACIN

2020A 05: 71% of candidates passed this question.
Most candidates had a structured answer to mechanisms of resistance that covered the major categories (alter target protein, prevent entry, efflux, degrade drug) and provided an example of a bacteria and the affected antibiotic, as was required to answer the question in full. Ciprofloxacin, whilst perhaps not a first line drug in the ICU, was not well known by many candidates. Better answers included a brief outline of class, mechanism of action (action on DNA gyrase to inhibit replication), spectrum (Gram negatives particularly mentioning Pseudomonas, lesser Grampositive cover, not anaerobes, some atypical), PK (with correct dose, wide penetration into tissues including bone/prostate etc., predominantly renal excretion), side effects/toxicity (common or specific to cipro e.g. QT, tendinitis, arthropathy) and an example of resistance.

AMINOGLYCOSIDES

Mechanism of Action

• Permeates into the bacterial cell down electronegative gradient (negative interior) via O₂ dependent process
  • Can be retarded by acidic, anaerobic environments (abscess)
• Inhibits bacterial 30S ribosomal subunit
  • Inhibits bacterial protein synthesis
  • Inhibition of bacterial growth (bacteriostatic) → bacteriocidal
• Synergism with cell wall inhibitors (β lactam antibiotics)
  • Penicillins inhibit peptidoglycan synthesis → increased permeability to aminoglycosides → inhibition of protein synthesis (including penicillin binding protein) → Further increase in cell permeability → death
• Displays concentration dependent killing and post-antibiotic effect
  • Peak plasma aminoglycoside >8 MIC required
  • Large AUC not required

Antimicrobial Spectrum

• Strong activity against aerobic gram negative bacteria
• Effective against gram positives esp. with β lactam synergism
• Ineffective against obligate anaerobes

Pharmacokinetics

• Absorption
  • Poor GI absorption, UNLESS inflammation or ulceration
• Distribution
  • Vd approximating extracellular fluid
  • Poorly protein bound
  • Poor CNS, ocular penetrance
• Metabolism
  • Minimal metabolism
• Elimination
  • Renal clearance via filtration
  • T_1/2b 2~3 hours
  • Can be removed by dialysis

GENTAMICIN

Gentamicin

• Covers a wide range of gram negative enterobacteria and has gram positive cover that includes staph and some streptococci.
• No anaerobic activity but is synergistic with beta lactams and vancomycin.
• Used for infections of the GUT, GIT, respiratory tract, skin and soft tissues, neutropenic sepsis, CNS infections, and surgical prophylaxis

Mechanism

• Bactericidal antibiotic, which inhibits the bacterial 30S ribosomal subunit
  • This impairs transcription and/or induces misreading of the mRNA, impairing protein synthesis
• di­ffuse across outer membranes via porins
• actively transported by oxygen dependent process across cell membrane to cytoplasm
  • low O2 and extracellular pH prevent this process

Toxicity

• Gentamicin is not metabolized in humans
• It is excreted in the urine unchanged
• The presence of transport molecules in the epithelial cells of the proximal and distal tubule and the cortical collecting ducts allows gentamicin to accumulate within the cytosol of these cells.
• In the cytosol, gentamicin acts on the endoplasmic reticulum, impairing protein synthesis, and on the mitochondria to impair ATP production, increasing oxidative stress via the production of free radicals and superoxides. It also acts on lysosomes to impair protease degradation, causing further cell damage
• Independent of the cellular damage, gentamicin also inhibits some of the epithelial cell transport processes. Tubular damage may then partially or totally obstruct the lumen, causing further disruption of the nephron resorptive processes à hence the rise in plasma creatinine and fall in eGFR
• The accumulation of drug within the cell means that the toxic effects can continue long after plasma drug levels have declined
• Ototoxicity may be caused through similar processes, via accumulation of the drug in the inner ear perilymph, where it disrupts mitochondrial protein synthesis and promotes formation of free radicals within the hair cells
• Nephrotoxicity usually reverses with cessation of drug, however ototoxicity may be permanent
• Gentamicin may also cause muscle weakness due to impairment of prejunctional release of ACh, use with caution with NMDR and in myasthenia gravis.

2009A 23: Pass rate: 50%
This answer was generally well done. Most answers showed good understanding of mechanism of action. The antibacterial spectrum and pharmacokinetics were done less well.
Clinical observation guiding your study would help in answering this question, such as renal dosing, monitoring drug levels and situations in which aminoglycosides are used.
Syllabus M2 2d
Reference: Katzung 10th edition p 755-762

2011A 10:
The first part of the question on bactericidal activity of gentamicin was better answered than the second part on its toxicity. Details on the cellular mechanisms of bactericidal action and toxicity were lacking in most answers.
Most candidates did not appreciate that gentamicin is avidly accumulated and retained by proximal renal tubular cells in concentrations many times higher than the plasma concentration. Also these high tubular cell concentrations of gentamicin are maintained long after the plasma concentrations have fallen to very low levels, thus enhancing its toxic effects. Gentamicin has multiple toxic effects within the tubular cell including adverse effects on protein synthesis, translation and folding, impairment of mitochondrial function and production of reactive oxygen species and damage to the nucleus.
Syllabus: M2a, 2d. Recommended sources: Pharmacological Basis of Therapeutics, Goodman and Gillman, Chp 45 and page 1162

2007B 05: 4 candidates (57%) passed this question.
It was expected candidates would specifically address both the spectrum of activity and mechanism of resistance.
Benzyl penicillin is highly active against Gram positive organisms, particulary streptococci but also effective against Meningococcus / Clostridia and other anaerobes, Listeria and is used in the treatment of syphilis (treponemma). It is readily hydrolysed by penicillinases or beta lactamases so any organisms that produce these are resistant i.e. most staphylococci.
Flucloxacillin contains a modified beta lactam ring so is not susceptible to hydrolysis by staphylococcal penicillinases, therefore the spectrum is Staphylococci not resistant to methicillin (i.e. not MRSA). Extra credit was given for comments that it won’t cover Listeria or some other organisms covered by Benzyl penicillin and it is much less active than Benzyl penicillin on organisms sensitive to both.
Ampicillin is an alpha amino benzyl penicillin (Aminopenicillin) and has a broader activity than Benzyl penicillin so covers the streptococci but aslo a variety of gram negative bacteria including some enterobacteriacae and Haemophilus influenzae. It also covers Helicobacter and Enterococci (better than Benzylpenicillin). It is destroyed by beta-lactamase.
Additional credit was given for discussion of other mechanisms of bacterial drug resistance.

2019B 20: 58% of candidates passed this question.
This question was most effectively answered using a tabular format. Only a minority of candidates demonstrated a comprehensive knowledge of these level 1 drugs and very few candidates compared the two in areas which lent themselves to comparison. The spectrum of activity generally lacked detail. Few candidates mentioned that piperacillin-tazobactam had superior gram-positive cover, both have extensive gram-negative cover including Pseudomonas.
Piperacillin-tazobactam is effective against anaerobes; whilst ciprofloxacin has some atypical cover against Mycoplasma. The mechanism of action was generally well described for piperacillin; many candidates incorrectly stated the mechanism of action for ciprofloxacin, confusing the drug with a macrolide.
Better answers included time- dependant and concentration-dependent killing. The concept of half-life was frequently confused with the dosing interval.
Minimal marks were awarded for “allergy” and “gastrointestinal side-effects”. Better candidates mentioned Liver function derangement, neutropenia, interstitial nephritis for piperacillin and tendonitis for ciprofloxacin.

2010B 03: 5 (33%) of candidates passed this question.
Most candidates used a table to compare these two drugs, which was an ideal means to structure their answers to this question and a useful way to present the information required. The use of a structured format for learning pharmacokinetic data about all drugs allows more useful information in a question such as this. Candidates should also give consideration to the effects of critical illness (such as cardiac output, plasma binding and volume of distribution) affect the pharmacokinetics of drugs used in intensive care. This particular section of the question was poorly answered.
Syllabus: M2a,2d
References: Goodman and Gillman, The Pharmacological basis of therapeutics Chp 46

2011B 22: 9 (36%) of candidates passed this question.
The question could have been answered succinctly using a table. Better answers included detail of how antibiotics inhibited enzymes, effects on ribosomal subunits, and impact on cell wall synthesis or inhibit DNA gyrase. The mechanism of resistance required an understanding of beta-lactam inhibition, gene mutation altering target enzymes and ribosomal subunits, and efflux mechanisms. Mention of Van A and Van B phenotypes was also sought.
Syllabus: M2a 2c,d
Recommended sources: Rang and Dale Pharmacology Chp 46, Katzung Chp 43, 45, 46.

2013A 08:
This question asked to compare and contrast, inviting candidates to tabulate their answers.
Details concerning other elements of pharmacology (apart from mechanism, spectrum and adverse effects) were not required and did not attract marks.
There was a lack of accurate detail in answers regarding clindamycin. Spectrum of activity mentioned by candidates was often quite narrow. The gram negative and anaerobic spectrum of activity afforded by benzyl penicillin was also not mentioned by many
candidates. Adverse reactions were an opportunity to score marks – all drugs can cause
nausea, vomiting, rash and hypersensitivity phenomena – especially the antibiotics. However it is important that specific side effects for each agent are also mentioned by candidates.
Information that related to the pharmaceutics, pharmacokinetic or pharmacodynamic
properties of these drugs was not requested and did not score marks.

Baltimore Classification system (for Viruses)

Key:
ss: Single stranded
ds: Double stranded
(-): – strand or antisense
(+): + strand or sense
RT – Reverse Transcriptase

Past Classifications (now not used):

By shape:

• filamentous
• isometric (or icosahedral)
• envelopedH
• Head and tail

By Genome Structure and Core:

• RNA / DNA
• Single-stranded / Double stranded
• Linear/Circular
• Non-segmented/Segmented

By capsid structure:

• Naked icosahedral – Hep A, Polio
• Enveloped icosahedral – EBV, HSV
• Enveloped helical – Influenza, Measles
• Naked Helical – Tobacco Mosaic virus
• Complex – Herper, Smallpox, Hep B

Mechanism of Action: Oseltamivir vs Aciclovir

Mooney / JC 2020

2010A 12: 1 (10%) of candidates passed this question
Viruses are classified according to:
a) genetic material
b) mode replication
c) structural proteins (capsids)
d) presence of an envelope

Thus DNA viruses, double or single stranded DNA usually replicate in the nucleus of the host cell via polymerase, not incorporated into the host genetic material. Examples being double stranded, herpes, adenovirus, poxvirus and single stranded, parvovirus. In comparison, RNA viruses, single strand and have 2 different reproduction strategies, being RNA sense(positive) and RNA antisense(negative), an example is paramyxovirus. For retroviruses, the single stranded RNA can’t act as mRNA and is transcribed into DNA by a reverse transcriptase. This DNA is incorporated into the host DNA, so the host makes the viral RNA, for example HIV.
Candidates were also expected to briefly mention capsids and viral envelopes. In relation to the second part of the question, candidates were expected to mention that acyclovir inhibits DNA polymerase in the terminal nucleic acid chain and that oseltamivir is a neuraminidase inhibitor which prevents the budding of new viruses from the infected cells. Most candidates had very little knowledge of this area.
Syllabus: M2 2a&d 8 Reference: Medical Microbiology and Infection at a Glance, Gillespie &, Bamford pgs 58,59, Basic and Clinical Pharmacology, Katzung pgs791,815

2021B 04: 6% of candidates passed this question.
This question exposed an area of the syllabus neglected by the candidates. Answers were generally vague in detail with lots of incorrect facts and generally displayed a very limited knowledge. Antifungal agents are regularly used in critically ill patients either as treatment or prophylaxis. An understanding of the aspects of these drugs with respect to spectrum of activity, mechanism of action, specific PK and PD properties as well as potential side effects would have been the basis for this compare and contrast question. Examiners want to be convinced that the candidates understand the strengths and weaknesses of each drug and in which circumstances one agent might be used in preference to the other.

2016B 23: 8% of candidates passed this question.
To pass this question each of the three components needed to be compared and contrasted for both agents. A tabulated answer helped in this regard but was not essential.
Some answers included information that could not gain marks, as it was not directly relevant to the question asked (e.g. presentation and dose).
In spectrum of activity, as well as what important organisms the agents were effective against, marks were also given for the important organisms that they were not effective against (e.g. MRSA and beta-lactamase producing organisms for penicillin G; and aspergillus for fluconazole).
In general, of the two agents, fluconazole was the least well answered. For example, a common omission either in mechanism of action or in adverse effects was that fluconazole inhibits microsomal P450 enzymes.
Some candidates confused fluoroquinolone with fluconazole.

• Disinfectants
  • Strong chemical compounds that kill of inhibit the growth of microbes
• Antiseptic
  • Disinfectants with sufficiently low toxicity to host cells, that can be used directly on skin, wounds or mucosa

Pharmacopeia - Antiseptics & Disinfectants (Level 3)

Sakurai 2016

2008A 14: No candidates (0%) passed this question.
It was expected candidates could define and distinguish between these terms with a specific comment that disinfectants are applied to inanimate objects and antiseptics can be applied to living tissue. The advantages and disadvantages could be addressed either tabulated or discussed in point form, either was acceptable.
It was expected answers would include a comment on each agent and specifically address areas such as general spectrum of activity, speed of onset ( agents that need to dry to be effective versus those with more rapid onset), duration of effect ( residual activity), limitations of use and potential hazards. Marks were awarded for identifying Glutaraldehyde as a disinfectant (as opposed to the other antiseptic agents) and its use for cleaning equipment such as endoscopes with the precautions required for potential toxicity.
Additional credit was given for discussion of relevant facts such as the proven benefit for chlorhexidine skin preparation for central venous line insertion. Candidates are referred to several of the recommended texts which cover this area well.