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Drug targets, beta-lactamases and the antibiogram

17 min

Skills you'll build4 skills
  • Match a major antimicrobial class to its cellular target
  • Select eligible isolates for a cumulative antibiogram
  • Distinguish ESBL, AmpC, and carbapenemase resistance patterns
  • Distinguish resistant-organism surveillance from diagnostic susceptibility testing

At the bench: Review susceptibility results for method validity and expected resistance

Try first

Try first

An Enterobacter cloacae complex isolate is resistant to cefoxitin and ceftriaxone. Adding clavulanate does not restore ceftriaxone activity. Carbapenems test susceptible. Which mechanism fits best?

Keep going to see the reasoning.

Keep going to see the reasoning.

Right. Keep going to follow the reasoning.

Keep going to see the reasoning.

Get the idea

Use the explanation to check your first decision.

Antimicrobial targets

Each class has one main target:1

  • Cell wall: beta-lactams bind penicillin-binding proteins, and vancomycin binds the D-Ala-D-Ala end of the precursor.
  • 30S ribosome: aminoglycosides and tetracyclines.
  • 50S ribosome: macrolides, clindamycin, chloramphenicol and linezolid.
  • Nucleic acids: fluoroquinolones inhibit DNA gyrase and topoisomerase IV, and rifampin inhibits RNA polymerase.
  • Folate: sulfonamides and trimethoprim.
  • Membrane: daptomycin and the polymyxins.

Three families of beta-lactamase

EnzymeSubstrates hydrolyzedInhibited byTypical host
ESBL (class A)Penicillins, oxyimino cephalosporins and aztreonam, with cephamycins and carbapenems sparedClavulanateEscherichia coli, Klebsiella
AmpC (class C)Cephamycins and oxyimino cephalosporinsBoronic acid and cloxacillin (clavulanate has no effect)Chromosomal in E. cloacae complex, Klebsiella aerogenes, Citrobacter freundii complex; plasmid in E. coli
Carbapenemase (KPC, class A; NDM, VIM, IMP, class B; OXA-48-like, class D)Carbapenems and most beta-lactamsClass B enzymes by EDTAEnterobacterales, Pseudomonas, Acinetobacter

Current breakpoints already account for ESBLs, so cephalosporin results are reported as tested.2 The modified carbapenem inactivation method (mCIM) detects a carbapenemase. An EDTA version (eCIM) with a zone at least 5 mm larger than the mCIM indicates a metallo-beta-lactamase.2,3

Carriage screens

A nasal MRSA test or a rectal VRE or CRE swab identifies colonized patients for infection prevention. It gives no susceptibility result for an infection. An isolate from the infected site gets its own identification and testing.2

The cumulative antibiogram

An antibiogram reports percent susceptible by species and drug, at least once a year. CLSI M39 sets the rules:4

  1. Use final, verified diagnostic results. Leave out surveillance cultures.
  2. Keep the first isolate of each species per patient in the period, regardless of its source or susceptibility pattern.
  3. Report species with at least 30 isolates.
  4. Count only susceptible results in the numerator. Intermediate and SDD results stay in the denominator.

Percent susceptible = susceptible isolates ÷ isolates tested for that drug × 100.4

Follow the bench demonstration

Sources for this step
References
  1. Mahon CR, Lehman DC. Textbook of Diagnostic Microbiology. 7th ed. Elsevier; 2023.
  2. Clinical and Laboratory Standards Institute. Performance Standards for Antimicrobial Susceptibility Testing. 36th ed. CLSI supplement M100. CLSI; 2026. Accessed September 27, 2026. https://clsi.org/shop/standards/m100/
  3. Infectious Diseases Society of America. 2026 guidance on the treatment of antimicrobial-resistant gram-negative infections. Accessed September 27, 2026. https://www.idsociety.org/practice-guideline/amr-guidance/
  4. Simner PJ, Hindler JA, Bhowmick T, et al. What's new in antibiograms? Updating CLSI M39 guidance with current trends. J Clin Microbiol. 2022;60(10):e02210-21. doi:10.1128/jcm.02210-21

Watch one

Read each decision and its explanation.

The stewardship team asks for last year's Pseudomonas aeruginosa cefepime percentage. The export contains 62 P. aeruginosa records, all final and verified.

  • 6 are surveillance cultures.
  • 11 are later diagnostic isolates from patients already in the list.
  • The first diagnostic isolates tested for cefepime read 36 susceptible, 4 intermediate and 5 resistant.

What percent susceptible goes on the antibiogram?

  1. Check the period and the status. All 62 are final and from last year.

    Only final, verified results from the period belong in the analysis.

  2. Remove the 6 surveillance cultures, leaving 56.

    Surveillance cultures document carriage and describe a different population.

  3. Keep the first isolate per patient. Removing 11 repeats leaves 45.

    Repeat isolates would let a few long-stay patients skew the results.

  4. Check the count. 45 is at least 30, so the species is reported.

    Fewer than 30 isolates give too imprecise a percentage for the routine report.

  5. Build the fraction. The numerator is the 36 susceptible, and the denominator is all 45 tested.

    Intermediate is a separate category, and counting it as susceptible overstates activity.

  6. Divide. 36 ÷ 45 × 100 = 80.0%.

    The percentage is the fraction multiplied by 100.

80.0% susceptible to cefepime, from 45 first isolates.

Practice this skill

Your turn

Problem 1 of 3 · Hints available

Which drug binds the 30S ribosomal subunit?

Macrolides such as erythromycin act on the 50S subunit.

Confused 30S and 50S ribosome inhibitors

Aminoglycosides and tetracyclines bind the 30S subunit, and macrolides, lincosamides, chloramphenicol, and linezolid act on the 50S subunit. Mixing them up makes resistance patterns harder to predict, because drugs that share a target can share a resistance mechanism. For example, methylation of 23S rRNA in the 50S subunit affects macrolides and lincosamides together.

Linezolid acts on the 50S subunit and prevents formation of the initiation complex.

Confused 30S and 50S ribosome inhibitors

Aminoglycosides and tetracyclines bind the 30S subunit, and macrolides, lincosamides, chloramphenicol, and linezolid act on the 50S subunit. Mixing them up makes resistance patterns harder to predict, because drugs that share a target can share a resistance mechanism. For example, methylation of 23S rRNA in the 50S subunit affects macrolides and lincosamides together.

Fluoroquinolones inhibit DNA gyrase and topoisomerase IV. They do not act on the ribosome.

Aminoglycosides such as gentamicin bind the 30S subunit and cause misreading of the message.

Hint
  1. Two drug classes in the table bind the 30S subunit.
  2. Linezolid and the macrolides bind the other subunit.

Review Mechanisms of action of the major antibiotic classes

Problem 2 of 3 · Hints available

A carbapenem-resistant Klebsiella pneumoniae is mCIM positive. The eCIM zone is 7 mm larger than the mCIM zone. Which enzyme family fits?

KPC is a serine enzyme. EDTA does not inhibit it, so the eCIM zone would not increase.

Class B enzymes need zinc. EDTA removes it, the meropenem is not hydrolyzed, and a zone at least 5 mm larger indicates a metallo-beta-lactamase.

AmpC with porin loss is not a carbapenemase, so the mCIM would be negative.

OXA-48-like enzymes are serine class D enzymes. EDTA does not inhibit them.

Hint
  1. A positive mCIM shows a carbapenemase. The eCIM shows whether EDTA inhibits it.
  2. EDTA chelates zinc. Ask which family depends on zinc.

Review Gram-negative β-lactamases: ESBL, AmpC, and carbapenemases

Problem 3 of 3 · On your own

A patient's admission nasal MRSA test was positive. Four days later a wound culture from an infected surgical site grows Staphylococcus aureus. What does the laboratory do with the wound isolate?

The nasal test documents carriage. The wound isolate may be a different strain, and its susceptibility category comes from its own testing.

Used a carriage screen as a complete infection workup

A surveillance screen, such as a nasal MRSA culture or a rectal VRE or CRE swab, documents carriage for infection prevention. It provides no susceptibility result for an infection, so a clinical isolate from the infected site still needs its own identification and susceptibility testing.

The screen serves infection prevention. The infected site's isolate gets its own identification and susceptibility results.

The nasal screen gave no susceptibility result. The wound isolate needs one for the infection.

Used a carriage screen as a complete infection workup

A surveillance screen, such as a nasal MRSA culture or a rectal VRE or CRE swab, documents carriage for infection prevention. It provides no susceptibility result for an infection, so a clinical isolate from the infected site still needs its own identification and susceptibility testing.

Review Haemophilus, Neisseria, and screening

Use it

Read the case evidence, then make each decision. The step is complete without it.

  • The laboratory prepares last year's E. coli antibiogram.
  • The export contains 41 E. coli records, all final and verified.
  • 4 are rectal ESBL surveillance swabs.
  • 6 are later diagnostic isolates from patients already counted.
  • The first diagnostic isolates read ceftriaxone 25 susceptible, 1 intermediate and 5 resistant.
  • One resistant isolate is also cefoxitin resistant, and clavulanate does not restore ceftazidime activity.
Decision 1 of 3

How many isolates enter the ceftriaxone calculation?

The export includes surveillance swabs and repeat isolates. Both are removed before the count.

Counted repeat isolates from one patient

An antibiogram counts the first diagnostic isolate of each species per patient in the period. Adding later isolates from the same patient, often resistant ones from a long admission, lets a few patients skew the percentage susceptible.

Removing the surveillance swabs is correct. The 6 repeats from patients already counted are also removed.

Counted repeat isolates from one patient

An antibiogram counts the first diagnostic isolate of each species per patient in the period. Adding later isolates from the same patient, often resistant ones from a long admission, lets a few patients skew the percentage susceptible.

41 − 4 surveillance − 6 repeats = 31 first diagnostic isolates, which also meets the 30-isolate minimum.

Review Antibiograms and stewardship

Decision 2 of 3

What percent susceptible is reported for ceftriaxone?

That counts the intermediate isolate as susceptible, 26 ÷ 31. Intermediate stays in the denominator only.

25 ÷ 31 × 100 = 80.6%. Only susceptible results enter the numerator.

That drops the intermediate isolate from the denominator, 25 ÷ 30. Every tested isolate belongs in it.

Review Antibiograms and stewardship

Decision 3 of 3

Which mechanism best fits the cefoxitin-resistant isolate?

Cefoxitin resistance with no clavulanate effect is the AmpC pattern. In E. coli it usually comes on a plasmid.

An ESBL spares cefoxitin and is inhibited by clavulanate. This isolate shows neither.

Nothing here suggests carbapenem hydrolysis. A metallo-beta-lactamase is shown by carbapenem resistance and a positive mCIM and eCIM.

Review Gram-negative β-lactamases: ESBL, AmpC, and carbapenemases

The antibiogram rule that matters is the first isolate per patient. The surveillance swabs and repeats would have added 10 records, and none of them represents a new patient's infection. The single AmpC isolate is reported as tested and counted like any other first isolate.

For reference

Sources checked