Lincosamides. Amphenicols (50S inhibitors)

Lincosamides. Amphenicols (50S inhibitors)

Clindamycin, for gram-positive cocci and anaerobes and to switch off bacterial toxins, with one of the highest risks of C. difficile colitis; and chloramphenicol, which reaches nearly everything and the brain, now kept for eye drops and a few grave infections because of what it does to the marrow.

At a glance

  1. Clindamycin and chloramphenicol bind the 23S ribosomal RNA of the 50S subunit at the peptidyl transferase centre, next to where macrolides bind, and stop the peptide bond from forming. Both mostly stop bacteria growing.
  2. Clindamycin is well absorbed by mouth, reaches bone and abscesses but not the cerebrospinal fluid, and is broken down by the liver. It reaches gram-positive cocci, some MRSA among them if the laboratory finds them susceptible, and anaerobes, above all those of the mouth, and it switches off bacterial toxins.
  3. It treats skin, soft tissue, bone and joint infections, aspiration pneumonia in penicillin allergy and some dental infections, and, with a β-lactam, toxic shock and necrotising fasciitis. Resistance shared with the macrolides (erm, MLSB) can be inducible: the D-test finds it.
  4. Clindamycin is one of the antibiotics most often followed by C. difficile colitis, which is why it was dropped from endocarditis prophylaxis.
  5. Chloramphenicol is broad, reaches the cerebrospinal fluid and the brain even without inflammation, and is cleared by glucuronidation. It suppresses the marrow, rarely as fatal aplastic anaemia, and builds up in newborns as the grey baby syndrome. In Europe it is mostly used as eye drops.
  6. Clindamycin is compatible with pregnancy and breastfeeding. Chloramphenicol eye drops can be used in pregnancy, and in breastfeeding with the baby watched; given into the body, it is kept for serious infections in pregnancy, and avoided in breastfeeding.

Drug classification

Clindamycin and chloramphenicol, with quinupristin–dalfopristin and lefamulin, are "other antibiotics binding to the 50S subunit". The syllabus groups the first two by their chemistry: the lincosamides, an amino acid joined to an amino sugar, and the amphenicols, a benzene ring with a dichloroacetyl tail; chloramphenicol's ring carries a nitro group, which its relative thiamphenicol's lacks. Quinupristin–dalfopristin and lefamulin are under Linezolid and other protein synthesis inhibitors.

Lincosamides

For gram-positive cocci and anaerobes. Clindamycin is lincomycin with a chlorine in place of a hydroxyl group, better absorbed and more active.

  • Clindamycinby mouth, injected, on the skin or in the vagina
  • Lincomycinby mouth or injected, the first, now little used

Amphenicols

Broad, and reaches the brain, but suppresses the marrow, so it is kept for eye drops and a few grave infections.

  • Chloramphenicoleye drops; by mouth or injected for grave infections

Lincomycin came from Streptomyces lincolnensis, found in soil from Lincoln, Nebraska, and clindamycin was made from it in the 1960s. Chloramphenicol came from Streptomyces venezuelae in 1947, and was the first antibiotic made wholly by chemical synthesis.

Pharmacokinetics

Clindamycin is about 90% absorbed by mouth, with or without food; the capsule is swallowed with a full glass of water, as it can ulcer the oesophagus. Into a vein it is given as clindamycin phosphate, by infusion, never as a bolus. It spreads well into tissues, bone, joints and abscesses, and into neutrophils and macrophages, but not usefully into the cerebrospinal fluid. The liver breaks it down, by CYP3A4, and its metabolites leave in urine and bile; its half-life is about 2 to 3 hours, so it is given three or four times a day. The dose is not changed in kidney failure.

Chloramphenicol is well absorbed by mouth, and into a vein is given as the succinate, which the body cleaves to the active drug. It is small and fat-soluble, and reaches the cerebrospinal fluid and brain even when the meninges are not inflamed, and the eye. The liver conjugates it with glucuronic acid and the kidneys excrete it; its half-life is about 3 hours. Newborns, whose glucuronyl transferase is still immature, clear it far more slowly. Its levels are measured in newborns, in liver or kidney failure and with drugs that interact, as over 25 mg/L is often toxic. It inhibits the liver's CYP enzymes, CYP2C19 and CYP3A4 in studies of human liver, and raises the levels of phenytoin, warfarin and sulfonylureas such as tolbutamide.

Pharmacodynamics

At the peptidyl transferase centre

Both bind the 23S ribosomal RNA of the 50S subunit where the peptide bond is made. Chloramphenicol sits in the A site and blocks the amino acid of the incoming tRNA from being joined to the chain; clindamycin overlaps the A and P sites and blocks the chain's first steps and its move along. Because macrolides bind next to them, the three compete, and one bacterial change, the erm methylation, defeats macrolides and clindamycin together. Both mostly stop bacteria growing; chloramphenicol kills H. influenzae, meningococci and pneumococci.

How chloramphenicol, clindamycin and linezolid stop a ribosome
A bacterial ribosome in section, reading a messenger RNA that runs across the picture: the small subunit below, holding the mRNA, with its E, P and A sites marked from left to right, and the large subunit above, with the exit tunnel running up through it and the peptidyl transferase centre on its underside beside the tunnel’s mouth. tRNAs stand on their codons in the E and P sites, the one in the P site holding the growing chain, which runs up into the tunnel. A third tRNA has docked in the A site, its amino acid in the peptidyl transferase centre beside the end of the chain. Step 1 of 6: A tRNA has docked. A tRNA has paired with the codon in the A site, and its amino acid sits in the peptidyl transferase centre, beside the end of the chain held by the tRNA in the P site.EPA

Step 1 of 6A tRNA has docked. A tRNA has paired with the codon in the A site, and its amino acid sits in the peptidyl transferase centre, beside the end of the chain held by the tRNA in the P site.

Point at a name or a part to light it.

Chloramphenicol, clindamycin and linezolid all bind the large subunit’s RNA at the peptidyl transferase centre, where the peptide bond is made, and keep the incoming amino acid from settling there. Clindamycin’s site overlaps the macrolides’, and one change to it, made by the erm gene, lets bacteria resist both. Our mitochondria have ribosomes much like a bacterium’s, which is how chloramphenicol causes a dose-related, reversible marrow suppression.

Simplified: not to scale, the drugs drawn larger than they are; the tRNAs drawn as flat cloverleaves, though each is folded in three dimensions; the elongation factors that bring each tRNA and move the ribosome along left out; the peptide bond and the move along the mRNA drawn as one step, the mRNA moving rather than the ribosome; one ribosome and one drug molecule, each drug shown in turn; each drug drawn as its rings, chains and heavy atoms, its hydrogens left out; the peptidyl transferase centre drawn as a patch at the large subunit’s underside, though the tRNAs’ ends reach into it; clindamycin’s block of the ribosome’s move along the mRNA left out; clindamycin shown on a ribosome well into a protein, though it acts as one is begun; the older account of linezolid, that it stops the first tRNA settling as a protein is begun, left to the text.

12 sources
  1. Parker N et al. Microbiology. OpenStax, 2016. 10.3 Structure and function of RNA
  2. Parker N et al. Microbiology. OpenStax, 2016. 11.4 Protein synthesis (translation)
  3. Parker N et al. Microbiology. OpenStax, 2016. 14.3 Mechanisms of antibacterial drugs
  4. Stevens CW. Brenner and Stevens' Pharmacology, 6th edition. Elsevier, 2023. Chapter 39, Antibiotics that inhibit bacterial protein synthesis
  5. Vázquez-Laslop N, Mankin AS. Trends Biochem Sci 2018;43:668–84. How macrolide antibiotics work
  6. Tenson T, Lovmar M, Ehrenberg M. The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome. J Mol Biol 2003;330:1005–14.
  7. Arenz S, Wilson DN. Cold Spring Harb Perspect Med 2016;6:a025361. Bacterial protein synthesis as a target for antibiotic inhibition
  8. Dunkle JA, Xiong L, Mankin AS, Cate JHD. Proc Natl Acad Sci USA 2010;107:17152–7. Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action
  9. Wilson DN et al. Proc Natl Acad Sci USA 2008;105:13339–44. The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
  10. PubChem. Chloramphenicol (CID 5959)
  11. PubChem. Clindamycin (CID 446598)
  12. PubChem. Linezolid (CID 441401)

What clindamycin reaches

  • Gram-positive cocci: streptococci and staphylococci, some MRSA among them, if the laboratory finds them susceptible; it isn't given blind when MRSA is suspected.
  • Anaerobes: those of the mouth (Prevotella, Fusobacterium, Peptostreptococcus, Actinomyces), Clostridium perfringens, and Bacteroides fragilis, though resistance in Bacteroides is now common.
  • Parasites, with a partner: Toxoplasma (with pyrimethamine), malaria (with quinine or artesunate), Pneumocystis (with primaquine), Babesia (with quinine).

It misses aerobic gram-negatives, enterococci and C. difficile.

Switching off toxins

Because it stops protein synthesis, clindamycin stops streptococci and staphylococci making their toxins: the superantigens of toxic shock, and the Panton–Valentine leukocidin. A β-lactam needs bacteria to be growing, and in a dense infection most have stopped; clindamycin doesn't. So in necrotising fasciitis and toxic shock it is given with the β-lactam.

Resistance

  • erm methylation of the 23S ribosomal RNA, which defeats macrolides, lincosamides and streptogramin B (MLSB). In some strains it is switched on only when a macrolide is present: such a strain resists erythromycin and looks susceptible to clindamycin, but can turn resistant during treatment, so the laboratory reports it resistant; it may still do for a short course in a minor skin infection. In the D-test, an erythromycin disc set beside a clindamycin disc flattens the clindamycin zone into a D.
  • Enzymes that inactivate lincosamides (the lnu genes) and, for chloramphenicol, chloramphenicol acetyltransferase, carried on plasmids.
  • The cfr gene, which methylates a nearby base and defeats chloramphenicol, clindamycin, linezolid, streptogramin A and the pleuromutilins at once.

What chloramphenicol reaches

Most gram-positives and gram-negatives, H. influenzae, Neisseria, Salmonella Typhi among them, anaerobes, rickettsiae, Chlamydia and Mycoplasma, but not Pseudomonas. It also binds the ribosomes of human mitochondria, much like bacterial ones, which is why, at high levels, it suppresses the marrow. The rare aplastic anaemia is a separate reaction, probably to metabolites of its nitro group.

Clinical indications

DrugTypical uses
Clindamycinskin and soft tissue infections, MRSA among them, if susceptible; bone and joint infections; toxic shock and necrotising fasciitis, with a β-lactam; aspiration pneumonia and lung abscess, mostly in penicillin allergy; on the skin for acne, with benzoyl peroxide; bacterial vaginosis; toxoplasmosis, malaria and Pneumocystis pneumonia, with a partner
Chloramphenicolbacterial conjunctivitis, as eye drops or ointment; meningitis or brain abscess when β-lactams can't be used; typhoid and rickettsial infections where other drugs aren't available or suitable
of clindamycin taken by mouth
90%absorbed
exposed to chloramphenicol develop aplastic anaemia
1 in 20,000 to 40,000patients
the chloramphenicol level above which it is often toxic
25mg/L

Adverse drug reactions

  • Life-threatening
    C. difficile colitis with clindamycin, from mild diarrhoea to pseudomembranous colitis and toxic megacolon, which can kill. It can start during the course or weeks after it. Marked or lasting diarrhoea means stopping clindamycin and testing for C. difficile.
  • Life-threatening
    Aplastic anaemia with chloramphenicol, idiosyncratic, unrelated to the dose, and often fatal, in about 1 in 20,000 to 40,000 patients exposed, even weeks or months after the course. Very rare cases have followed eye drops.
  • Serious
    Dose-related marrow suppression with chloramphenicol: anaemia, and low white cells and platelets, as it blocks the mitochondrial ribosomes of the marrow's cells and their use of iron for heme. It is common at high levels and recovers when the drug is stopped. The blood count is checked about every two days during the course and the drug stopped at the first fall, though the counts don't warn of aplastic anaemia.
  • Life-threatening
    The grey baby syndrome: in newborns, chloramphenicol builds up and causes vomiting, a swollen abdomen, grey skin, a low temperature and circulatory collapse, sometimes fatally.
  • Serious
    Optic and peripheral neuritis with long courses of chloramphenicol.
  • Life-threatening
    Severe skin reactions with clindamycin, rarely: Stevens–Johnson syndrome, toxic epidermal necrolysis, DRESS and acute generalised exanthematous pustulosis. Anaphylaxis is rare with both drugs.
  • Serious
    Liver injury and acute kidney injury with clindamycin, rarely.

Side effects

  • Mild
    Diarrhoea, common with clindamycin, nausea and abdominal pain. Marked or lasting diarrhoea may be C. difficile (above).
  • Mild
    Rash, a maculopapular rash, among the commoner effects of clindamycin.
  • Mild
    A metallic taste with clindamycin into a vein, and stinging with chloramphenicol eye drops.

Contraindications

  • Contraindicated
    An allergy to clindamycin or lincomycin, which cross-react.
  • Contraindicated
    A past allergic or toxic reaction to chloramphenicol, in its licence, marrow suppression among them.
  • Contraindicated
    A personal or family history of a blood disorder, aplastic anaemia among them, for chloramphenicol eye drops too.
  • Avoid
    Chloramphenicol by mouth or into a vein for a minor infection or as prophylaxis, or when a safer antibiotic would work. Its licence keeps it for serious infections where less toxic drugs fail or can't be used.
  • Avoid
    Chloramphenicol with other drugs that suppress the marrow, which its licence says to avoid.
  • Avoid
    Clindamycin after C. difficile colitis, or in inflammatory bowel disease, if another antibiotic will do. Its licence is less strict, asking for caution in gut disease, colitis above all.
  • Avoid
    Clindamycin with erythromycin, which competes with it on the ribosome; they are not given together.
  • Caution
    Chloramphenicol in newborns, whose doses are cut and levels measured.
  • Caution
    Chloramphenicol with phenytoin, warfarin or a sulfonylurea, whose levels it raises, so their doses may need cutting.
  • Caution
    Clindamycin with warfarin, whose effect it can raise, so the INR is checked more often, or with rifampicin, which speeds its breakdown.
  • Caution
    Clindamycin with neuromuscular blockers, or in myasthenia gravis, as it can deepen neuromuscular blockade.
  • Caution
    Clindamycin into a vein, only diluted and infused, never as a bolus, which has caused low blood pressure and cardiac arrest.
  • Caution
    Severe liver disease. Chloramphenicol builds up, so its dose is cut and its levels measured; clindamycin is cleared more slowly too, but its dose isn't usually changed.

Pregnancy and lactation

  • Compatible
    Clindamycin in pregnancy. It crosses the placenta. Most human studies have not found more birth defects (one large cohort found a small rise, not confirmed), animal studies found harm only at doses toxic to the mother, and it is used for bacterial vaginosis, malaria with quinine, and other infections in pregnancy. Its licence asks that it be used only if clearly needed.
  • Compatible
    Chloramphenicol eye or ear drops in pregnancy, which leave too little in the blood to harm the baby; the eye drops are the usual first choice for an eye infection in pregnancy. Their licences don't recommend them in pregnancy, as safety hasn't been established.
  • Avoid
    Chloramphenicol by mouth or into a vein in pregnancy. It is given for a serious infection when the benefit is likely to outweigh the risk, but there are few data, it can harm the mother's marrow, and near delivery it can reach the newborn, who can't clear it. Its licence contraindicates it in pregnancy.
  • Compatible
    Clindamycin in breastfeeding. Small amounts pass into milk. The baby may get diarrhoea or a rash, and rarely blood in the stool, which is worth watching for. Its licence says it is no reason to stop breastfeeding, though another drug may be preferred.
  • Caution
    Chloramphenicol eye or ear drops in breastfeeding. Very little reaches the milk, and they are probably compatible, with the baby watched for poor feeding, vomiting or unusual bruising. In the UK fusidic acid or gentamicin drops are preferred where they will do, and the drops are ruled out if the mother or her family has had a blood disorder. Their licences don't recommend them in breastfeeding.
  • Avoid
    Chloramphenicol by mouth or into a vein in breastfeeding, because it passes into milk and could suppress the baby's marrow; another antibiotic is used, or breastfeeding is paused. Its licence contraindicates it in breastfeeding.

Check yourselfAnswer, then say how sure you were: a lucky guess still counts as a weak point.

1Which of these antibiotics is among those most often followed by Clostridioides difficile colitis?

2A Staphylococcus aureus resists erythromycin but tests susceptible to clindamycin. The D-test is positive. What does that mean?

3Why is clindamycin added to a β-lactam in necrotising fasciitis caused by Streptococcus pyogenes?

4Why is chloramphenicol dangerous for a newborn?

5Which of chloramphenicol's effects on the bone marrow is not related to the dose, and often fatal?

6A patient with a prosthetic heart valve, allergic to penicillin, needs a dental extraction. Is clindamycin still given to prevent endocarditis?

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Bacterial ribosome

Clindamycin and chloramphenicol bind the 50S subunit too.