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Common infective organisms

In order to understand which antibiotics patients require, it is necessary to know which infective organisms you needs to cover (outlined on this page) and which antibiotics cover which organisms (outlined here).


Community-acquired pneumonia

  • Streptococcus pneumoniae
  • Haemophilus influenzae (if not vaccinated)
  • Atypicals 

If immunocompromised (e.g. malnourished, alcoholic, diabetic, on long-term steroids), also: Staphylococcus aureus, coliforms, TB

If severely immunosuppressed (e.g. HIV with CD4 <200, transplant recipient), also: Pneumocystis cariniiCryptococcus, CMV, Varicella zoster virus, influenza, fungal infections

Hospital-acquired pneumonia

  • Staphylococcus aureus (including MRSA)
  • Anaerobes
  • Coliforms
  • Pseudomonas

Colonising bacteria in chronic respiratory diseases

  • Streptococcus pneumoniae
  • Haemophilus influenzae
  • Moraxella catarrhalis
  • Staphylococcus aureus 
  • Pseudomonas 

In cystic fibrosis, also: Burkholderia cepacia

Upper respiratory tract infections

  • Streptococcus pneumoniae
  • Streptococcus pyogenes
  • Haemophilus influenzae
  • Moraxella catarrhalis

Cavitating pneumonia

  • Streptococcus pneumoniae
  • Staphylococcus aureus
  • Klebsiella
  • TB
  • Anaerobes


Intra-abdominal (including biliary)

Normal bowel flora:

  • Anaerobes, e.g. Bacteroides
  • Coliforms
  • Enterococcus


  • Salmonella enteritidis
  • Shigella
  • Campylobacter
  • Escherichia coli (enterotoxic)

Less common: Yersinia enterocoliticaBacillus cereusStaphylococcus aureus

If risk factors, also: Clostridium difficileVibrio choleraeSalmonella typhi

If dysentery: ShigellaVibrio choleraeamoebiasis

Don’t forget viral, parasitic and non-infectious causes!



  • Staphylococcus aureus
  • Streptococcus pyogenes

For wound/ulcer infections or severe/necrotising cellulitis, also: anaerobes 

For burns, also: anaerobes, Pseudomonas

For post-surgical wounds, also: Gram negative bacilli (e.g. E. coliKlebsiellaPseudomonas), Enterococci, MRSA, CONS

NB: wound-colonising bacteria (i.e. bacteria present in exudate without necessarily causing infection) include: coliforms, Enterococcus, anaerobes 



  • Neisseria meningitidis (meningococcal) 
  • Streptococcus pneumoniae (pneumococcal)
  • Haemophilus influenzae (if not vaccinated)
  • Listeria (if >65 years or immunocompromised)

If neonatal: group B StreptococcusE. coli/coliforms, Listeria (rare)


Urine infections

  1. Escherichia coli
  2. Staphylococcus saprophyticus
  3. Non-E. Coli enterobacteriaceae (Klebsiella, Enterobacter, Proteus), PseudomonasEnterococciStaphylococci (CONS/aureus)

Less common organisms (3) are associated with: catheters, hospitals, structural abnormalities and instrumentation  


Infective endocarditis

  • Viridans group Streptococci and other Streptococci (e.g. bovis)
  • Enterococci
  • Staphylococcus aureus and coagulase-negative Staphylococci (e.g. epidermidis)
  • Coxiella burnetii
  • HACEK organisms


Surgical prophylaxis

  • Need to cover skin Β± intra-abdominal organisms

Sepsis of unknown origin

  • Need to cover skin, chest, urine, intra-abdominal organisms

Test yourself!

Here are some syndromes associated with group A streptococcus (Streptococcus pyogenes). Outline the cause, timeframe and clinical features of each.

Scarlet fever

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Streptococcal toxic shock syndrome

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Post-streptococcal glomerulonephritis

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Rheumatic fever

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Some of our OSCE stations require antibiotic prescribing. Try some now!

  1. Neutropenic sepsis prescribing
  2. Acute assessment – shortness of breath II
  3. Acute assessment – abdominal pain
  4. Sepsis
  5. Find lots more stations here

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