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Common infective organisms

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 (may or may not cause infections/exacerbations)

  • 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


→ ceftriaxone/ciprofloxacin/azithromycin

  • 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)


  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 ± intra-abdominal organisms

Sepsis of unknown origin

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