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).

Respiratory

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 carinii, Cryptococcus, 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

Abdominal

Intra-abdominal (including biliary)

Normal bowel flora:

Anaerobes, e.g. Bacteroides
Coliforms
Enterococcus

Gastroenteritis/diarrhoea

Salmonella enteritidis
Shigella
Campylobacter
Escherichia coli (enterotoxic)

Less common: Yersinia enterocolitica, Bacillus cereus, Staphylococcus aureus

If risk factors, also: Clostridium difficile, Vibrio cholerae, Salmonella typhi

If dysentery: Shigella, Vibrio cholerae, amoebiasis

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

Skin/joints/bone

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. coli, Klebsiella, Pseudomonas), Enterococci, MRSA, CONS

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

Neurological

Meningitis

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

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

Urinary

Urine infections

Escherichia coli
Staphylococcus saprophyticus
Non-E. Coli enterobacteriaceae (Klebsiella, Enterobacter, Proteus), Pseudomonas, Enterococci, Staphylococci (CONS/aureus)

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

Cardiac

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

Other

Surgical prophylaxis

Need to cover skin ± 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.