Common Sense Pathology

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Initial investigations

CXR is advised in all patients with pneumonia because it helps to:

  • confirm the diagnosis;
  • delineate the infiltration, nature and extent of the consolidation;
  • indicate the presence of underlying disorders; and
  • detect the presence of complications.

An extensive initial diagnostic workup is usually not necessary, and may include some of the laboratory tests listed. 

The following investigations are recommended in the hospitalised patient:

WCC > 15000/mm3 suggests bacterial 
WCC < 3000/mm3 and > 25000/mm3 are regarded as poor prognostic features.
Anaemia may indicate mycoplasma infection, chronic disease, or complicated pneumonia.
Blood cultures - two sets
Sputum - microscopy, culture and sensitivities
- AFB and TB culture

Occasionally, in severe pneumonia unresponsive to initial therapy, investigation may include:
Bronchial brushings/lavage: MCS
Bronchial biopsy: MCS and histology

Pleural fluid examination, including white cell and differential count, MCS and TB culture or PCR and cytology; protein and glucose may be indicated if pleural effusion is present.
If clinically indicated, U&E and blood gases may be required.
HIV serology should be considered especially in young adults with pneumonia sufficiently severe to require hospitalisation, or in patients who fail to respond to initial antibiotic therapy.




Community acquired pneumonia


1. Conventional bacteria
Streptococcus pneumoniae
Haemophilus influenzae
Moraxella catarrhalis 

Aerobic Gram negative bacilli e.g.
Klebsiella pneumoniae
E coli

Staphylococcus aureus

Microscopy, culture and sensitivities
The preferred specimens include:
Expectorated sputum
Blood cultures
Transtracheal aspirates 
Pleural fluid

It should be noted that Legionella,
Mycoplasma, Chlamydia pneumoniae
and M tuberculosis are not detected using
conventional cultures.

2. Atypical pathogens including:
Mycoplasma pneumoniae

Chlamydia pneumoniae
Legionella spp. 

Mycoplasma pneumoniae serology
Cold agglutinins
Chlamydia-specific serology
Legionella serology
- the major indications
include: severe or life-threatening pneumonia; pneumonia in the compromised host; associated features that strongly suggest this diagnosis; and pneumonia in the patient who fails to respond to β-lactam antibiotics.

3. Tuberculosis

Tuberculosis should be considered in any patient 
with pneumonia
Acid-fast stain and mycobacterium culture
If a rapid answer is required, TB PCR 

4. Repiratory viruses including:
Influenza A and B 
Respiratory syncytial virus

Serology for influenza, parainfluenza, 
adenovirus and RSV
Direct fluorescent antibody staining of
respiratory tract specimens
Virus culture

Nosocomial pneumonia


Conventional bacteria

Microscopy, culture and sensitivities

Aerobic Gram-negative bacilli esp.
Klebsiella pneumoniae
Enterobacter spp.
Serratia spp.
Pseudomonas aeruginosa
Acinetobacter spp.
Staphylococcus aureus
Streptococcus pneumoniae
Haemophilus influenzae


Anaerobic bacteria 

Anaerobic culture can be performed on specimens not contaminated with upper airway flora e.g. lung abscess, pleural effusions

Legionella spp.

Legionella serology

Pneumonia in the immunocompromised host

Cell-mediated immunity defects (e.g. HIV) 
Pneumocystis carinii

Preferred samples include bronchoscopically
collected specimens. The yield on sputum is less than 50%.
Pneumocystis carinii PCR
Silver stain

Cryptococcus, Aspergillus
M. tuberculosis, M. avium
Nocardia spp. 

Fungal culture
Acid-fast stain and mycobacterium culture
Conventional culture
(warn laboratory if suspected)

Common pyogenic bacteria, incl.
Streptococcus pneumoniae
Haemophilus influenzae

Conventional culture

Cytomegalo- and Herpes simplex virus

Lung biopsy for histology 
Respiratory samples for:
Viral culture

Streptococcus pneumoniae
Haemophilus influenzae

Conventional culture

Streptococcus pneumoniae
Haemophilus influenzae
Neisseria meningitidis

Conventional culture

Gram negative bacilli
Nocardia spp.

Conventional culture



  1. Working Group of the South African Pulmonology Society. Management of Community-acquired pneumonia in adults. S Afr M J 2002; 92 (8): 647 - 655
  2. Bartlett JG, Mundy LM. Community acquired pneumonia. NEJM 1995; 333: 1618 - 1624
  3. Harrison 's Principles of Internal Medicine 12 Edition. pp1064 - 1068
  4. Mandell, Douglas and Bennett's Principles and Practice of Infectious Diseases p 2000.
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