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close this bookBasic Laboratory Procedures in Clinical Bacteriology (WHO; 1991; 128 pages)
View the documentPreface
View the documentIntroduction
open this folder and view contentsQuality assurance in microbiology
close this folderPart I. Bacteriological investigations
open this folder and view contentsBlood
open this folder and view contentsCerebrospinal fluid
open this folder and view contentsUrine
open this folder and view contentsStool
close this folderLower respiratory tract infections
View the documentIntroduction
View the documentThe most common infections
View the documentCollection of sputum specimens
View the documentProcessing of sputum in the laboratory (for non-tuberculous infections)
View the documentCulture for Mycobacterium tuberculosis
View the documentGeneral note on safety
open this folder and view contentsUpper respiratory tract infections
open this folder and view contentsSexually transmitted diseases
open this folder and view contentsPurulent exudates, wounds, and abscesses
open this folder and view contentsAnaerobic bacteriology
open this folder and view contentsAntimicrobial susceptibility testing
open this folder and view contentsPart II. Essential media and reagents for isolation and identification of clinical pathogens
View the documentSelected further reading
View the documentSelected WHO publications of related interest
View the documentBack Cover

The most common infections

Acute and chronic bronchitis

In patients with acute bronchitis (usually following an acute viral infection, such as a common cold or influenza), sputum is not usually cultured unless the patient fails to show signs of clinical improvement.

Chronic bronchitis is a long-lasting disabling respiratory disease with periodic acute attacks. Most patients generally cough up sputum every day, which is usually grey and mucoid; the disease also has episodes when the condition of the patient becomes worse and obviously purulent sputum is coughed up. This is termed an acute exacerbation of chronic bronchitis. The typical respiratory pathogens (Haemophilus influenzae, Streptococcus pneumoniae, or less often Branhamella catarrhalis) are frequently found in sputum samples.

Lung abscess

An abscess may form in the lung following the inhalation of a foreign body, of the stomach contents, or of upper respiratory tract (mouth or throat) secretions. This is sometimes termed “aspiration pneumonia”. Attempts may be made to culture coughed-up sputum (which is often extremely foul-smelling), but when there is an abscess (as demonstrated by radiography) the pus contained in it should be examined microscopically and cultured. Unfortunately, there is no medical agreement on how this pus should be obtained, but direct puncture and withdrawal of pus is one of the possibilities. Anaerobic bacteria such as Bacteroides melaninogenicus, Peptococcus spp, and Peptostreptococcus spp, derived from the mouth or throat flora, are often very important causative agents. Pus should be collected, transported, and examined according to standard methods for anaerobic culture of pus.

Pneumonia and bronchopneumonia

Acute lobar pneumonia usually affects only a single lobe of the lung. This infection is nearly always caused by S. pneumoniae and blood cultures taken at the same time frequently show the presence of this organism. This form of disease occasionally occurs in epidemic form. A rare cause of a rather similar form of pneumonia is Klebsiella pneumoniae.

While a few patients infected with S. pneumoniae or K. pneumoniae will have classical pneumonia, the most frequent form of the disease is bronchopneumonia, with patches of infiltration and inflammation (termed “consolidation”) distributed over one or often both lungs.

Many different kinds of viruses or bacteria can be associated with bronchopneumonia. Apart from S. pneumoniae, and sometimes H. influenzae, Staphylococcus aureus is a cause of bronchopneumonia, particularly during influenza or measles epidemics. Gram-negative rods (in particular, E. coli and K. pneumoniae) and P. aeruginosa are also frequently found. These infections are all too common in intensive-care departments, especially when broad-spectrum antibiotics are widely used or mechanical respiration is carried out, and are indicative of indiscriminate use of antibiotics and failure to monitor patients carefully for early signs of infection.

If there is a pleural effusion, the fluid should be examined microscopically and cultured according to the procedures described for pus and exudates.

Pulmonary tuberculosis

The sputum of patients with pulmonary tuberculosis is usually not highly purulent, but should not be rejected for tuberculosis investigation because of this. An acid-fast stained smear (Ziehl-Neelsen) should be examined microscopically to detect immediately any patients who have acid-fast bacteria in their sputum.1 After the stained smear has been made, the sputum should be treated by a decontamination procedure in order to kill as many of the non-mycobacterial organisms as possible and to leave the tubercle bacilli viable and thus suitable for culture on Löwenstein-Jensen medium.


1 See Manual of basic techniques for a health laboratory. Geneva, World Health Organization, 1980.

Because the bacteriological procedures for the diagnosis of pyogenic respiratory infections, such as bronchitis and pneumonia, are so fundamentally different from those for tuberculosis, they will be considered separately. The physician must make it clear to the laboratory whether he or she wishes examinations for:


• pyogenic bacteria (H. influenzae, S. pneumoniae, etc.),
• tubercle bacteria (M. tuberculosis), or
• both types of bacteria.
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