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Laboratory diagnosis of paediatric lower respiratory tract infection.

The burden of respiratory tract infections (RTIs) in children is extremely high in industrialised and developing countries, with nearly 50% of paediatric consultations in industrialised countries related to RTIs. (1)

Viruses have been shown to cause up to 90% of pneumonias, especially in the first year of life, with the respiratory syncytial virus the most important pathogen. This percentage decreases to approximately 50% by school-going age. Viral pneumonias are frequently complicated by bacterial infections, and mixed infections are common. Streptococcus pneumoniae is common in all age groups, and complications are usually associated with pneumococcal infections or co-infections.

The majority of patients with viral lower respiratory tract infections (LRTIs) are admitted to hospital because of bronchiolitis and pneumonia.

Laboratory diagnosis

Laboratory confirmation of the diagnosis is difficult and colonising flora may hamper the detection of true pathogens.

Although respiratory virus infections cause significant morbidity and mortality, laboratory diagnosis may not be needed in all patients or under all conditions. The indications for laboratory diagnosis of viral LRTIs are not clearly defined. However, infections that lead to hospital admission or prolong hospital stay, such as moderate to severe LRTI or fever syndrome, especially in young infants or immunocompromised children, warrant laboratory investigation. Other possible indications include an effort to stop unnecessary prescription of antimicrobials, to decrease further unnecessary diagnostic testing, to direct antiviral therapy or to define seasonal or epidemic disease in a specific community. (2)

In the past tissue culture techniques, which were the gold standard, were used to detect respiratory viruses. However, these techniques are time consuming, with decreased sensitivity, compared with molecular testing that is only performed in a few specialised laboratories. Serology is rarely helpful during acute disease owing to the possible time delay before seroconversion. Several antigen-based rapid diagnostic assays are available, including immunofluorescence and ELISA assays, but nucleic acid amplification tests such as the multiplex polymerase chain reaction (PCR) offer a broad range of diagnostic capabilities where multiple aetiologies can be detected. These can include the detection of influenza virus A, B and C, adenovirus, metapneumovirus, RSV A and B, rhinovirus A, parainfluenza virus 1, 2 and 3, echovirus, bocavirus and coronavirus in a single test.

A range of samples, such as nasopharyngeal aspirates or swabs and bronchoalveolar lavage specimens, are appropriate for PCR processing. Nasopharyngeal swabs present an easy method of obtaining a specimen if other respiratory samples are difficult to obtain. Samples should preferably not be frozen or stored for more than 72 hours before processing.

Confirmation of bacterial aetiology can be performed by conventional culture of the organism or by antigen detection from a urine sample, e.g. in the case of Legionella or S. pneumoniae. Several PCR assays are available for the detection of typical and atypical bacterial agents.

An adequate, expectorated sputum specimen should contain many neutrophils and few or no squamous epithelial cells. The latter are indicative of contamination with saliva. If possible, patients should brush their teeth and/or rinse their mouths well with water before attempting to collect the specimen in order to reduce the possibility of contaminating it with food particles or oropharyngeal secretions. An induced sputum sample should be considered if expectorated sputum cannot be obtained.

In bronchoscopy and aspirated specimens reduction of contamination may be accomplished by a head-down position to reduce gravitational flow of saliva. Oral contamination may successfully be reduced by using a telescoping double catheter with a plug to protect the brush or by a sheathed brush. The use of the telescoping plugged catheter and bronchoalveolar lavage increases the overall diagnostic yield.

A processing delay of more than a few hours may result in loss of recovery of fastidious pathogens and overgrowth of oropharyngeal flora.


(1.) Schaad UB. Prevention of paediatric respiratory tract infections: emphasis on the role of OM-85. Eur Respir Rev 2005; 14: 7477.

(2.) Henrickson KJ. Advances in the laboratory diagnosis of viral respiratory disease. Pediatr Infect Dis J 2004; 23(1S): S6-S10.


Clinical Microbiologist, Pathcare Reference Laboratory, Goodwood
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Title Annotation:More about ... Microbiology
Author:Senekal, Marthinus
Publication:CME: Your SA Journal of CPD
Geographic Code:6SOUT
Date:Nov 1, 2008
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