Table 22.12.

Respiratory Specimens and Diagnostic Testing

Specimen Type	Microbiological Investigations	Comment
Sputum/induced sputum	Microscopy; culture; susceptibilities; DFA; PCR	Provided it is a good-quality specimen, it can be a highly informative specimen; can be difficult to obtain in children
Nasopharyngeal aspirate/swab	Microscopy; culture; susceptibilities; DFA; PCR	Most useful in viral infections; requires a skilled operator to obtain specimen; in some ways, it is easier to obtain than a throat swab, because the nares are always accessible
Nasal swab	Microscopy; culture; susceptibilities; DFA; PCR	Limited usefulness as it only recovers organisms present in the nasal cavity and not beyond
Throat swab	Microscopy; culture; susceptibilities; DFA; PCR	Probably the most representative specimen for disease of the upper respiratory tract; many bacterial pathogens are also common colonizers at various stages of childhood; can be difficult to obtain without child and parent cooperation; may represent organisms present in the nose as well as the oropharynx
Endotracheal aspirate	Microscopy; culture; susceptibilities; DFA; PCR	Invasive specimen, but is likely to represent pathogens from the lower respiratory tract; can be contaminated by organisms present in the oropharynx that can make result interpretation difficult
Bronchoalveolar lavage fluid	Microscopy; culture; susceptibilities; DFA; PCR	Invasive specimen but is likely to represent pathogens from the lower respiratory tract; can be contaminated by organisms present in the oropharynx, which can make result interpretation difficult
Transthoracic needle aspiration	Microscopy; culture; susceptibilities; DFA; PCR	Highly invasive specimen; risk of complications; microbiologically of high value provided the correct area has been biopsied
Lung tissue	Microscopy; culture; susceptibilities; DFA; PCR	Highly invasive specimen; risk of complications; microbiologically of high value provided the correct area has been biopsied
Pleural fluid	Microscopy; culture; susceptibilities; DFA; PCR	Invasive specimen but is the specimen of choice in a child with empyema
Blood cultures	Microscopy; culture; susceptibilities;	Very helpful if positive, but the positivity rate in pneumonia is relatively low
Serum/whole blood	Immunoassays; DFA; PCR	Serology per se is of limited value, since a diagnosis is dependent on paired sera that then makes it a retrospective tool; a single high titer can occasionally be obtained in acute disease; PCR on whole blood may be helpful in severe disease to detect viremia, but viremia is generally short lived
Urine	Antigen detection tests; microscopy; culture	Antigen detection tests are of limited value in children; pathogen is rarely cultured from urine

DFA, Direct fluorescent antibody; PCR, polymerase chain reaction.