Microscopy and culture
Microscopy and sputum or other LRT samples (bronchoalveolar lavage [BAL]) and blood cultures, have historically been the main diagnostic tools used to identify the microbial etiology of pneumonia. Respiratory pathogen identification in high quality samples directly obtained from the infection site or a normally sterile site (blood), provides good evidence on the probable causative agents.
LRT samples are generally cultured in standard microbiologic media such as the combination of blood, chocolate and MacConkey agars, isolating the most commonly found bacterial pneumonia pathogens. Some bacteria require special media (Legionella sp; buffered charcoal yeast extract-based media) or cells (Chlamydophila pneumoniae), or cannot be cultured in a diagnostic laboratory (Mycoplasma pneumoniae).
The process of sample collection is pivotal to microscopy and culture results as well as to their interpretation. LRT samples may become contaminated by upper respiratory tract (URT) secretions during collection or the collected sample may harbor URT secretions. The presence of 25 PMN per low power field (X 100) [10], or ≥10 leukocytes for every SEC [11], is indicative of a high quality expectorated sputum sample in adults. Sputum with relatively low numbers of PMN cells and a high number of SEC is highly suggestive of oropharyngeal contamination. However, the application of these criteria to sputum samples (including induced sputum) in children remains to be determined.