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©2013 UpToDate ® Print Email Studies on bronchoalveolar lavage fluid for the assessment of pneumonia in immunocompromised hosts* Type of infection Stain Culture Other Bacteria Gram stain Aerobic and anaerobic culture Fungi KOH smear • Fungal culture • Aspergillus galactomannan antigen Mycobacteria AFB Mycobacterial culture Pneumocystis jirovecii (formerly P. carinii) Fluorescein-conjugated monoclonal antibody Δ N/A PCR Nocardia spp Modified AFB Fungal culture Legionella spp N/A Legionella culture using BCYE medium ◊ Mycoplasma pneumoniae N/A N/A PCR Viruses Cytomegalovirus N/A Shell vial culture, conventional culture § PCR, cytology § Influenza virus N/A Viral culture Reverse transcriptase PCR, direct or indirect fluorescent antibody, rapid antigen test������ Parainfluenza virus N/A Viral culture Direct or indirect fluorescent antibody, PCR Respiratory syncytial virus N/A Viral culture PCR, rapid antigen test ������ Adenovirus N/A Viral culture PCR Herpes simplex virus N/A Viral culture ������ Direct fluorescent antibody ������ Varicella-zoster virus N/A Viral culture Direct fluorescent antibody

Reverse transcriptase PCR, direct or indirect fluorescent antibody, rapid antigen test������ Parainfluenza virus N/A Viral culture Direct or indirect fluorescent antibody, PCR Respiratory syncytial virus N/A Viral culture PCR, rapid antigen test ������ Adenovirus N/A Viral culture PCR Herpes simplex virus N/A Viral culture ������ Direct fluorescent antibody ������ Varicella-zoster virus N/A Viral culture Direct fluorescent antibody KOH: potassium hydroxide; AFB: acid fast bacillus; N/A: not applicable; BCYE: buffered charcoal yeast extract; PCR: polymerase chain reaction.   * The decision of which studies to send depends upon the individual patient's clinical findings and on availability at specific hospital laboratories. When the diagnosis is not established by studies of bronchoalveolar lavage fluid or non-invasive testing, histopathology of lung tissue is often helpful. For detailed discussions regarding the diagnosis of specific causes of pneumonia, see individual topic reviews. • The detection of Candida species from respiratory specimens should generally be interpreted as reflecting colonization of the oropharynx since Candida pneumonia is extremely rare. Δ Other stains for P. jirovecii include calcofluor white, cresyl echt violet, Gomori methenamine silver, and toluidine blue. ◊ If Legionella pneumonia is suspected, a Legionella urinary antigen should also be obtained. § If cytomegalovirus infection is suspected, a peripheral blood sample should also be sent for PCR (from whole blood or plasma) or antigenemia assay (from peripheral blood polymorphonuclear leukocytes). ‡ Rapid antigen testing lacks sensitivity. Thus, PCR is considered the gold standard for the detection of respiratory viruses in bronchoalveolar lavage fluid. For patients with a negative rapid antigen test in whom a respiratory virus is suspected, PCR should also be sent. † The detection of herpes simplex virus may represent contamination of the specimen from reactivation within the oropharynx rather than pneumonia.