Studies on bronchoalveolar lavage fluid for the assessment of pneumonia in immunocompromised hosts*

Type of infection or condition	Direct smear/stain	Culture	Other
Bacteria	Gram stain	Aerobic and anaerobic culture
Fungi – molds	Calcofluor white/KOH preparation, silver stain	Fungal culture^¶	Aspergillus galactomannan antigen, PCR
Fungi – endemic	Calcofuor white/KOH preparation	Fungal culture	Histoplasma antigen
Mycobacteria	AFB stain	Mycobacterial culture
Pneumocystis jirovecii (formerly P. carinii)	Fluorescein-conjugated monoclonal antibody^Δ, cytology	N/A	PCR
Nocardia spp	Modified AFB stain	Culture^◊
Legionella spp	Modified Gimenez stain	Legionella culture using BCYE medium^§	Direct fluorescent antibody
Mycoplasma pneumoniae	N/A	N/A	PCR
Viruses
Cytomegalovirus	N/A	Shell vial culture, viral culture^¥	PCR, cytology^¥
Influenza virus	N/A	Viral culture	PCR, direct or indirect fluorescent antibody, rapid antigen test^‡
Parainfluenza virus	N/A	Viral culture	PCR, direct or indirect fluorescent antibody
Respiratory syncytial virus	N/A	Viral culture	PCR, rapid antigen test^‡
Adenovirus	N/A	Viral culture	PCR
Human metapneumovirus	N/A	N/A	PCR, direct fluorescent antibody
Herpes simplex virus	N/A	Viral culture^†	PCR, direct fluorescent antibody^†
Varicella-zoster virus	N/A	Viral culture	PCR, direct fluorescent antibody
Middle East respiratory syndrome coronavirus	N/A	N/A	PCR
Malignancy**	Cytology (Wright-Giemsa stain, Papanicolaou stain)	N/A

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 noninvasive testing, histopathology of lung tissue is often helpful. For detailed discussions regarding the diagnosis of specific causes of pneumonia, refer to the individual UpToDate topic reviews. If mucormycosis is suspected, do not grind culture samples.
¶ 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.
◊ Most routine aerobic bacterial, fungal, and mycobacterial culture media can support Nocardia, but selective media, such as BCYE, modified Thayer-Martin agar, or Lowenstein-Jensen (LJ) media, may be beneficial in decreasing the overgrowth of other organisms in specimens derived from nonsterile sites.
§ 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.
** Cytology is often performed on BAL fluid in immunocompromised hosts to evaluate for malignancy.

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Studies on bronchoalveolar lavage fluid for the assessment of pneumonia in immunocompromised hosts*