Version July 2025
| 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, Blastomyces antigen, Coccidioides serology |
| Mycobacteria | AFB stain | Mycobacterial culture | Nucleic acid amplification (NAA) tests: Xpert MTB/RIF, Xpert MTB/XDR, DNA sequencing |
| Pneumocystis jirovecii (formerly P. carinii) | Fluorescein-conjugated monoclonal antibodyΔ, cytology | N/A | PCR (may reflect colonization) |
| Nocardia spp | Modified AFB stain | Culture◊ | |
| Legionella spp | Modified Gimenez stain | Legionella culture using BCYE medium§ | Direct fluorescent antibody |
| Mycoplasma pneumoniae | N/A | Mycoplasma/Ureaplasma culture | PCR |
| Viruses | |||
| Coronavirus disease 2019 | N/A | Viral culture | PCR, rapid antigen test‡ |
| 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 | |
AFB: acid-fast bacillus; BCYE: buffered charcoal yeast extract; KOH: potassium hydroxide; N/A: not applicable; 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.