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 antibodyΔ, 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 |
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