TABLE 2.
Diagnostic studies for specific agents of lower respiratory tract infectionsa
| Pathogens | Available assays | Comments |
|---|---|---|
| Bacteria | ||
| Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, gram-negative bacilli, other | Gram stain and culture of expectorated sputum, BAL, or other deep respiratory secretions; Gram stain and culture of pleural fluid; blood cultures | NOW S. pneumoniae (Binax, Inc.) urinary antigen test is available; high specificity; sensitivity, 52 to 80% |
| Atypical agents | ||
| Legionella species | Culture of respiratory secretions and tissues on BCYE, selective BCYE | Considered the “gold standard” |
| Urine antigen detection | Several kits available; reliably detects only Legionella pneumophila serogroup 1 | |
| Serology | Serology with acute- and convalescent-phase specimens; 1-3 months may be required for seroconversion | |
| PCRb with respiratory secretions | Most promising | |
| Mycoplasma pneumoniae | Serology | Method of choice |
| Culture | Rarely performed; requires specialized media, prolonged incubation | |
| PCRb | Available through reference laboratories | |
| Chlamydia pneumoniae | Serology | MIF is best assay |
| Culture | Not widely available; sensitivity, 50 to 70% | |
| PCRb | ||
| Chlamydia psittaci | Serology | Culture not recommended in routine clinical labs due to safety risks |
| Bordetella species | Culture | NP swabs, aspirates, and washings are specimens of choice; requires specialized media for transport and culture |
| DFA | Sensitivity of 65% and specificity of 99.6% with monoclonal antibody reagents | |
| Serology | IgA and IgG antibodies to PT and FHA | |
| PCRb | Rapid, sensitive; calcium alginate swabs are inhibitory to PCR | |
| Coxiella burnetii | Serology | Titer of antibody to phase II IgG, ≥200 by IFA |
| Nocardia species | Gram stain and modified acid fast stain; culture of respiratory specimens and tissues | |
| Mycobacterium species | Acid-fast stain; culture with combination of broth and solid media | |
| Direct amplification techniques available | Two amplification assays have been cleared by FDA: Gen-Probe AMTDT and Roche Amplicor and COBAS assays (Roche Molecular) | |
| Viruses | ||
| Influenza virus, respiratory syncytial virus, and parainfluenza viruses 1 to 4 | NP aspirates, washings, and swabs are preferred specimens; virus isolation is test of choice with exception of detection of respiratory syncytial virus (for which antigen detection is test of choice) | |
| Adenovirus | Antigen detection methods have variable sensitivities and specificities | Point-of-care rapid tests are least sensitive |
| PCR | Commercial multiplex PCR assay available as RUO for RNA viruses | |
| Herpes simplex virus | Virus isolation | |
| PCRb | Available through reference laboratories | |
| Cytomegalovirus | Shell vial culture in combination with early antigen detection by DFA | Detection of antigen on peripheral blood leukocytes and amplification techniques with plasma and serum used to monitor at-risk patients |
| Varicella-zoster virus | Virus isolation | |
| DFA | ||
| Hantavirus | Serology: EIA for IgM and IgG | Serology is available through most state health laboratories |
| Fungi | ||
| Pathogenic | Fungal stains—GMS, calcofluor white, PAS | |
| Blastomyces, Histoplasma, Coccidioides immitis, Sporothrix schenckii | Recovery in culture from tissue, respiratory secretions, etc. | Probes available for rapid confirmation of culture isolates for Blastomyces, Histoplasma, and Coccidioides; Histoplasma antigen (blood, urine, respiratory secretions) available for acute disseminated infections |
| Serology | May be unreliable in immunocompromised host/PICK> | |
| Cryptococcus species | Stains as listed above | Serum cryptococcal antigen by LA or EIA |
| Recovery in culture | ||
| Opportunistic | ||
| Candida species | Gram stain or fungal stain | Recovery from culture alone is insufficient to make a diagnosis; histology is required |
| Aspergillus | GMS or calcofluor stain | |
| Recovery in culture | Recommended, as other hyaline molds may have similar histopathologic appearance | |
| Zygomycetes | GMS or calcofluor stain | Nonseptate broad hyphae are suggestive of a zygomycete |
| Recovery in culture | ||
| Histopathology of tissue section | ||
| Pneumocystis | Giemsa stain, GMS, other; DFA stain | Induced sputum; bronchoscopy gives higher yield |
a
The information in this table is compiled from references 3, 10, 11, 12, 16, 19, 25, and 26. Abbreviations: BCYE, buffered charcoal yeast extract; MIF, microimmunofluorescence; NP, nasopharyngeal; IgA, immunoglobulin A, DFA, direct fluorescent-antibody test; PT, pertussis toxin; FHA, filamentous hemagglutinin; IFA, immunofluorescent antibody; AMTDT, amplified Mycobacterium tuberculosis direct test; EIA, enzyme immunoassay; GMS, Gomori's methenanine silver; PAS, periodic acid-Schiff; LA, latex agglutination; FDA, U.S. Food and Drug Administration; RUO, research use only. Not standardized; not cleared by the U.S. Food and Drug Administration.