Diagnostic studies for specific agents of lower respiratory tract infectionsa

PathogensAvailable assaysComments
    Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, gram-negative bacilli, otherGram stain and culture of expectorated sputum, BAL, or other deep respiratory secretions; Gram stain and culture of pleural fluid; blood culturesNOW S. pneumoniae (Binax, Inc.) urinary antigen test is available; high specificity; sensitivity, 52 to 80%
Atypical agents
    Legionella speciesCulture of respiratory secretions and tissues on BCYE, selective BCYEConsidered the “gold standard”
Urine antigen detectionSeveral kits available; reliably detects only Legionella pneumophila serogroup 1
SerologySerology with acute- and convalescent-phase specimens; 1-3 months may be required for seroconversion
PCRb with respiratory secretionsMost promising
    Mycoplasma pneumoniaeSerologyMethod of choice
CultureRarely performed; requires specialized media, prolonged incubation
PCRbAvailable through reference laboratories
    Chlamydia pneumoniaeSerologyMIF is best assay
CultureNot widely available; sensitivity, 50 to 70%
    Chlamydia psittaciSerologyCulture not recommended in routine clinical labs due to safety risks
    Bordetella speciesCultureNP swabs, aspirates, and washings are specimens of choice; requires specialized media for transport and culture
DFASensitivity of 65% and specificity of 99.6% with monoclonal antibody reagents
SerologyIgA and IgG antibodies to PT and FHA
PCRbRapid, sensitive; calcium alginate swabs are inhibitory to PCR
    Coxiella burnetiiSerologyTiter of antibody to phase II IgG, ≥200 by IFA
    Nocardia speciesGram stain and modified acid fast stain; culture of respiratory specimens and tissues
    Mycobacterium speciesAcid-fast stain; culture with combination of broth and solid media
Direct amplification techniques availableTwo amplification assays have been cleared by FDA: Gen-Probe AMTDT and Roche Amplicor and COBAS assays (Roche Molecular)
    Influenza virus, respiratory syncytial virus, and parainfluenza viruses 1 to 4NP 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)
    AdenovirusAntigen detection methods have variable sensitivities and specificitiesPoint-of-care rapid tests are least sensitive
PCRCommercial multiplex PCR assay available as RUO for RNA viruses
    Herpes simplex virusVirus isolation
PCRbAvailable through reference laboratories
    CytomegalovirusShell vial culture in combination with early antigen detection by DFADetection of antigen on peripheral blood leukocytes and amplification techniques with plasma and serum used to monitor at-risk patients
    Varicella-zoster virusVirus isolation
    HantavirusSerology: EIA for IgM and IgGSerology is available through most state health laboratories
    PathogenicFungal stains—GMS, calcofluor white, PAS
        Blastomyces, Histoplasma,     Coccidioides immitis,     Sporothrix schenckiiRecovery 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
SerologyMay be unreliable in immunocompromised host/PICK>
        Cryptococcus speciesStains as listed aboveSerum cryptococcal antigen by LA or EIA
Recovery in culture
        Candida speciesGram stain or fungal stainRecovery from culture alone is insufficient to make a diagnosis; histology is required
        AspergillusGMS or calcofluor stain
Recovery in cultureRecommended, as other hyaline molds may have similar histopathologic appearance
        ZygomycetesGMS or calcofluor stainNonseptate broad hyphae are suggestive of a zygomycete
Recovery in culture
Histopathology of tissue section
        PneumocystisGiemsa stain, GMS, other; DFA stainInduced 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.