. 2013 Aug 15;57(4):e22–e121. doi: 10.1093/cid/cit278

Table VI-2.

Laboratory Diagnosis of Community-acquired Pneumonia

Etiologic Agents	Diagnostic Procedures	Optimum Specimens	Transport Issues; Optimal Transport Time
Bacteria
Streptococcus pneumoniae	Gram stain	Sputum, bronchoscopic specimens	Sterile container, RT, 2 h; >2–24 h, 4°C
	Culture	Sputum, bronchoscopic specimens	Sterile container, RT, 2 h; >2–24 h, 4°C
	Urine antigen^a	Urine	Sterile container, RT, 24 h; >24 h–14 d, 2–8°C
Staphylococcus aureus	Gram stain	Sputum, bronchoscopic specimens	Sterile container, RT, 2 h; >2–24 h, 4°C
Haemophilus influenzae	Culture
Enterobacteriaceae
Pseudomonas aeruginosa
Legionella species	Urine antigen	Urine	Sterile container, RT, 24 h; >24 h–14 d, 2–8°C
	L. pneumophila serogroup 1	Urine	Sterile container, RT, 24 h; >24 h–14 d, 2–8°C
	Selective culture on BCYE	Induced sputum, bronchoscopic specimens	Sterile container, RT, 2 h; >2–24 h, 4°C
	NAAT^b	Induced sputum, bronchoscopic specimens	Sterile container, RT, 2 h; >2–24 h, 4°C
Mycoplasma pneumoniae	NAAT^b	Throat swab, NP swab, sputum, bronchoalveolar lavage (BAL)	Transport in M4 media or other Mycoplasma-specific medium at RT or 4°C up to 48 h; ≥48 h, −70°C
Mycoplasma pneumoniae	Serology IgM, IgG antibody detection	Serum	Clot tube, RT, 24 h; >24 h, 4°C
Chlamydophila pneumoniae	NAAT^b	NP swab, throat washings, sputum, bronchial specimens	Transport in M4 or other specialized medium at RT or 4°C up to 48 h;≥48 h, −70°C
Chlamydophila pneumoniae	Serology (MIF) IgM antibody titer; IgG on paired serum 2–3 wk apart	Serum	Clot tube, RT, 24 h; >24 h, 4°C
Mixed anaerobic bacteria (Aspiration pneumonia)	Gram stain	Bronchoscopy with protected specimen brush	Sterile tube with 1 mL of saline or thioglycolate; RT, 2 h; >2–24 h
	Aerobic and anaerobic culture	Bronchoscopy with protected specimen brush
	Aerobic and anaerobic culture	Pleural fluid (if available)	Sterile container RT, without transport ≤60 min; Anaerobic transport vial RT, 72 h
Mycobacteria
Mycobacterium tuberculosis and Nontuberculous mycobacteria	AFB smear	Expectorated sputum; induced sputum; bronchoscopically obtained specimens	Sterile container, RT,≤2 h; ≤24 h, 4°C
	AFB culture
	NAAT (No FDA-cleared direct test available)
Fungi
Histoplasma capsulatum	Calcofluor-KOH or other fungal stain	Expectorated sputum; induced sputum, bronchoscopically obtained specimens; tissue	Sterile container, RT, <2 h; ≤24 h, 4°C
	Fungal culture		Sterile container, RT, <2 h; ≤24 h, 4°C
	Histology	Tissue	Sterile container 4°C; Formalin container, RT, 2–14 d
	Antigen Tests	Serum, urine, pleural fluid (if available)	Clot tube, RT, 2 d; 2–14 d. 4°C
	Antigen Tests	Serum, urine, pleural fluid (if available)	Sterile container (urine), RT 2 h; >2–72 h, 4°C
	Serum antibody (CF)	Serum	Clot tube, RT, 24 h; 4°C, >24 h
Coccidioides immitis/posadasii	Calcofluor- KOH or other fungal stain	Expectorated sputum; induced sputum, bronchoscopically obtained specimens	Sterile container, RT, <2 h; ≤24 h, 4°C
	Fungal culture		Sterile container, RT, <2 h; ≤24 h, 4°C
	Histology	Tissue	Formalin container, RT, 2–14 d; Sterile container 2–14 d, 4°C
	Serum antibody IgM (ID, LA, EIA)	Serum	Clot tube, RT, 24 h;>24 h, 4°C
	IgG antibody (CF, EIA)	Serum	Clot tube, RT, 24 h;>24 h, 4°C
Blastomyces dermatitidis	Calcofluor -KOH or other fungal stain	Expectorated sputum; induced sputum, bronchoscopically obtained specimens; tissue	Sterile container, RT, < 2 h; ≤24 h, 4°C
	Fungal culture		Sterile container, RT, < 2 h; ≤24 h, 4°C
	Histology	Tissue	Sterile container 4°C, Formalin container, RT, 2–14 d
	Antigen Tests	Serum,	Clot tube, RT, 24 h
		Urine, pleural fluid (if available)	Sterile container 4°C, 2–14 d
	Serum antibody (CF)	Serum	Clot tube, RT, 24 h; >24 h, 4°C
Viruses
Influenza viruses A, B	Rapid antigen detection	Nasal aspirates, nasal washes, NP swabs, throat washes, throat swabs, bronchoscopically obtained samples
	DFA	Transport in viral transport media, RT <2 h; 5 d, 4°C; >5 d, −70°C
	Viral culture methods
	NAAT^c
Adenovirus	DFA
	Viral culture methods
	NAAT^c
Parainfluenza viruses 1–4	DFA
	Viral culture methods
	NAAT^c
Respiratory syncytial virus	Rapid antigen detection
	DFA
	Viral culture methods
	NAAT^c
Human metapneumovirus	DFA
Human metapneumovirus	NAAT^c
Coronaviruses	NAAT^c
Rhinovirus	Viral culture methods
Rhinovirus	NAAT^c
Enteroviruses	Viral culture methods
Enteroviruses	NAAT^c
Parasites
Paragonimus westermani	Direct microscopic examination of pleural fluid and sputum for characteristic ova	Pleural fluid	Sterile container, fresh samples 4°C, 60 min; preserved samples, RT, >60 min–30 d
Paragonimus westermani		Sputum

Abbreviations: BAL, bronchoalveolar lavage; BCYE, buffered charcoal yeast extract; CF, complement fixation; DFA, direct fluorescent antibody test; EIA, enzyme immunoassay; ID, immunodiffusion; KOH, potassium hydroxide; LA, latex agglutination; NAAT, nucleic acid amplification test; NP, nasopharyngeal; RT, room temperature.

^a Sensitivity in nonbacteremic patients with pneumococcal pneumonia is 52%–78%; sensitivity in bacteremic cases of pneumococcal pneumonia is 80%–86%; specificity in adults is > 90%. However, studies have reported a 21%–54% false positive rate in children with NP carriage and no evidence of pneumonia [87].

^b Currently there is one FDA approved platform (see text). Availability is laboratory specific. Provider needs to check with the laboratory for optimal specimen source, performance characteristics and turn around time.

^c Several FDA cleared NAAT platforms are currently available and vary in their approved specimen requirements and range of analytes detected. Readers should check with their laboratory regarding availability and performance characteristics including certain limitations.