. 2018 Jun 28;67(6):e1–e94. doi: 10.1093/cid/ciy381

Table 23.

Laboratory Diagnosis of Pulmonary Infections in Cystic Fibrosis

Etiologic Agents	Diagnostic Procedures	Optimum Specimens	Transport Issues and Optimal Transport Time
Bacteria
Staphylococcus aureus Haemophilus influenzae Streptococcus pneumoniae Enteric bacilli Pseudomonas aeruginosa Stenotrophomonas maltophilia Achromobacter spp	Culture	Expectorated sputum; throat swabs^a; other respiratory samples	Sterile container, RT, 2 h; >2–24 h, 4°C
Burkholderia cepacia complex	Culture using B. cepacia selective agar	Throat swabs^a, expectorated sputum; other respiratory cultures	Sterile container, RT, 2 h; >2–24 h, 4°C
Opportunistic glucose nonfermenting gram-negative rods Burkholderia gladioli Inquilinus spp Ralstonia spp Cupriavidus spp Pandoraea spp	Culture	Expectorated sputum; throat swabs^a; other respiratory samples	Sterile container, RT, 2 h; >2–24 h, 4°C
Mycobacterium spp
Mycobacterium abscessus	Mycobacterial culture Mycobacterial culture	Expectorated sputum, bronchoscopically obtained cultures; other respiratory cultures	Sterile container, RT, 2 h; >2–24 h, 4°C
Mycobacterium avium complex	Mycobacterial culture Mycobacterial culture		Sterile container, RT, 2 h; >2–24 h, 4°C
Fungi
Aspergillus spp	Calcofluor-KOH or other fungal stain Fungal culture	Expectorated sputum, bronchoscopically obtained cultures; other respiratory cultures	Sterile container, RT, 2 h; >2–24 h, 4°C
Scedosporium spp
Trichosporon
Viruses
RSV	Rapid antigen detection DFA Viral culture methods NAAT^b	Nasal aspirates, nasal washes, NP swabs, throat washes, throat swabs; bronchoscopically obtained specimens	Transport in viral transport media, RT or 4°C, 5 d; –70°C, >5 d
Influenza Adenovirus Rhinovirus Coronavirus Parainfluenza virus Human metapneumovirus	Rapid antigen detection DFA Viral culture methods NAAT^b

Abbreviations: DFA, direct fluorescent antibody; KOH, potassium hydroxide; NAAT, nucleic acid amplification test; NP, nasopharyngeal; RSV, respiratory syncytial virus; RT, room temperature.

^aYoung children < 8 years of age only; often called “gag sputum.”

^bSeveral US Food and Drug Administration–cleared NAAT platforms are currently available and vary in their approved specimen requirements and range of analytes detected. Readers should check with their laboratories regarding availability and performance characteristics, including certain limitations.