Throat and Pharyngeal Culture, Patients with Cystic Fibrosis


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Subject: Throat and Pharyngeal Culture, Patients with Cystic Fibrosis

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  • This culture is used to screen for the bacterial pathogens that commonly cause lower respiratory tract infections in patients with CF. Pharyngeal specimens are most useful to document carriage/chronic infection, whereas lower respiratory specimens are recommended for the evaluation of clinically evident, acute infection.

  • Pneumonia is a cause of significant morbidity and mortality in patients with CF. The etiology of these infections is different than that seen in other patient groups. P. aeruginosa (including mucoid variants), Burkholderia cepacia complex organisms, Stenotrophomonas maltophilia, H. influenzae, and other glucose-fermenting and nonfermenting gram-negative bacilli, as well as mycobacteria, S. aureus, and S. pneumoniae, are commonly isolated from lower and upper respiratory tract specimens submitted from patients with CF.

  • Sputum from patients with CF should not be screened by Gram stain, as recommended for routine sputum cultures submitted from patients without CF.

  • Special collection and transport instructions:

    • Posterior pharyngeal swabs may be submitted.

    • Expectorated sputum or invasively obtained lower respiratory specimens are recommended for evaluation of chronic carriage/infection and acute exacerbation of pulmonary infection.

    • Specimens are transported as for routine sputum specimens.

  • Method:

    • A variety of supportive, selective, and differential agar media are inoculated. Commonly inoculated media include

      • SBA as a supportive medium capable of supporting the growth of many pathogens, including S. pneumoniae.

      • CNA agar for gram-positive pathogens; mannitol–salt agar for isolation of S. aureus.

      • MacConkey agar for nonfastidious gram-negative bacilli, including P. aeruginosa and S. maltophilia.

      • B. cepacia–selective agar.

      • Chocolate agar for isolation of H. influenzae.

    • Cultures for mycobacterial, fungal, viral, or other respiratory pathogens are also recommended in addition to bacterial cultures.

  • Turnaround time: Cultures are examined daily for 96 hours. Several days are required for isolation, susceptibility testing, and identification of suspected isolates.


  • Patients with CF often show respiratory tract colonization that changes little over time, even in response to antimicrobial therapy. The interpretation of cultures demonstrating such “abnormal flora” may be challenging; clinical and therapeutic decisions must be based on a variety of clinical and other factors, in addition to culture results.

  • The workup and interpretation of CF respiratory cultures are typically based on several factors, including type of specimen submitted, organism(s) isolated, and the predominance of a specific pathogen compared to other flora.


  • Although rapidly growing mycobacteria and mold may be isolated with CF respiratory cultures, special cultures are needed for sensitive detection of nontuberculous mycobacteria, Aspergillus species and other molds, and viruses that may cause acute respiratory infections in these patients. It is difficult to differentiate isolates that represent chronic colonization versus acute exacerbation on the basis of laboratory criteria.

  • Common pitfalls:

    • Clinicians must order special throat or lower respiratory cultures specifically designed for evaluation of patients with CF; routine cultures are not optimized for evaluation of the flora typically isolated from such specimens. Laboratories should not apply sputum rejection criteria based on Gram stain screening recommended for routine sputum cultures submitted from other patients.