Upper Respiratory Culture, Routine

Additional Information:

UFHPL Epic order code: LAB2012

Thrush, oral candidiasis, and Candida esophagitis frequently complicate antineoplastic therapy, hyperalimentation, transplantation immunosuppression, pregnancy, and the acquired immunodeficiency syndrome (AIDS). In addition to a fungal culture, a saline wet preparation, Gram stain, or KOH preparation demonstrating yeast cells or pseudohyphae may also be useful in rapidly establishing the diagnosis of oral or mucocutaneous candidiasis.

Streptococcus pyogenes: Group A β-hemolytic strep) and other β-hemolytic streptococci in groups B, C, D, and G are generally susceptible to penicillin and its derivatives. Therefore, susceptibility need not be routinely determined. The principal reason for considering an alternative drug for individual patients is allergy to penicillin. Erythromycin, a cephalosporin, or clindamycin might be substituted in these cases. Patients allergic to penicillins may also be allergic to cephalosporins.

In the late 1980s, a resurgence of serious Streptococcus pyogenes infection was observed. Complications including rheumatic fever, sepsis, severe soft tissue invasion,and toxic shock-like syndrome (TSLS) are reported to be most common with the M1 serotype and a unique invasive clone has become the predominant cause of severe streptococcal infections.3

Ear: Normal flora of the skin of the healthy ear includes Staphylococcus epidermidis, Corynebacterium sp, and Staphylococcus aureus. Correlation of nasopharyngeal cultures with results of tympanocentesis culture is poor and lacks predictive value in identification of the causative agent of otitis media. In decreasing order of frequency, the following organisms have been recovered from tympanocentesis: S pneumoniae (50 to 75 percent), H influenzae (10 to 30 percent), Moraxella (Branhamella) catarrhalis (5 to 10 percent), Streptococcus pyogenes (5 to 10 percent), Staphylococcus aureus (1 to 5 percent), Pseudomonas aeruginosa (0.1 to 1 percent). E coli, Klebsiella pneumoniae, Pseudomonas aeruginosa may be isolated from neonates. In therapeutic failures, S aureus, and P aeruginosa are most frequently recovered. Tympanocentesis is not usually performed in primary infections. It is to be considered in treatment failures and neonates. Candida superinfection may complicate therapy for recurring ear infections and may be a cause of persistent otorrhea. Otitis externa is frequently caused by P aeruginosa and less frequently by Candida sp, Proteus sp, S aureus, and Trichophyton sp.


  1. Bibler MR, Rouan GW. Cryptogenic group A streptococcal bacteremia: Experience at an urban general hospital and review of the literature. Rev Infect Dis. 1986 Nov-Dec; 8(6):941-951. PubMed 3541128
  2. Lang SD, Singh K. The sore throat. When to investigate and when to prescribe. Drugs. 1990 Dec; 40(6):854-862. PubMed 2079000
  3. Cleary PP, Kaplan EL, Handley JP, et al. Clonal basis for resurgence of serious Streptococcus pyogenes disease in the 1980s. Lancet. 1992 Feb 29; 339(8792):518-521. PubMed 1346879


  • Brodsky L. Modern assessment of tonsils and adenoids. Pediatr Clin North Am. 1989 Dec; 36(6):1551-1569. PubMed 2685730
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  • Givner LB. Abramson JS, Wasilauskas B. Apparent increase in the incidence of invasive group A beta-hemolytic streptococcal disease in children. J Pediatr. 1991 Mar; 118(3):341-346. PubMed 1999773
  • Gregory DW. Saturday Conference: Candida infections. South Med J. 1982 Mar; 75(3):339-345. PubMed 7038888
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CPT Code(s):


Collection Procedure:

Throat: Depress tongue and rub swab vigorously over each tonsillar area and posterior pharynx. Any exudate should be touched, and care should be taken to avoid the tongue and uvula. Place the used swab in a transport tube.
Nasopharynx: With the patient’s head immobilized, insert a flexible wire swab into the patient’s nostril until it reaches the posterior nares. Leave the swab in place for 15 to 30 seconds. Rotate and remove the swab; then, place it in a transport tube.

Specimen Requirements:

Type: Throat swab, nasopharynx swab, nares swab, ear swab

Container/Tube: Bacterial culture transport swab
  • Both tonsillar pillars and the oropharynx should be swabbed. Do not allow the swab to touch the patient’s tongue.

Sample Volume: One swab or aspirated material

Storage: Store specimens at room temperature.
Rejection Criteria:

  • Unlabeled specimen or name discrepancy between specimen and request label
  • Inappropriate specimen transport device
  • Leaking specimen
  • Specimen received after prolonged delay (usually more than 72 hours)
  • Expired transport


This test is used to:

  • Isolate and identify potentially pathogenic organisms from a patient’s throat, sinus, etc.
  • Evaluate pharyngitis
  • Evaluate nares for staph
The test includes:

  • Culture
  • Isolation of potential aerobic pathogens and identification (additional charges/CPT codes may apply)
  • Susceptibility testing if the culture results warrant (additional charges/CPT codes may apply). CPT coding for microbiology and virology procedures often cannot be determined before the culture is performed.


Interpretation requires a significant level of experience and technical proficiency in order to avoid false-positives and false-negatives.1 Many other etiologic agents can be responsible for pharyngitis.2

Note: This procedure does not include screening for Neisseria gonorrhoeae or Corynebacterium diphtheriae. Anaerobic organisms that are frequently implicated in chronic infection of the tonsils and adenoids are not recovered by aerobic culture methods.



Reference Values:

Upper Respiratory Culture

*Rare because of vaccination.

† Not recovered by
upper respiratory culture.

Organisms Implicated in
Infections of the Oropharynx

Bordetella pertussis*†

Candida albicans

Corynebacterium diphtheriae

Leptotrichia buccalis

Neisseria gonorrhoeae

Respiratory viruses†:



Epstein-Barr virus†

Parainfluenza virus†



Streptococcus pyogenes

Organisms Commonly Present
in the Normal Oropharynx

Actinomyces israelii (tonsils)†

Bacteroides sp (tonsils)†

Candida albicans

Candida sp

Corynebacterium sp (diphtheroids)

E coli


Fusobacterium sp (tonsils)

Haemophilus influenzae

Haemophilus parainfluenzae

Klebsiella sp

Neisseria meningitidis

Nonhemolytic streptococci

Proteus sp

Staphylococcus aureus

Staphylococcus epidermidis

Streptococcus pneumoniae

Streptococcus pyogenes

Veillonella sp