Nasopharyngeal Culture

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Nasopharyngeal Culture


A nasopharyngeal culture is a microbiology test used to identify pathogenic organisms present in the nasal cavity that may be the cause of an upper respiratory tract illness or may be transmitted by carriers to persons susceptible to infection.


Some of the organisms responsible for upper respiratory infections are carried primarily in the nasopharynx. Nasopharyngeal cultures are performed to isolate these organisms. These include viruses such as influenza, parainfluenza, and respiratory syncytial virus, which are the most common causes of respiratory infection in young children, and pathogenic bacteria such as Bordetella pertusis and Corynebacterium diphtheriae, which are infrequent causes of infections in the United States. In addition, nasopharyngeal cultures are used to identify carriers of Staphylococcus aureus, Streptococcus pneumoniae, and Neisseria meningitidis. These organisms usually do not cause disease in the nasopharynx or throat. However, asymptomatic carriers may transmit these organisms via nasal secretions to others that will develop serious infections. Staphylococcus aureus and Streptococcus pneumoniae can cause pneumonia and septicemia and N. meningitidis can cause outbreaks of meningitis.

Bacteria that cause pharyngeal infection (sore throat ) such as Haemophilus influenzae, Streptococcus pyrogenes (group A streptococcus), Candida albicans, and Mycoplasma pneumoniae may also be isolated from the nasopharynx. The procedure can also be used as a substitute for a throat culture in infants, elderly patients, debilitated patients, or in cases where a throat culture is difficult to obtain.


For best results, the specimen should be obtained prior to initiating any therapy. The health care worker obtaining the specimen should wear gloves to prevent spreading infectious organisms.


Collection and transport

A sample is obtained from the nasopharynx by means of a swab, aspirate, or wash. Swabbing is most commonly used for collection. A calcium algenate (wool) or polyester swab on a flexible wire is most commonly used. The nose is cleared of mucus and the swab is inserted into the nasal cavity and moved forward along the septum until it reaches the rear of the pharynx. The swab is rotated several times and then removed. For viral culture, the swab should be transported in a small amount of veal infusion or sucrose-phosphate broth. For bacterial culture, the swab should be placed in Stuart's or Amie's transport medium. If pertussis is suspected, the swab should be placed directly onto Regan-Lowe media before transporting to the lab. Aspirates are collected by placing a thin flexible catheter or plastic tube onto the end of a 10 mL syringe and applying suction. Washings are collected by irrigating the nasal cavity with 7-10 mL of sterile phosphate buffered saline using a suction bulb and then aspirating the fluid.

VIRUSES. Nasopharyngeal swabs are most often used to collect samples from neonates or young children who have an upper respiratory infection. Most respiratory infections in young children are caused by viruses. Cultures are not routinely ordered for influenza, parainfluenza, or respiratory syncytial virus. Influenza and parainfluenza are cultured in primary monkey kidney cells or chick egg embryos. RSV is most often cultured in HEp2 cells (malignant human epithelioma cells). Since viral cultures can take up to seven to 12 days, tests for viral antigens using fluorescent or enzyme immunoassay are performed frequently.

BACTERIA. Bacterial culture and Gram stain are performed routinely for nasopharyngeal specimens. Gram stain is helpful in suggesting the presence of Candida albicans (gram-positive budding yeast), Corynebacterium diphtheriae (small gram-positive rods arranged like Chinese letters), and Neisseria meningitidis (small gram-negative diplococci).

The Gram stain is performed by:

  • Transferring a small portion of the specimen to the center of a glass slide, which is then heat-fixed and cooled before staining.
  • Placing a few drops of crystal violet on the slide and allowing it to set for 30-60 seconds.
  • Rinsing off the crystal violet, gently, with water.
  • Applying a few drops of Gram's iodine on the slide and allowing it to set for 60 seconds.
  • Rinsing off the iodine, gently, with water.
  • Decolorizing by rinsing with 95% ethanol, drop by drop, until the alcohol rinses clear.
  • Placing a few drops of safranin on the slide and allowing it to set for 30 seconds.
  • Rinsing off the safranin, gently, with water.
  • Blotting excess water with bibulous paper.
  • Allowing the slide to air dry.
  • Observing the slide under oil immersion.

Gram-positive cells retain the crystal violet and appear dark purple, while gram-negative cells do not retain the crystal violet. They are stained with the safranin and appear red.

Specimens should be plated on sheep blood agar, which supports the growth of most of the pathogenic bacteria encountered in nasopharyngeal specimens except Chlamydia, Haemophilus, and Mycoplasma; chocolate (heated blood) agar for Haemophilus; and a selective medium for gram-positive cocci such as colistin-nalidixic acid (CNA). If Corynebacterium diphtheriae is suspected, the specimen should be plated on Loeffler or Tinsdale agar, which permits faster growth than blood agar. If Bordetella pertusis is suspected, the specimen should be plated on Regan-Lowe (charcoal-horse blood agar) or Bordet-Gengou agar. Cultures should be incubated at 35°C in air at high humidity. Plates should be examined for growth each day and suspect colonies Gram-stained and subcultured (that is, transferred to an appropriate medium). If C. diphtheriae or B. pertussis is suspected, plates should be held for six to seven days. Otherwise, plates showing no growth of suspected pathogens may be discarded after 48 hours. Preliminary identification of the organism can be made from catalase, coagulase, urease, nitrate reduction, sucrose fermentation, and characteristic colonial morphology.

Antibiotic susceptibility testing is performed by the Kirby-Bauer or broth microdilution method for Haemophilus, Neisseria, Streptococcus pneumoniae, or Staphylococcus aureus. Antibiotics usually included are ampicillin, chloramphenicol, cephalosporins, meropenem, oxacillin, vancomycin, and trimethoprim-sulfamethoxazole. Antibiotic susceptiblity is not performed for C. diphtheriae, B. pertussis, or M. pneumoniae because they are susceptible to erythromycin, and are difficult to grow in MIC broth for susceptibility testing. Streptococcus is susceptible to penicillin.

Alternative procedures

In most cases of upper respiratory tract infections, a throat culture is more appropriate than a nasopharyngeal culture. However, the nasopharyngeal culture should be used in cases where throat cultures are difficult to obtain or to detect the carrier states especially meningococcal disease.


The patient should clear their nose of excess secretions prior to sample procurement. To prevent contamination, the swab should not touch the patient's tongue or side of the nostrils.




There is little to no risk of complications involved in a nasopharyngeal culture.


Preliminary results may be reported in one or two days followed by confirmation which usually takes additional time depending upon the organisms isolated. Bacteria that normally grow in the nasal cavity will be identified by a nasopharyngeal culture. These include nonhemolytic streptococci, alpha-hemolytic streptococci, some Neisseria species, diphtheroids, and some types of staphylococci.

Pathogenic organisms that might be identified by this culture include:

  • group A beta-hemolytic streptococci
  • Bordetella pertussis, the causative agent of whooping cough
  • Corynebacterium diptheriae, the causative agent of diptheria
  • Neisseria gonorrhoeae, the causative agent of gonorrhea that may be isolated from persons who have engaged in oral sex
  • Chlamydia trachomatis, the causative agent of pelvic inflammatory disease and urethritis that may cause a nasopharyngeal infection in the neonate from transmission in the womb

Antibiotic— A drug given to stop the growth of bacteria. Antibiotics are ineffective against viruses.

Bacilli— Rod-shaped bacterium.

Cocci— Spherical shape bacterium.

Nasopharynx— The back wall of the nasal cavity, where it meets the throat.

In addition, some bacteria normally present in the nasal cavity may be the cause of infection or disease when they are present in large amounts. These include:

  • Haemophilus influenzae, a causative agent of bronchitis, inner ear infection, and meningitis
  • Streptococci pneumoniae, a causative agent of pneumonia
  • Candida albicans, the causative agent of thrush

Asymptomatic carriers may contain the following organisms in the nasopharynx:

  • Neisseria meningitidis, a causative agent of meningitis
  • Streptococci pneumonia, a causative agent of pneumonia
  • Staphylococcus aureus, the causative agent of many Staph infections

Health care team roles

A physician orders a nasopharyngeal culture. A physician, physician assistant, or nurse collects the specimen. A clinical laboratory scientist/medical technologist who specializes in microbiology performs the culture and antibiotic sensitivity test when required. The physician determines the appropriate antimicrobial treatment.



Byrne, J., D.F saxton, P.K. Pelikan, and P.M. Nugent. Laboratory Tests, Implication for Nursing Care, 2nd ed. Menlo Park, CA: Addison-Wesley Publishing Company.

Chernecky, Cynthia C, and Barbara J. Berger. Laboratory Tests and Diagnostic Procedures. 3rd ed. Philadelphia, PA: W. B. Saunders Company, 2001.

Loeb, S., ed. Illustrated Guide to Diagnostic Tests. Springhouse, PA: Springhouse Corporation, 1994.


The American Medical Association, Kids Health. 〈〉.

National Center for Infectious Disease, Centers for Disease Control and Prevention. 1600 Clifton Rd., NE, Atlanta, GA 30333. 〈〉 and 〈〉.