Collection of Upper Respiratory Tract Specimens

Last updated on June 7th, 2021

Infections of the upper respiratory tract usually involve the ears, the mucus membranes lining the nose and throat above the epiglottis and the sinuses. Upper respiratory tract specimens should be collected within 3 days of symptom onset and no later than 7 days, ideally prior to the initiation of antimicrobial chemoprophylaxis or therapy.

Procedure for Nasopharyngeal aspirate and Swab
Procedure for Nasopharyngeal aspirate and Swab

Most infections involving the nose and throat are caused by viruses. Oropharyngeal (OP) and nasopharyngeal (NP) swabs and nasopharyngeal wash/aspirate are the common upper respiratory tract specimens submitted for virologic assays.  Nasopharyngeal wash/aspirate is the preferred sample. Use mask, gloves and eye protection while collecting the specimen.

Oropharyngeal (OP) and nasopharyngeal (NP) swabs

Only sterile dacron or rayon swabs with plastic shafts are appropriate for oropharyngeal and nasopharyngeal swabs.

DO NOT use calcium alginate swabs or swabs with wooden sticks, as they may contain substances that inactivate some viruses and inhibit some molecular assays. 

Procedure for the collection of Oropharyngeal (OP) Swab

  1. Insert the swab into the posterior pharynx and tonsillar areas.
  2. Rub swab over both tonsillar pillars and posterior oropharynx and avoid touching the tongue, teeth, and gums.

Procedure for the collection of Nasopharyngeal (NP) Swab

  1. Insert flexible wire shaft swab through the nares parallel to the palate (not upwards) until resistance is encountered or the distance is equivalent to that from the ear to the nostril of the patient indicating contact with the nasopharynx.
  2. Gently, rub and roll the swab. Leave the swab in place for several seconds to absorb secretions before removing it.

Place NP and OP swabs immediately into a sterile vial containing 2 ml of viral transport media. Both swabs can be placed in the same vial if desired. Aseptically, cut or break the applicator sticks off near the tip to permit the tightening of the cap.

 Procedure for collection of Nasopharyngeal wash/aspirate

  1. Have the patient sit with the head tilted slightly backward.
  2. Instill 1 ml-1.5 ml of nonbacteriostatic saline (pH 7.0) into one nostril.
  3. Flush a plastic catheter or tubing with 2 ml-3 ml of saline.
  4. Insert the tubing into the nostril parallel to the palate (not upwards).
  5. Aspirate nasopharyngeal secretions. If permitted, repeat this procedure for the other nostril.
  6. Collect nasopharyngeal aspirate in sterile vials


Label each specimen container with:

  1. Name of the patient
  2. Hospital or lab identification number
  3. Type of specimen collected
  4. Date of collection

Transport and Storage

Send specimens to the lab immediately (testing sensitivity decreases over time). If specimens will be examined within 48 hours after collection, keep specimen at 4oC and ship on wet ice or refrigerant gel-packs, otherwise store frozen at ≤-70oC and ship on dry ice.

Viability of some pathogens (e.g. respiratory syncytial virus) from specimens that are frozen and then thawed is greatly diminished and may result in false-negative test results.

About Acharya Tankeshwar 473 Articles
Hello, thank you for visiting my blog. I am Tankeshwar Acharya. Blogging is my passion. I am working as an Asst. Professor and Microbiologist at Department of Microbiology and Immunology, Patan Academy of Health Sciences, Nepal. If you want me to write about any posts that you found confusing/difficult, please mention in the comments below.

1 Comment

  1. Do you have details about Time and temperature storage of both upper and lower respiratory tract specimens
    for microbiological studies (bacterial culture specifically)?
    Do you agree that for upper resp. specimens “throat, nasal, oral, NP swabs” , the ideal time and temp. Storage is ≤24 h, RT
    while for lower resp. specimens “sputum, BAL, BBW” , the ideal time and temp. Storage is ≤24 h, 4C
    Or do you think the answer depends on the expected bacteria you try to isolate.
    finally what about fungal culture and temperature storage of the clinical samples requested for fungal culture?

    thanks in advance for reply

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