Respiratory Specimen Collection

RESPIRATORY SPECIMEN COLLECTION INSTRUCTIONS

All specimens submitted to the laboratory should be labeled with at least two patient identifiers:

• Patient name
• Medica Record Number or Date of Birth

The samples should also be labeled with:

• The specimen type
• The collection date and time
• The collector's initials or employee ID number

 

Appropriate personal protective equipment (PPE) must be used during all collection procedures. Refer to department policies or Infection Control for more information. 

 

 

Nasopharyngeal (NPH) Swab

Equipment:

• For SARS-CoV-2/Influenza A&B/RSV PCR (4-PLEX); Respiratory FilmArray; Bordetella pertussis/parapertussis PCR; Influenza A/B, Qualitative NAAT; RSV, Qualitative NAAT; Rapid SARS-CoV-2;
  • NPH flocked swab BD 220251,
  • M4 Remel 12520 viral transport media (VTM)
• For Respiratory Culture
  • ESwab minitip collection kit (green capped) BD 220246

 

Specimen Collection:

1. Insert the swab into the nare until the posterior nasopharynx is reached.
2. Gently rotate the swab for 5-10 seconds or as tolerated. Withdraw the swab.
3. Repeat the process on the other nare.
4. Break the swab off into the appropriate media and secure the cap.

 

Transport

1. Send to the laboratory immediately.
2. If the sample cannot be sent immediately, transport refrigerated to the laboratory.

 

 

Nasal Swab

Equipment:

• ESwab, mini-tip collection kit BD 220246

 

Specimen Collection

1. Insert the swab into a nare until resistance is met at the level of the turbinate.
2. Rotate the swab against nasal mucosa.
3. Remove the swab from the patient's nare.
4. Break the swab off into the transport tube containing 1.0mL of liquid media.

 

Transport

1. Send to the laboratory immediately.
2. If the sample cannot be sent immediately, transport refrigerated to the laboratory.

 

 

Nasal Wash

Equipment:

• Sterile normal saline for irrigation
• Luki-trap
• Suction catheter

 

Specimen Collection

1. Have the patient clear any nasal congestion before obtaining the specimen by blowing his nose or by nasal suctioning.
2. Connect the suction catheter to the luki-trap and then connect the luki-trap to wall suction.
3. "Wash" for nasal cells by irrigating both nares with 0.5 ml normal saline. Suction each nares to obtain cells not mucus.
4. Rinse the suction catheter with 1.0-1.5ml normal saline which helps move the specimen from the suction catheter into the luki-trap.
5. If using a bulb syringe, empty the contents of the bulb syringe directly into the sterile container.

 

Transport

1. Send to the laboratory immediately.
2. If the sample cannot be sent immediately, transport refrigerated to the laboratory.

 

 

Sputum (Expectorated)

Equipment:

• Sterile cup (clear plastic, screw cap)

 

Specimen Collection

Note: Do not have the patient gargle with non-sterile water before collecting a sample, as non-sterile water may introduce bacterial and mycobacterial contaminants. Gargling with a sterile saline or water is acceptable. 

1. Instruct the patient to cough deeply. Instruct the patient not to expectorate saliva or postnasal drippings.
2. Collect the resulting specimen into a sterile cup.
   • Notify the physician if unable to obtain a specimen.
3. A specimen may be obtained by sterile suction technique using a Luki-trap by passing a sterile suction catheter along the floor of the nose to the nasopharynx. When the patient coughs, suction the specimen into the trap. Obtain the specimen by suction only with physician order.
4. If submitting a sputum sample for ABF Culture and Stain, first morning sputum samples of 3.0-5.0 mL is optimal for possible recovery of mycobacterial organisms.

 

Transport

1. Send to the laboratory immediately.
2. If the sample cannot be sent immediately, transport refrigerated to the laboratory.

 

Sample Rejection

The Microbiology Laboratory will perform a Gram stain on all sputum specimens submitted for analysis. A sputum specimen containing > 25 epithelial cells per low power field indicates that the sample has been contaminated with oropharyngeal secretions during collection, which is suboptimal for culture. In these scenarios, the Microbiology Laboratory will notify the provider and allow them to choose whether to proceed with the culture on the suboptimal sample or recollect the sputum.

 

Tracheal Aspirate

Equipment:

• Luki trap (with tubes)
• Sterile suction catheter
• Sterile normal saline for irrigation
• Disposable clean graduated cup.

 

Specimen Collection

1. Connect the suction catheter to the rubber tubing side on the aspirating trap and connect the other side of the aspirating trap to the tubing from wall suction.
2. Draw up the appropriate amount (based on patient age) of preservative-free sterile saline for irrigation into a syringe:
   • Under 1 year: 0.5 mL
   • 1-3 years: 1 mL
   • 3 years and older: 2 mL
3. Pour the remaining normal saline for irrigation into the graduated cup.
4. Suction the patient by putting on sterile gloves, instilling saline from the syringe (without the needle), suction the patient while keeping the aspirating trap in a vertical position.
5. If the specimen is in the catheter, suction a small amount of normal saline for irrigation from graduated cup to move secretions into the aspirating trap. Disconnect the aspirating trap from the suction tubing and catheter. Connect tubing on the aspirating trap to the other side of the trap.

 

Transport

1. Send to the laboratory immediately.
2. If the sample cannot be sent immediately, transport refrigerated to the laboratory.
3. Specimen should not be transported in the tube system with Luki trap top. Rupture of the trap due to pressure changes while in the tube system can occur.

 

 

Broncheoalveolar Lavage (BAL) and other bronchoscopy collected samples

Equipment:

• Sterile cup

 

Specimen Collection

1. These procedures are performed by pulmonologists, intensivists, and other trained providers. Providers should refer to their own department procedures for instructions on specimen collection.
2. Once a sample has been collected, it should be placed into a sterile cup.

 

Transport

1. Deliver the sample to the laboratory immediately. 
2. If the sample cannot be sent immediately, transport refrigerated to the laboratory.
3. It is not recommended to send irretrievable or difficult to recollect specimens through the tube system, as samples are lost on occasion. 

 

 

Throat (Oropharyngeal)

NOTE: Do not obtain throat cultures if the epiglottis is inflamed. Sampling may cause serious respiratory obstruction.

 

Equipment:

• For Group A Strep Antigen and Streptococcus Culture:
  • Rayon dual swab
  • Tongue depressor
• For GC Culture or Respiratory Culture:
  • ESwab collection kit BD 220245 or 220246 mini swab
  • Tongue depressor

 

Specimen Collection

1. Remove the swab(s) from the collection kit package.
2. Depress the tongue gently with the tongue depressor to visualize the throat area for obvious purulent areas.
3. Swab between the tonsillar pillars and behind the uvula. Avoid touching the cheeks, tongue, uvula or lips.
4. Swab back and forth across the posterior pharynx, tonsillar area and any inflamed or ulcerated areas.
5. Place swab(s) in appropriate transport device.
   • If using the Rayon dual swab, place swabs in the provided container and secure the cap.
   • If using the Eswab, break the swab off into the provided transport media and close the tube. 

 

Transport ​​​

1. Sent to the laboratory immediately.
2. If unable to send to the laboratory immediately, transport refrigerated.

 

 

 

Throat (Oropharyngeal) - Cystic Fibrosis Patients

The following section provides instructions on the deep pharyngeal specimens. This procedure applies only to Cystic Fibrosis patients who cannot produce sputa.

NOTE: Do not obtain throat cultures if the epiglottis is inflamed. Sampling may cause serious respiratory obstruction.

 

Equipment:

• Tongue depressor
• ESwab collection kit BD 220245 or 220246 mini swab

 

Specimen Collection

1. Remove the swab(s) from the collection kit package.
2. Depress the tongue gently with the tongue depressor to access the back of the throat.
3. Place the swab at the back of the patient's throat. 
4. Instruct the patient to cough.
5. Collect secretions.
6. Remove the swab from patient's throat.
7. Break the swab off into the provided transport media and close the tube. 

 

Transport ​​​

1. Sent to the laboratory immediately.
2. If unable to send to the laboratory immediately, transport refrigerated.

 

 

 

Last updated: 11/20/2025

 

REFERENCES

1. Bowden, V.R., Smith Greenberg, C.(2008). Pediatric Nursing Procedures, 2nd Ed.
2. Philadelphia: Wolters Kluwer/Lippincott Williams & Wilkins.
3. Clinical Microbiology Procedures Handbook, 5th Edition. (2023). Washington, D.C.: The ASM Press.
4. E swab Package insert. BD 220245 or BD 220246 mini Eswab. Becton 08/2016
5. BioFire Package Insert.
6. Respiratory FilmArray Verification Study CHMCA 2016