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Collecting, transporting and prioritizing specimens

15 min

  • Choose a collection device compatible with the requested microbiology test
  • Choose room temperature or refrigeration for a specimen and its requested test
  • Prioritize a limited or irreplaceable microbiology specimen

Read the full reference

Try first

Try first

A clinic orders a Neisseria gonorrhoeae and Chlamydia trachomatis nucleic acid amplification test (NAAT). Which swab goes to the patient?

The next section explains it.

The next section explains it.

Right. The next section explains why.

The next section explains it.

Get the idea

The right material in the right device

A culture grows only what reached the laboratory alive. Collect before antimicrobials when possible, because even one dose can suppress growth. Take material from the true site of infection, in a sterile container for everything except stool.1 The label carries the patient's identifier, the source and the collection time. The source tells the reader which resident flora to expect, and the time starts every transport limit.1,2

Swabs trap material in their fibers and deliver less than an aspirate or tissue. Send fluid or tissue for anaerobes, mycobacteria and fungi whenever the site allows.1 Swab materials matter too:

  • Calcium alginate inhibits PCR, and aluminum shafts inhibit it after long contact.3
  • Cotton may inhibit gonococci, and wooden shafts can inhibit chlamydiae.4
  • A plastic-shafted Dacron, rayon or nylon swab suits culture and NAAT. An FDA-cleared assay lists the devices it accepts.4

Temperature follows the organisms

Sterile fluids, blood and gonococcal specimens can carry organisms that cold injures. Urine, respiratory secretions and stool carry heavy resident flora that overgrows a pathogen at room temperature.1,5 Your laboratory's instructions set the exact limits.

Keep at room temperatureRefrigerate when delayed
CSF and other sterile fluidsUnpreserved urine, after about 30 minutes
Blood and inoculated culture bottlesUnpreserved stool, after about 1 hour
Swabs for N. gonorrhoeae cultureRespiratory specimens, after about 2 hours
Stool in Cary-Blair mediumViral transport medium

Never refrigerate CSF for culture.1,5

Irreplaceable specimens

A replaceable specimen that fails the acceptance criteria is recollected. A CSF, a tissue or another specimen that cannot be collected again gets a different path:2

  1. Contact the ordering service promptly.
  2. Resolve any identity discrepancy before a result is assigned. A clinician's request to go ahead does not establish identity.
  3. When volume is short, ask the clinician to rank the tests.
  4. Document the decision and put the limitation on the report.
References
  1. Tille PM. Bailey & Scott's Diagnostic Microbiology. 15th ed. Elsevier; 2021.
  2. Laboratory requirements. 42 CFR part 493, §493.1242, §493.1291 (2026). Accessed September 27, 2026. https://www.ecfr.gov/current/title-42/chapter-IV/subchapter-G/part-493
  3. Wadowsky RM, Laus S, Libert T, States SJ, Ehrlich GD. Inhibition of PCR-based assay for Bordetella pertussis by using calcium alginate fiber and aluminum shaft components of a nasopharyngeal swab. J Clin Microbiol. 1994;32(4):1054-1057. doi:10.1128/jcm.32.4.1054-1057.1994
  4. Papp JR, Schachter J, Gaydos CA, Van Der Pol B. Recommendations for the laboratory-based detection of Chlamydia trachomatis and Neisseria gonorrhoeae—2014. MMWR Recomm Rep. 2014;63(RR-2):1-19. Accessed September 27, 2026. https://www.cdc.gov/mmwr/preview/mmwrhtml/rr6302a1.htm
  5. Miller JM, Binnicker MJ, Campbell S, et al. Guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2024 update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. Published online March 5, 2024. doi:10.1093/cid/ciae104

Watch one

A single tube of CSF arrives from a lumbar puncture with 1.0 mL of fluid. The label and the requisition carry the same name and medical record number. The orders are Gram stain and bacterial culture, fungal culture and mycobacterial culture.

What do you do with the tube?

  1. Check the label against the requisition: two identifiers match, so identity is settled.

    Identity comes first, because no result can be assigned to an unverified specimen.

  2. Classify the specimen: CSF is kept and worked up, whatever its shortfalls.

    A second lumbar puncture cannot recover this moment in the illness, so the specimen is irreplaceable.

  3. Compare volume with need: Gram stain and bacterial culture need 0.5 to 1.0 mL, and mycobacterial and fungal cultures target 5 to 10 mL. One milliliter cannot support all three.

    Each test needs its own volume, and the smallest share goes furthest.

  4. Call the ordering service and ask which test comes first.

    The clinician knows which question matters most for this patient.

  5. Keep the tube at room temperature and process the ranked tests at once.

    Cold injures organisms such as *Neisseria meningitidis*, and delay costs recovery.

  6. Document the call and add a comment naming the insufficient volume for the tests left out.

    The reader needs to know which tests were not done and why.

Accept the CSF, call the ordering service to rank the tests, process them at once at room temperature, and document the volume limitation on the report.

Your turn

Problem 1 of 3

A swab for Neisseria gonorrhoeae culture and an unpreserved urine for culture will both be delayed about 3 hours before reaching the laboratory. How is each kept?

Correct. Gonococci are refrigeration-sensitive, so the swab stays at room temperature. Unpreserved urine carries resident flora that multiplies at room temperature and inflates the colony count, so delayed urine is refrigerated after about 30 minutes.

Incorrect. Gonococci are refrigeration-sensitive, so the swab stays at room temperature whatever the delay.

Incorrect. Delayed unpreserved urine is refrigerated after about 30 minutes, because resident flora multiplies at room temperature and inflates the colony count.

Hint
  1. Decide which organisms each specimen is meant to recover.
  2. Decide which temperature each organism survives best.

Review Transport

Problem 2 of 3

A pediatric unit sends a nasopharyngeal swab for Bordetella pertussis PCR. The swab has a calcium alginate tip on an aluminum shaft and sat in its tube for 2 days before shipping. What do you do?

PCR does detect nonviable organisms. Alginate fibers and a long-soaked aluminum shaft inhibit the reaction itself, so a negative result could be false.

Used a swab the molecular assay does not accept

Calcium alginate fibers and aluminum shafts inhibit PCR, and cotton and wooden shafts can inhibit gonococci and chlamydiae in culture. An FDA-cleared molecular assay accepts only the devices it lists, and any other device needs validation for that assay. A swab chosen for culture can give a false-negative NAAT.

Calcium alginate inhibits PCR after brief contact, and aluminum shafts inhibit it after about 48 hours. A flocked or synthetic swab on a plastic shaft, as the assay lists, gives a result that can be trusted.

A comment cannot rescue an inhibited reaction. A negative result would still be reported as the patient's result.

Hint
  1. Think about what the tip fibers and the shaft do to the amplification enzymes.
  2. Check the assay's instructions for the devices it accepts.

Review Collection

Problem 3 of 3

A surgeon sends a bone biopsy from the operating room for bacterial and fungal culture. The container's medical record number differs by one digit from the requisition's. The surgeon calls and asks you to go ahead, since the name is right. What do you do?

A bone biopsy cannot be collected again without another operation. Rejecting it loses the only chance at this culture.

Discarded an irreplaceable specimen without consultation

A CSF, tissue, or other specimen that cannot be recollected may be the only chance at a diagnosis, and rejecting it for a minor problem loses that chance. The laboratory contacts the ordering service, resolves identity discrepancies before reporting, asks the clinician to rank the tests when volume is short, and states the limitation on the report.

The specimen is irreplaceable, so it is processed without delay. The laboratory's documented exception procedure settles identity, and no result reaches a patient's record until it does.

A clinician's request does not establish identity. Reporting under the requisition could put the result on the wrong record.

Relabeling by the laboratory hides the discrepancy. The documented exception procedure decides how identity is resolved.

Review Receipt, prioritization, and rejection

Use it

  • A courier from an outpatient clinic arrives at 16:10 with three specimens from one patient, all collected at 13:00.
  • An unpreserved clean-catch urine for culture. It rode in the courier bag at room temperature.
  • An endocervical swab for N. gonorrhoeae culture in charcoal transport medium, also at room temperature.
  • A wooden-shafted cotton swab placed in the collection tube of a gonorrhea and chlamydia NAAT kit. The kit's instructions list a plastic-shafted synthetic swab.
Decision 1 of 3

What do you do with the urine?

Resident flora multiplied for about 3 hours at room temperature. The colony count would be inflated and could look like infection.

Cooling now cannot undo 3 hours of growth. The count is already unreliable.

Unpreserved urine is refrigerated after about 30 minutes. This one exceeded its transport limit, so it is recollected and delivered promptly or refrigerated.

Review Transport

Decision 2 of 3

What do you do with the gonococcal culture swab?

Room temperature is the right transport for gonococci. The swab is acceptable and goes to media without further delay.

Cold injures N. gonorrhoeae. Refrigeration could lose the organism and give a false-negative culture.

Refrigerated a specimen carrying cold-sensitive organisms

Refrigeration protects urine, stool, and respiratory specimens from overgrowth by resident flora. It injures Neisseria meningitidis and N. gonorrhoeae, so refrigerating CSF, sterile fluids, blood, or a gonococcal swab can lose the pathogen. Delayed, unpreserved urine left at room temperature gives an inflated colony count.

Charcoal transport medium at room temperature supports gonococci through a delay of this length. Rejecting it throws away a usable specimen.

Review Transport

Decision 3 of 3

What do you do with the NAAT tube?

The medium preserves nucleic acid. The swab itself is outside the assay's list, and cotton and wood are not validated for this test.

Used a swab the molecular assay does not accept

Calcium alginate fibers and aluminum shafts inhibit PCR, and cotton and wooden shafts can inhibit gonococci and chlamydiae in culture. An FDA-cleared molecular assay accepts only the devices it lists, and any other device needs validation for that assay. A swab chosen for culture can give a false-negative NAAT.

An FDA-cleared assay accepts only the devices it lists. A new collection with the listed swab gives a result the laboratory can stand behind.

A culture was not ordered on this swab, and cotton may inhibit gonococci. The ordered test needs the right device.

Review Collection

The clue that settled this delivery is what each specimen is meant to recover. The gonococcal swab needed warmth, and it arrived warm. The urine needed cooling within 30 minutes and waited 3 hours. The NAAT needed the swab its instructions name.

Keep

Sources checked