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Collecting, transporting and prioritizing specimens

15 min

Skills you'll build3 skills
  • 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

At the bench: Select specimen preparation, media, and incubation for a culture

Try first

Try first

A clinic orders a Neisseria gonorrhoeae and Chlamydia trachomatis nucleic acid amplification test (NAAT). Which swab is used for the collection?

Keep going to see the reasoning.

Keep going to see the reasoning.

Right. Keep going to follow the reasoning.

Keep going to see the reasoning.

Get the idea

Use the explanation to check your first decision.

Collection devices and material

A culture grows only the organisms that arrive viable. 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 gives the patient's identifier, the source and the collection time. The source shows which resident flora to expect, and the collection time starts every transport limit.1,2

Swabs retain material in their fibers and deliver less specimen 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 is suitable for culture and NAAT. An FDA-cleared assay lists the devices it accepts.4

Transport temperature

Sterile fluids, blood and gonococcal specimens can contain organisms that cold injures. Urine, respiratory secretions and stool contain 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 is handled differently:2

  1. Contact the ordering service promptly.
  2. Resolve any identity discrepancy before a result is assigned. A clinician's request to proceed 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.

Follow the bench demonstration

Sources for this step
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

Read each decision and its explanation.

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 confirmed.

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

  2. Classify the specimen: CSF is accepted and worked up even when the volume is short.

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

  3. Compare the volume with what the tests require: 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.

  4. Call the ordering service and ask which test to prioritize.

    The clinician knows which question matters most for this patient.

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

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

  6. Document the call and add a comment stating that the volume was insufficient for the tests not performed.

    The report has to show which tests were not done and why.

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

Practice this skill

Your turn

Problem 1 of 3 · Hints available

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 contains resident flora that multiplies at room temperature and falsely raises the colony count, so delayed urine is refrigerated after about 30 minutes.

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

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

Hint
  1. Consider which organisms each specimen is collected to recover.
  2. Consider which transport temperature each organism survives best.

Review Transport

Problem 2 of 3 · Hints available

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 specifies, gives a reliable result.

A comment does not correct an inhibited reaction. A negative result would still be reported as the patient's result.

Hint
  1. Consider how the tip fibers and the shaft affect the amplification enzymes.
  2. Check the assay's instructions for the devices it accepts.

Review Collection

Problem 3 of 3 · On your own

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 discards the only specimen available for this culture.

Discarded an irreplaceable specimen without consultation

A CSF, tissue, or other specimen that cannot be recollected may be the only specimen available, and rejecting it for a minor problem leaves nothing to test. 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 resolves 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 conceals the discrepancy. The documented exception procedure specifies how identity is resolved.

Review Receipt, prioritization, and rejection

Use it

Read the case evidence, then make each decision. The step is complete without 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 falsely high and could be mistaken for infection.

Refrigeration now does not reverse 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 correct transport for gonococci. The swab is acceptable and goes to media without further delay.

Cold injures N. gonorrhoeae. Refrigeration can kill 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 discards a usable specimen.

Review Transport

Decision 3 of 3

What do you do with the NAAT tube?

The medium preserves nucleic acid. The swab is not on 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 a listed swab gives a reportable result.

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

Review Collection

Each specimen is judged by what it was collected to recover. The gonococcal swab needed room-temperature transport, and it arrived that way. The urine needed refrigeration within about 30 minutes and sat for 3 hours. The NAAT needed a swab from the assay's device list.

For reference

Sources checked