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Urine specimens and storage

15 min

Skills you'll build3 skills
  • Decide whether a urine specimen meets the requested test's requirements
  • Predict changes caused by delayed urine examination
  • Select a urine collection type suited to the requested measurement

At the bench: Check specimen identity and suitability before analysis · Reconcile urine appearance, chemistry, and microscopy findings

Try first

Try first

A urinalysis and a urine culture are ordered on one specimen. It arrives 30 minutes after collection in a clean, nonsterile routine cup, labeled on the container body. What do you do?

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.

Check the specimen before you test

Each laboratory writes its own rejection criteria. The common reasons to reject a urine specimen are:2

  • a missing, illegible or mismatched label, or a label on the lid only
  • visible fecal or tissue-paper contamination
  • too little urine for the ordered tests
  • an unpreserved specimen past the laboratory's stability limit
  • a culture specimen in a nonsterile container
  • a collection method that does not fit the ordered test

The collector labels the container body in the patient's presence, because a lid can be removed or exchanged.2 A fixed-dose boric-acid culture tube is filled to its line. Underfilling raises the preservative concentration, which can inhibit organisms and give a falsely low or negative culture.4

Match the collection to the test

  • Random: routine urinalysis and screening.
  • First morning: the concentrated void after overnight recumbency, for low-concentration constituents and orthostatic proteinuria.
  • 24-hour: total daily excretion.
  • Midstream clean-catch: routine urinalysis and culture.
  • Catheterized or suprapubic: culture when a voided specimen is unsuitable.
  • Pediatric bag: screening urinalysis only. Perineal flora contaminate it, so a positive bag culture cannot establish infection.2

Changes during a delay

For routine urinalysis, College of American Pathologists (CAP) requirements direct accredited laboratories to examine urine within 2 hours of collection unless it is refrigerated or chemically preserved.3 Urine for culture has its own time limit. IDSA/ASM guidance calls for processing within 30 minutes, or refrigeration or a preservative when processing is delayed. Follow your laboratory's procedure for a delayed specimen.5 Unpreserved urine at room temperature changes in predictable directions:1

ResultAfter a delayWhy
pHRisesBacteria convert urea to ammonia
TurbidityRisesBacteria grow and crystals form
NitriteRisesBacteria reduce nitrate
GlucoseFallsCells and bacteria consume it
KetonesFallAcetoacetate degrades and acetone evaporates
Bilirubin and urobilinogenFallLight oxidizes them
Intact cells and castsFallThey lyse, faster in dilute or alkaline urine

When several of these changes appear together in a late specimen, the results describe the storage. Request a fresh specimen and record the reason. Refrigeration slows the changes and can precipitate amorphous urates and phosphates that cloud the sediment.1,2

Follow the bench demonstration

Sources for this step
References
  1. Kouri TT, Hofmann W, Falbo R, et al. The EFLM European urinalysis guideline 2023. Clin Chem Lab Med. 2024;62(9):1653-1786. doi:10.1515/cclm-2024-0070
  2. Clinical and Laboratory Standards Institute. Processes for the Collection of Urine Specimens. 1st ed. CLSI guideline PRE05. Clinical and Laboratory Standards Institute; 2024. Accessed September 27, 2026. https://clsi.org/shop/standards/pre05/
  3. College of American Pathologists. Urinalysis Checklist. December 9, 2025 ed. Requirement URN.22300. Accessed September 27, 2026. https://www.cap.org/laboratory-quality-solutions/accreditation/accreditation-checklists/
  4. UK Health Security Agency. Diagnosis of urinary tract infections: quick reference tools for primary care. Updated July 7, 2025. Accessed September 27, 2026. https://www.gov.uk/government/publications/urinary-tract-infection-diagnosis/diagnosis-of-urinary-tract-infections-quick-reference-tools-for-primary-care
  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 Section XI, Urinary Tract Infections. Full text

Watch one

Read each decision and its explanation.

An outpatient urine arrives at the urinalysis bench at 12:20. The label says it was collected at 07:40, and the cup is at room temperature.

What do these results describe?

TestResultReference intervalFlag
pH8.5 High4.5–8.04.5–8.0High
NitritePositiveNegativeNegative
Leukocyte esteraseSmallNegativeNegative
GlucoseNegativeNegativeNegative
WBC0–2 /hpf0–5 /hpf0–5
BacteriaManyNone seenNone seen

Specimen: Not measured on urine. Random urine, collected 07:40, received 12:20 unrefrigerated

  1. Check the collection time first: 4 hours 40 minutes at room temperature, well past the 2-hour limit for unpreserved urine.

    Time and temperature determine whether the urine still matches what the patient passed.

  2. Read the pH: 8.5 is above the usual range for fresh urine and fits bacterial growth after collection.

    Bacteria growing in the cup make ammonia from urea, which raises the pH.

  3. Read the nitrite with the bacteria: many bacteria and a positive nitrite can both come from hours of growth in the cup.

    Nitrite keeps forming while bacteria remain in contact with the urine's nitrate.

  4. Compare the leukocyte esterase with the count: a positive pad with 0–2 WBC/hpf fits white cells that lysed in alkaline urine.

    The esterase pad reacts with enzyme from lysed white cells that microscopy can no longer count.

  5. Conclude: the pattern reflects the delay, so request a fresh specimen and record the late, unrefrigerated arrival as the reason.

    Retesting the same urine only repeats what the storage did.

The results show deterioration during 4 hours 40 minutes at room temperature. None of them can be reported as the patient's urine, and a fresh specimen is needed.

Practice this skill

Your turn

Problem 1 of 3 · Hints available

Bacteria grow from a pediatric bag urine culture. What should happen next?

Correct. Perineal flora frequently contaminate bag specimens and can grow from outside the urinary tract, so diagnostic culture needs urine collected by catheterization or suprapubic aspiration.

Incorrect. Perineal flora can grow to high counts in a bag specimen, so bag growth cannot establish a urinary tract infection at any colony count.

Incorrect. A second bag specimen has the same risk of perineal contamination. Diagnostic culture needs catheterized or suprapubic urine.

Hint
  1. Consider what the bag is in contact with while it collects.
  2. Consider which collections take urine directly from the bladder.

Review Routine collections

Problem 2 of 3 · Hints available

A fixed-dose boric-acid urine culture tube is substantially underfilled. Why can this affect culture recovery?

Correct. The tube holds a fixed boric-acid dose sized for its fill line, so less urine raises the concentration enough to inhibit organisms and produce a falsely low or negative culture.

Incorrect. The number of organisms per milliliter does not depend on how much urine enters the tube. The problem is the higher preservative concentration.

Incorrect. Boric acid is meant to keep counts stable. In an underfilled tube its excess concentration inhibits organisms and lowers recovery.

Hint
  1. The tube contains the same amount of boric acid regardless of how much urine is added.
  2. Consider the effect of less urine on the preservative's concentration.

Review Refrigeration and preservatives

Problem 3 of 3 · On your own

An unpreserved urine sat for 5 hours on a counter under room lights before testing. Which result is most likely to read falsely low?

Bacteria keep converting urea to ammonia during the delay, so the pH rises.

Bacteria keep reducing nitrate in the cup, so nitrite tends to rise with time.

The pads measure the urine as it is now. After 5 hours, that urine no longer matches what the patient passed.

Interpreted storage changes as the original specimen state

After hours at room temperature, bacteria raise pH and nitrite, cells and casts lyse, glucose falls, and bilirubin fades in light. Reporting results from such a specimen gives falsely alkaline, nitrite-positive, cell-poor findings. Request a fresh collection.

Light oxidizes bilirubin and the delay adds to the loss, so the pad can read low or negative.

Review Changes during storage

Use it

Read the case evidence, then make each decision. The step is complete without it.

  • Dana Reade, 17, had protein on a sports physical dipstick.
  • Orders: routine urinalysis, urine culture, and a urine protein check on a first morning specimen for orthostatic proteinuria.
  • One sterile cup arrives at 16:05, labeled on the body: midstream clean-catch, collected 15:20.
  • The cup stayed at room temperature.
  • Urinalysis procedure: test unpreserved urine within 2 hours of collection. Recollect if it sat longer at room temperature.
  • Culture procedure: process within 30 minutes, or refrigerate or preserve the urine. Document a longer room-temperature delay and let microbiology decide whether to accept it.
  • Protein procedure: use the first void after overnight recumbency.
Decision 1 of 3

What do you do with the urinalysis and the culture?

A midstream clean-catch in a sterile cup is a standard culture specimen. The 45 minutes at room temperature is what microbiology needs to review.

The cup is 45 minutes old, inside the 2-hour urinalysis limit. The culture needed processing within 30 minutes or refrigeration, so microbiology decides whether to accept it.

The 2-hour limit is for urinalysis. Culture needs processing within 30 minutes or refrigeration, so this 45-minute delay goes to microbiology.

The 30-minute limit is for culture, and a late culture goes to microbiology for review. Urinalysis has 2 hours, so it can go ahead.

Review Acceptability

Decision 2 of 3

What do you do about the orthostatic protein check?

A 24-hour collection mixes upright and recumbent urine, so it cannot separate the two.

This void follows a day of upright activity, when orthostatic protein appears. It cannot show whether protein clears during recumbency.

Assumed one urine specimen suits every test

A random void cannot show 24-hour excretion, a later void cannot replace the first morning void in an orthostatic protein check, and a bag specimen cannot support a diagnostic culture. The wrong collection gives a valid-looking result that does not measure what was ordered.

That void collects urine formed while recumbent overnight, which is the specimen the check requires.

Review Routine collections

Decision 3 of 3

The urinalysis is set aside by mistake and found at 18:50, still at room temperature. What do you do?

At 3 hours 30 minutes unrefrigerated, pH, nitrite, glucose and cell counts may describe the storage. A fresh specimen gives results that describe Dana's urine.

A comment does not show which results changed or by how much.

Refrigeration slows further change. It cannot undo the changes that happened during the delay.

Past the 2-hour limit, the results can show bacterial growth and cell lysis that happened in the cup.

Interpreted storage changes as the original specimen state

After hours at room temperature, bacteria raise pH and nitrite, cells and casts lyse, glucose falls, and bilirubin fades in light. Reporting results from such a specimen gives falsely alkaline, nitrite-positive, cell-poor findings. Request a fresh collection.

Review Changes during storage

Each order follows its own procedure. On arrival the urinalysis could be tested, and the culture delay went to microbiology. The protein check needed the first morning void. Once the urinalysis sat past 2 hours at room temperature, it needed a new specimen.

For reference

Sources checked