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Specimen collection: urine, stool, sputum and swabs

  • Procedure

A poorly taken specimen gives a false result: collect it at the right time, uncontaminated, correctly labelled and sent promptly.

Updated

What it is

The quality of a lab result starts at the bedside. Each specimen has its own technique: a midstream urine needs cleansing first and the first stream discarded; urine from a catheterized patient is taken from the sampling port; sputum must come from the lungs, not be saliva; stool follows the laboratory's instructions; and nasal or throat swabs touch the right area with the right swab. Cultures are taken, whenever possible, before antibiotics are started. Every container is labelled in front of the patient and travels in a sealed bag with the request on the outside.

Indications

  • Urine: urinalysis and urine culture when urinary infection is suspected.
  • Stool: occult blood, parasites or other tests per the order.
  • Sputum: culture, acid-fast bacilli testing or cytology.
  • Nasal, nasopharyngeal or oropharyngeal swabs: respiratory viruses or other tests.
  • A wound swab when new signs of infection appear and a culture is ordered.

Contraindications and precautions

  • Follow the laboratory's instructions for each test: container, transport medium, fasting, diet or medicines to stop.
  • Use standard precautions and, for sputum or respiratory swabs, the droplet or aerosol protection the protocol requires.
  • Nasopharyngeal swabs are taken by trained staff; children need help to keep still.
  • Use synthetic swabs with plastic or wire shafts; not calcium alginate or wooden shafts for molecular tests.
  • Avoid mouthwash or toothpaste before sputum: they alter the microorganisms in the sample.

Equipment

  • Sterile containers or transport tubes for each test, labelled.
  • Wipes or gauze for cleansing, gloves and a transport bag with an outside pocket for the request.
  • For catheterized patients: disinfectant and a sterile needle-free syringe.
  • Suitable synthetic swabs and transport medium for swabs.
  • Eye protection, a mask or respirator according to the risk.

Step by step (and why)

  1. Check the order, the test and its requirements, and identify the patient with two identifiers — it avoids wrong or useless specimens.
  2. Explain what will be collected and how; for sputum, how it differs from saliva — a patient who understands gives a better sample.
  3. Midstream urine: cleanse the genitals, first stream into the toilet, collect the middle — the first stream carries germs from the urethra.
  4. Catheterized patient: disinfect the port and aspirate with a sterile syringe — urine in the bag is contaminated.
  5. Sputum: several deep breaths and a deep cough; spit straight into the container without touching the inside — so it comes from the lungs.
  6. Nasopharyngeal swab: head back, swab parallel to the palate to resistance, rotate and withdraw — it reaches the site being tested.
  7. Oropharyngeal swab: rub tonsils and back of the throat without touching tongue or teeth — saliva and the mouth contaminate it.
  8. Close, label in front of the patient and send promptly in a sealed bag — an unlabelled or late specimen is rejected or misleads.
  9. Record the time, specimen type and what you observed — the lab and the team interpret the result better.

Complications

  • Specimen contamination, causing false positives and unnecessary treatment.
  • Too little sample, or saliva instead of sputum, which means repeating it.
  • Identification errors from labelling away from the patient.
  • Injury to the nasal cavity if the patient moves during the swab; children need help to keep still.
  • Staff exposure to droplets or aerosols without adequate protection.

Next step: when to call for help

  • If you cannot get an adequate sample (for example, the patient cannot expectorate), ask; other measures or suctioning may be needed.
  • Report a striking specimen appearance: bloody urine, bloody sputum or black stools.
  • If the specimen was contaminated, mislabelled or delayed, do not send it: report it and collect a new one per protocol.
  • Report if the patient had already received an antibiotic before a culture was taken, so it is considered when interpreting.

Test yourself

Think of the answer, then tap the question to see it.

Why is the first stream discarded in a midstream urine sample?

Because it carries germs from the urethra and skin; the middle stream better represents the urine in the bladder.

Where is urine taken from in a patient with an indwelling catheter?

From the sampling port, after disinfecting it, with a sterile syringe. Never from the bag, because that urine is contaminated.

How is sputum told apart from saliva?

Sputum is thick and opaque; saliva is clear, thin and watery. A saliva sample is no good for culture.

Which swabs are recommended for molecular respiratory tests?

Synthetic swabs with plastic or wire shafts. Calcium alginate swabs and wooden shafts are not used because they may inhibit the test.

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Connections

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Educational content for students; it does not replace your institution's protocols, supervised clinical training or a prescriber's order. Dose-calculation examples use made-up numbers: they are educational, not a clinical order.

Sources: Nursing Skills, 9.5: Sputum Specimen Collection (Open RN, Chippewa Valley Technical College (via LibreTexts), 2021); Nursing Skills, 11.5: Obtaining Urine Specimen for Culture (Open RN, Chippewa Valley Technical College (via LibreTexts), 2021); Clean catch urine sample (MedlinePlus, U.S. National Library of Medicine, 2024); Interim Guidelines for Collecting and Handling of Clinical Specimens for COVID-19 Testing (Centers for Disease Control and Prevention (CDC), 2024).

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Representative model, for educational purposes only.