Pathology tests can be performed on many different types of samples (also called specimens). Most commonly these are blood, urine, saliva, sputum, faeces, semen and other bodily fluids, as well as tissue.
 
Some tests can be performed on more than one type of sample. For example, glucose testing can be performed on  blood, urine and other samples. The sample used for testing is often determined by the purpose of the particular test. A blood glucose test is used to help diagnose diabetes and monitor blood glucose levels in diabetics while urine glucose is one of the substances tested when a urinalysis is performed, such as when a urinary tract infection or kidney disorder is suspected.
 
Sample collection usually takes place in your doctors’ rooms or in a testing laboratory collection centre where there are trained specimen collectors (phlebotomists). Samples can also be collected at hospitals and day clinics. Samples can even be taken for analysis during a surgical procedure.  Some samples are collected at home either self-collected or by domicillary staff. 
 
Most of the common tests can be collected without an appointment. However, some specialised tests involve complicated collection procedures and must be performed by someone who is specially trained or performed under a doctor’s supervision.
 
Check with your doctor and if you are uncertain, ask the pathology laboratory beforehand about their preferred process. If you are taking a child to have a sample collected, check that the collection centre is equipped to handle paediatric collections. For more information on helping children with sample collection see Tips to help children.
 
Once the sample is taken it will be sent to the testing laboratory. Sometimes it has to reach the lab within a certain time frame to ensure it is valid for testing. Some samples need to be transported under strict conditions to preserve their validity.
 
 

Last Review Date: September 1, 2018

Blood, swabs & bodily fluids

The following is general information on how samples are collected to help you understand what to expect. Specific instructions will be provided by your doctor.
 
Blood 

Blood samples can be collected from blood vessels (capillaries, veins, and sometimes arteries) by someone trained to do this (typically a phlebotomist, doctor or nurse). The sample is obtained by using a needle to draw off blood into special collection tubes. Different types of tubes can be used for different types of tests. Some blood samples can be obtained by a finger puncture that produces just a drop of blood, such as that used for glucose testing. For more information:  What to expect when having a blood test 

Sputum 

Sputum is formed in the lungs and lower airways. It is often used to investigate the cause of a respiratory tract (chest) infection.    Some doctors like you to give a sample at their medical practice under supervision, others are happy for you to collect yourself at home. You need to get a container from them or from your local pathology laboratory collection centre.
 
The best time to collect sputum is when you wake up in the morning. However, if you are coughing up sputum all day, you can collect it at any time.  You need to cough up sputum from as far down the lungs as you can.    It is important you don’t mistake saliva for sputum. Whereas, sputum is usually thick and opaque in consistency, saliva is clear and colourless. Examining saliva will not reveal the cause of a chest infection.
 
Usually, you will need to rinse out your mouth with water beforehand. (You must not use toothpaste or mouth wash.) Then you need to cough as vigorously as you can until you feel the sputum at the back of your throat. You spit this into the plastic container.   You need to deliver the sample as soon as you can. The sample is fine stored at room temperature but if you can’t deliver it in a couple of hours you need to keep it in the fridge. 

Saliva 

Typically, saliva is collected with a swab or if larger amounts are needed, it is expectorated into a container. In some situations a special collection device may be used. Directions will be given by your doctor or the pathology laboratory performing your tests. 

Stool 

You will usually be asked to collect this sample yourself when you go to the toilet.  It is important to prevent the sample from becoming contaminated by urine or from other material in the toilet bowl and to wash your hands well after handling the sample. Depending on the test, you may be instructed to collect the sample into a container, scoop a small portion into a vial, or smear a small amount on special test paper. 

Urine 

You will usually be asked to collect this sample yourself by urinating into a container or receptacle. It is important to make sure the sample is not contaminated by anything outside the urinary tract. For some tests, a first-void morning urine sample is required. This is when the urine is at its most concentrated. Other tests require a mid-stream urine sample – for example, when a test is being performed to look for infection. The first part of the urine can contain organisms.   This means collecting after a small amount of urine has been passed. For certain tests, 24-hour urine samples are collected at home and may need to be refrigerated. If urine is being collected for a drugs test you may be asked to provide it under supervision. This usually means the collector stands outside the toilet while you collect the sample. 

When a swab is required 

Many samples are collected by running a sterile swab over an affected area. Throat, nasal, vaginal, and superficial wound cultures are obtained in this way.   Often a trained health professional will take the swab or sometimes you may be asked to do it yourself.  Taking a swab can be uncomfortable, but it is generally quick, relatively painless and has no after-effects.

Typically, swabs are taken of open wounds and sores by brushing the swab over the area and gathering a sample of fluid or pus. Touching the open wound area may be temporarily painful since the wound is likely to be tender and sore. If a wound or infection is deep, however, a needle and syringe may be used to aspirate a sample of fluid or pus from the site.

Samples of fluids from the nose or throat are collected by running a swab over the area. People typically respond to swabbing of their throat with a momentary gag reflex. If the throat is sore, the sample collection, brief as it is, can be uncomfortable. Similarly, a nasal swab may be uncomfortable as the swab is inserted and reaches areas inside the nose that are typically never touched. If you are uncomfortable, discuss this with the person performing the collection. They are trained to take a sensitive approach to minimise discomfort.

Samples of vaginal secretions are obtained by running a cotton swab over the walls of the vagina. Endometrial tissue samples are obtained by inserting a thin, flexible, hollow tube into the uterus, during which a slight pinch or brief cramping might be felt. 

HPV or Pap smear 

The collection procedure for the HPV test and the Pap smear are the same. A tiny brush is used to collect cells to be sent to the lab for testing. Usually this is performed by your GP, specialist doctor or practice nurse. 

Semen 

Usually you will be asked to do this at home then to deliver it to the laboratory or a collection centre immediately or within a short time frame. Any delay may affect the sample and the test results will not be accurate. If this happens, you will need to give another semen sample and repeat the test.
 
You will be given a collection container by your doctor or testing laboratory. The test will measure the number and viability of sperm you have produced over a defined time period. Your laboratory will provide instructions about how to prepare. This will explain when you need to ejaculate in the days leading up to the test.  For example, you may be asked to ejaculate in the previous 3 – 7 days, but not in the previous 48 hours before you collect your semen sample. Check with your doctor or lab. 

Hydrogen and methane breath testing 

In this test you will be required to drink a small sample of carbohydrate mixed with water and then collect breath samples by exhaling into a bag. This is sent to the lab for analysis. There are strict conditions covering diet and medications in the preceding weeks and you may be asked to fast and then empty your bowels beforehand. It is important to follow your doctor’s instructions otherwise results of the test may be invalid and the procedure may need to be repeated. 

Helicobacter pylori breath test (urea breath test) 

This test examines your breath for detecting the presence of Helicobacter pylori bacteria in your stomach, which can cause gastritis or ulcers. The test requires you to swallow a small amount of urea (in a mildly radioactive form) with water. After a short waiting period you will be asked to blow into a balloon to collect your exhaled breath. The amount of radioactivity you will be exposed to is very small. There are strict conditions concerning diet and medications that may interfere with results and fasting immediately before the test. It is important to follow your doctor’s instructions otherwise results of the test may be invalid and the procedure may need to be repeated. 

Other samples 

  • Hair – rarely a hair sample can be required for nicotine/cotinine test, heavy metals testing, fungal tests, and  drugs of abuse)
  • Fingernail clippings or skin scrapes– for fungal tests.
  • Sweat – special collection for babies to screen for babies at risk of cystic fibrosis



 

Biopsies, needle aspirations, surgery, CSF & bone marrow

Biopsies and fine needle aspiration
 
Samples of tissue and fluid may be required for laboratory analysis that necessitate a small invasive procedure. These are usually performed by a medical practitioner in a day hospital or clinic. Tissue biopsies can be collected using procedures, such as:

  • Needle biopsy (fine needle aspiration) — A needle is inserted into the site and cells and/or fluid are withdrawn using a syringe. A slight pinch may be felt at the site of needle insertion. Usually no recovery time is required and slight discomfort may be experienced afterwards.
  • An excisional biopsy is a minor surgical procedure in which an incision is made and a portion or all of the tissue is cut from the site.
  • A closed biopsy is a procedure in which a small incision is made and an instrument is inserted to help guide the surgeon to the appropriate site to obtain the sample. These biopsies are usually performed in a hospital operating room. A local or general anaesthetic is used, depending on the procedure, so the patient remains comfortable. If a general anaesthetic is used, recovery may take one to several hours.
Cerebrospinal fluid (CSF) — A sample of cerebrospinal fluid is obtained by lumbar puncture, often called a spinal tap. It is a special but relatively routine procedure. IIf you need to have this it can be performed while you are lying on your side in a curled up fetal position or sometimes, in a sitting position. Your back will be cleaned with an antiseptic and a local anaesthetic is injected under the skin. A special needle is inserted through the skin, between two vertebrae, and into the spinal canal. The health practitioner collects a small amount of CSF in multiple sterile vials; the needle is withdrawn and a sterile dressing and pressure are applied to the puncture site. You will then be asked to lie quietly in a flat position, without lifting your head, for one or more hours to avoid a potential post-test spinal headache. The lumbar puncture procedure usually takes less than half an hour. Discomfort levels can vary greatly. The most common sensation is a feeling of pressure when the needle is introduced. Let your healthcare practitioner know if you experience a headache or any abnormal sensations, such as pain, numbness, or tingling in your legs, or pain at the puncture site.
 
Other body fluids such as synovial fluid, peritoneal fluid, pleural fluid, pericardial fluid and cyst fluid are collected using procedures similar to that used for CSF in that they require aspiration of a sample of the fluid through a needle into a collection vessel. These are generally more complex type of collections and often require some patient preparation, use of a local anaesthetic, and a resting period following sample collection. For details, see the descriptions for arthrocentesis, paracentesis, thoracentesis, and pericardiocentesis.
 
Bone marrow — The bone marrow aspiration and/or biopsy collects small samples of marrow and bone from the hip. In some instances, marrow collection may be collected from the breastbone (sternum).These procedures are performed under local anaesthesia and sometimes, under sedation. You will be asked to lie down on your stomach or side for the collection. The site is cleaned with an antiseptic and injected with a local anaesthetic. When the site has numbed, a needle is inserted through the skin and into the bone. For an aspiration, a syringe is attached to the needle and bone marrow fluid is aspirated. For a bone marrow biopsy, a special needle is used to collect a core (a cylindrical sample) of bone and marrow. Even though your skin has been numbed, it is possible to feel brief but uncomfortable pressure (pulling and/or pushing) sensations) during these procedures. After the needle has been withdrawn, a sterile bandage is placed over the site and pressure is applied. In some instances, the procedure may be repeated on the opposite hip (bilateral bone marrow), most often done as part of the initial diagnostic workup. It is important to lie quietly until blood pressure, heart rate, and temperature are back to normal, and then to keep the collection site dry and covered for about 48 hours.

Diagnostic tests in pregnancy

Diagnostic tests (karyotyping, FISH, microarrays) can be carried out during pregnancy to detect specific chromosomal abnormalities in an unborn baby.  Procedures are required to collect samples.
 
  • Chorionic villus sampling (CVS) collects a sample of cells, called ‘chorionic villi cells’ which are found in the placenta. Under ultrasound guidance a needle is inserted into the mother’s womb either through the abdomen or through the neck of the cervix. Small fragments of placental tissue are drawn into a syringe. The procedure is performed under local anaesthetic.  There can be some discomfort and there may be some cramps afterwards.
  • Amniocentesis takes amniotic fluid from the sac around the baby. Under ultrasound guidance, a needle is inserted into the lower abdomen and into the mother’s womb to extract a small amount of amniotic fluid. This contains cells shed from the baby. The procedure is performed under local anaesthetic.  There can be some discomfort and there may be some cramps afterwards.
  • Noninvasive Prenatal Testing (NIPT) is a newer test done at 10 weeks pregnancy where a blood sample is collected from the pregnant women.  The sample is analysed to detect the presence of cell-free DNA from the fetus and this DNA is used to assess the risk of common genetic disorders in the fetus.  NIPT has a high diagnostic accuracy for detecting Down syndrome and some other chromosomal abnormalities in the developing fetus.