A cerebrospinal fluid (CSF) smear is part of a series of laboratory tests performed on samples of your CSF. A CSF smear is often combined with a CSF Gram stain to diagnose certain infectious diseases of your central nervous system. These diseases include meningitis and encephalitis. Such diseases are caused by viruses, fungi, bacteria, or other pathogens and result in inflammation of your central nervous system.

CSF is a clear liquid that cushions, nurtures, and surrounds your brain and spinal cord. It delivers nutrients and carries away waste. It’s continually produced by the choroid plexus in your brain and absorbed into your blood stream. Your body completely replaces its CSF every few hours.

Obtaining a spinal fluid sample is difficult. However, testing CSF is one of the best ways to correctly diagnose specific types of infections of your central nervous system because CSF is in direct contact with your brain and spine.

The most common method of collecting CSF is a lumbar puncture, which is sometimes called a spinal tap.

A CSF smear is used to analyze the color of your spinal fluid, as well as the number and shape of cells it contains. Your doctor will order this test to check for signs of infection. A CSF Gram stain looks for microorganisms. It’s ordered when your doctor suspects you have meningitis or encephalitis caused by bacteria or fungi.

Meningitis is an inflammation of the membranes surrounding your spinal cord and brain. It progresses quickly and can be life-threatening in some cases. You should seek medical attention if you experience:

  • a sudden high fever
  • a severe headache
  • an extreme sensitivity to light
  • a stiff neck

Bacterial encephalitis causes inflammation of the brain. The symptoms of it can range from mild flu-like symptoms to more severe symptoms. They can include:

  • drowsiness
  • confusion
  • vomiting
  • a severe headache
  • a sudden fever
  • seizures

Cases of bacterial and fungal meningitis are less common than viral meningitis, but people who have trouble fighting infections are more likely to get them.

A lumbar puncture requires a signed release stating that you understand the risks of the procedure.

Be sure to tell your doctor if you take any blood-thinning medications, such as warfarin (Coumadin) or aspirin. You may need to stop taking them for several days before the procedure.

You’ll be asked to empty your bowels and bladder before the procedure.

How CSF Samples Are Taken

Lumbar puncture usually takes less than 30 minutes. A doctor who’s trained to safely collect CSF performs it. CSF is usually withdrawn from your lower back area. It’s very important to remain completely still during the procedure to avoid incorrect needle placement or trauma to your spine. During the procedure the following will occur:

  1. You’ll either be seated with your spine curled forward or you’ll lie on your side with your spine curved and your knees drawn up to your chest. Curving your spine allows your doctor to find ample space to insert a thin spinal needle between the vertebrae, or bones, in your lower back. Sometimes fluoroscopy, a type of X-ray, is used to guide the needle safely between your vertebrae.
  2. When you’re in position, a healthcare provider will clean your back with a sterile solution, such as iodine. A sterile area will be maintained throughout the procedure to reduce your risk of infection.
  3. They’ll apply numbing cream to your skin.
  4. Then, they’ll inject the site with an anesthetic, or pain-killing, solution.
  5. When the site is numb, your doctor will insert the spinal needle.
  6. Once the needle is in, your CSF pressure will usually be measured using a manometer, or pressure gauge. This reading is called your opening pressure. High CSF pressure can be a sign of certain conditions, including meningitis, a tumor, or an intracranial hemorrhage, which is bleeding that occurs in the brain.
  7. Your CSF pressure may also be measured at the end of the procedure. This reading is called your closing pressure.
  8. The doctor will also take CSF samples up through the needle and into an attached syringe. Several vials of fluid may be taken.
  9. When fluid collection is complete, your doctor will take the needle out of your back. The puncture site will be cleaned again with sterile solution, and a bandage will be applied.

You must remain lying down for about one hour to avoid a headache, which is a common side effect of the procedure.

If you have a back deformity, an infection, or a possible brain herniation, your doctor may need to use more invasive CSF collection methods. A brain herniation occurs when structures in your brain have shifted out of place.

More invasive collection methods usually require hospitalization. In a ventricular puncture, your doctor drills a hole into your skull and inserts a needle directly into one of the ventricles of your brain. In a cisternal puncture, your doctor inserts a needle below the base of your skull.

How CSF Samples Are Analyzed

When doing a CSF smear, a laboratory technician spreads or smears a small amount of your CSF fluid on a glass slide and looks at it under the microscope. Infection can make it cloudy instead of clear. The appearance of the fluid and the presence of any abnormalities will help your doctor make a diagnosis.

With a CSF Gram stain, a lab technician adds special dyes, or stains, and other solutions to the CSF smear to help identify microorganisms. Certain types of bacteria and fungi are known to absorb the stains.

If there are no microorganisms found, it’s possible you don’t have an infection caused by bacteria or fungi. However, if you’re on antibiotics, bacteria may not be present in your CSF sample. Further tests will be needed to rule out a bacterial infection.

If microorganisms are found, it likely means that you have one of the following diseases of the central nervous system:

  • meningitis
  • encephalitis
  • tuberculosis, which is a bacterial infection that usually starts in your lungs but may spread to your spinal cord

Other types of bacterial and fungal infections are also possible.

Primary risks associated with lumbar puncture include:

  • bleeding from the puncture site into your spinal fluid, which is known as a traumatic tap
  • discomfort during and after the procedure
  • an allergic reaction to the anesthetic
  • an infection at your puncture site
  • a headache after the test
  • damage to your spinal cord nerves, which can occur if you move during the procedure

Your risk of bleeding is higher if you take blood thinners.

You face serious additional risks if you have a brain mass, such as a tumor, that’s putting pressure on your brain stem. An abscess, or a pocket of pus surrounded by inflamed tissue, can also put pressure on your brain stem. In these cases, lumbar puncture can cause brain herniation. Brain herniation results in high intracranial pressure, which can eventually cut off the supply of blood to your brain. This can result in brain damage or even death. Lumbar puncture won’t be performed if a brain mass is suspected.

Cisternal and ventricular puncture have additional risks. They include:

  • damage to the spinal cord
  • damage to the brain
  • bleeding within the brain
  • disturbance of the blood-brain barrier in your skull

Lumbar puncture is extremely dangerous for people who have thrombocytopenia, which is a low platelet count, or other blood clotting problems.

Bacterial Meningitis

Bacterial meningitis is a medical emergency. Early treatment can help prevent serious illness and death if you have meningitis. However, this infection is hard to diagnose because its symptoms are similar to viral meningitis, a less life-threatening illness.

Prompt treatment is essential. Your doctor may begin broad-spectrum antibiotics while conducting additional tests to find the exact cause of your infection. These are a type of medication used to treat a variety of bacteria types. Bacterial meningitis vaccines can also prevent some types of the infection. Students living in college dorms or common housing should consider getting the vaccine.


In mild cases of encephalitis, you may get better with bed rest, forced fluids, and over-the-counter pain and fever medications. “Forced fluids” means drinking more than usual to ensure hydration. For severe cases of encephalitis, hospitalization is usually needed.

Cases of encephalitis are uncommon in the United States.