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What is being tested?

Fungi are microorganisms that exist in nature as single-celled yeasts or as multi-cellular moulds. There are more than 50,000 species of fungi in the environment, but less than 200 species are associated with human disease. Of these, only about 20 to 25 species are common causes of infection.

Fungal infections represent the invasion of tissues by one or more species of fungi and range from superficial skin infections to serious deep tissue, blood, lung or systemic diseases. Superficial fungal infections are very common. They may cause nail infections or itchy red scaly skin infections such as those commonly known as tinea, including athlete’s foot, jock itch, and ringworm. Other fungi cause yeast infections, which may present with white patches in the mouth (oral thrush) or vaginal itching and discharge (vaginal thrush). According to the US Centre for Disease Control and Prevention (CDC), almost 75% of women will have at least one yeast infection in their lifetime.

Much less commonly, some fungi may spread from their original location to penetrate to deeper tissues or may cause serious lung infections, septicaemia, or systemic infections that can affect any organ in the body. Fungal lung infections typically start with the accidental inhalation of microscopic fungal spores. Serious lung or systemic fungal infection is rare in healthy people with normal immune systems. However, people that are immunocompromised, such as those with advanced HIV or AIDS, those who have had an organ transplant, and those with an underlying condition such as diabetes or lung disease are at an increased risk of having a severe fungal infection, a systemic infection, and/or recurrent infections. There are a few fungi which may cause lung or systemic infection in healthy people but these are uncommon in Australia.

Fungal tests are used to detect and identify fungi in order to diagnose infections and help guide their treatment. Fungal testing typically includes a microscopic examination of the sample on a slide, sometimes using a preparation or stain to aid in detection of fungal elements. This may be sufficient to determine that the infection is due to a fungus and, with superficial infections, no more tests may be required. However, in cases of persistent, deep, or systemic infections when a more definitive diagnosis is needed, it may be followed by additional tests such as culture and susceptibility testing, antigen, and/or antibody tests, or molecular tests, such as PCR.

How is it used?

Fungal tests are used to help detect and diagnose a fungal infection, to help guide treatment, and/or sometimes to monitor the effectiveness of treatment. For many superficial skin and yeast infections, a clinical examination of the patient and microscopic examination of the sample may be sufficient to determine that a fungal infection is present. The specific organism is not always identified. The doctor has several topical and oral antifungal treatment options and bases their choice(s) on practice guidelines and their experience.

Fungal cultures are used to identify the specific fungi present in persistent fungal infections and in those that penetrate into deeper tissues, affect the lungs, or cause systemic infections. Many fungi are slow-growing. The nutrient media used to recover them typically inhibits bacterial growth and must support fungal growth for several weeks. Susceptibility testing performed on fungi isolated from a culture is used to determine which antifungal drug is best to use for treatment.

Blood tests for fungal antigens, antibodies or molecular tests may be used to determine if a patient has, or recently had, a specific fungal infection. They are more rapid than fungal cultures but only test for a few specific fungal species which cause systemic infections, so the doctor has to know what fungal organism to test for. 

When is it requested?

Fungal tests are ordered whenever a doctor suspects that a patient may have a fungal infection. They may also be ordered after or periodically during treatment to evaluate its effectiveness. In some patients, fungal tests may be ordered periodically to monitor for infection recurrence. Many signs and symptoms of fungal infections are similar to those caused by bacteria and/or viruses, and fungal tests are often ordered when it is not clear what is causing the condition.

For superficial infections, tests may be ordered when symptoms involving skin, nails, or mucous membranes appear, for example:

  • Itchy, red, scaly areas of skin
  • Nails that are thickened, brittle, and/or deformed
  • White patches in the mouth (thrush)
  • Vaginal itching and thick white or creamy discharge (yeast infection)

Deep and systemic fungal infections may cause a variety of symptoms depending on the part of the body that is affected. Some examples include:

  • Lung infections may produce flu-like symptoms such as coughing, fever, muscle aches, headaches, and rashes.
  • Blood infections (septicaemia) may cause chills, fever, nausea, rapid heartbeat
  • Central nervous system (CNS) infections (meningitis) may cause severe persistent headache, stiff neck, and sensitivity to light.

What does the result mean?

Superficial Infections

Many superficial fungal infections are diagnosed based on a physical examination. In addition to general symptoms, many skin infections have characteristic signs (such as the appearance of infected nails) and typical locations on the body (such as athlete’s foot between the toes). A clinical evaluation cannot, however, definitively tell the doctor which microorganism is causing a fungal infection. A few laboratory tests may be useful in detecting and confirming a fungal infection and may help guide treatment. These may include:

KOH prep (potassium hydroxide solution)Skin scrapings, hair or nail clippings, tissue, vaginal swab, body fluids, sputumDissolves non-fungal elements in a sample. Reveals yeast cells and fungal hyphae (branching filaments) on a microscope slide.Primary screening tool. Detects fungi but does not tell what specific fungus is presentRapid
Calcofluor white stainSkin scrapings, hair or nail clippings, vaginal swab, body fluids, sputumStain binds to fungal elements in a sample and fluoresces under ultraviolet light. Allows visualisation on microscope slide. More sensitive means of visualising fungi.Detects fungi but does not tell what specific fungus is present.Rapid
Fungal CultureVaginal swabA sample is inoculated onto or into nutrient media and incubated to grow any fungi present in sample.Primary tool to diagnose a fungal infection. Grows fungi for identification tests and subsequent susceptibility testing.Weeks


Deep and Systemic Infections

When a more definitive diagnosis is needed, as in cases of persistent, deep, or systemic infections, more extensive testing may be required to identify which fungus is causing the infection and how it may best be treated. This usually involves a combination of the tests mentioned above plus the following tests:

Fungal cultureBody fluids, tissue, vaginal swab, sputum, bloodA sample is inoculated onto or into nutrient media and incubated to grow any fungi present in the samplePrimary tool to diagnose a fungal infection. Grows fungi for identification tests and subsequent susceptibility testingDays to weeks
Susceptibility testingSample of fungus isolated in cultureFollow-up to fungal culture. When a pathogenic fungus has been identified, susceptibility is sometimes ordered to determine the most effective antifungal agent(s) to use.Guide treatmentDays to weeks after culture
Antigen testingBlood, CSF, body fluidsDetects proteins associated with a specific fungus. This type of test available for a small variety of fungi.Diagnose infection by specific fungus (e.g. CryptococcusDay(s)
Antibody testingBlood, CSF, body fluidsDetects immune response to a specific fungus. Diagnose current or recent infection by specific fungus; monitor treatmentDay(s) to weeks
Molecular tests for DNABlood, CSF, tissue or sample of fungus isolated in cultureDetects genetic material of a specific fungus.Specific tests for some fungi (e.g. Aspergillus) others tests for multiple fungi (panfungal PCR); not yet widely availableDays to weeks


If fungal elements are identified in a KOH prep or Calcofluor white stain, then a fungus is present in the sample and may be causing the symptoms a patient is experiencing or be present as a harmless coloniser of the skin. The presence of multiple organisms in a fungal culture may indicate multiple pathogens or a mixture of pathogens and normal flora. If there is only normal flora present in the culture, then the infection may be due to an opportunistic fungus (part of the normal flora), the pathogen may have been missed in the sample, or the condition may be due to another cause.

If an antigen test is positive, then it is likely that the fungus identified is the cause of the person’s infection. A positive antibody test result in a single serum sample may indicate exposure to a specific fungus, but it may not indicate when the exposure occurred. Rising levels of antibodies in two serum samples, measured as acute and convalescent tests, can indicate an active or recent fungal infection. Some infected patients with compromised immune systems may have lower than expected antibody levels.

If there are no fungi recovered in the sample, then the patient may not have a fungal infection or the pathogen was not successfully recovered with the sample and test.

Is there anything else I should know?

Fungal infections must frequently be distinguished from infections due to other microorganisms, such as bacteria. In some cases, an infection may have both bacteria and fungi present. Tests that may be used to identify or rule out other causes include:

  • Gram stain – A rapid test performed to microscopically detect bacteria and/or fungi in a sample.
  • Bacterial culture – Used to rule out a bacterial infection or determine if concurrent bacterial infection exists.
  • Acid fast bacilli culture – Ordered when a mycobacterial infection such as tuberculosis is suspected.
  • Blood culture – Ordered when septicaemia is suspected.

Fungi thrive in moist environments, such as public swimming pool and gym lockers, inside sweaty shoes, constrictive clothing, and in skin folds. Fungal skin infections can be minimised by wearing thongs or sandals to limit direct exposure, by changing socks frequently, drying out shoes, and keeping moist areas of the body clean and dry.

Common questions

  • If I have a persistent cough and fever, why would my doctor ask me where I have been travelling and what activities I have been doing?

Some fungi are found in distinct geographical regions, such in the southwestern and midwestern United States of America. Others are associated with particular activities or exposures: for example, if you have been around excavation or spelunking in caves, you may have been exposed to fungal spores which can cause histoplasmosis. Another fungus which can affect healthy people, called Cryptococcus gattii, is often found near River Red Gum trees. This information is important, even if travel or exposure was not recent. Lung infections caused by some fungi may emerge months to even years after exposure. 

  • If my doctor thinks I have a fungal infection, why am I being tested for tuberculosis?

Many of the signs and symptoms associated with fungal lung infections could also be due to a tuberculosis infection. Generally, a doctor would order tuberculosis testing (such as an Acid fast bacilli culture) to rule out a mycobacterial infection as the cause of your symptoms. The organisms that cause both conditions tend to be slow-growing – both in the body and in the laboratory.

  • Why would my doctor take multiple kinds of samples?

Multiple samples may be taken to evaluate how far into the body an infection has spread and sometimes to increase the likelihood that the fungus will be recovered.

  • Will my fungal infection eventually resolve itself without treatment?

Some may, but most persist without treatment. Lung and systemic infections may grow progressively worse and cause permanent tissue and organ damage even when symptoms are not severe. Some deep infections are almost uniformly fatal without treatment. Superficial infections such as tinea rarely cause serious disease and may even resolve on their own but some can be troublesome and uncomfortable for a long time without treatment. Medications or creams can often hasten recovery.

  • Is it really necessary to continue treatment for a long period of time?

Yes. Even if you start feeling better in a short period of time, you should follow your doctor’s recommendations. While yeast infections may resolve within a few days to weeks, some fungal infections may require months or even years of consistent treatment.

Last Updated: Thursday, 1st June 2023

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