Diagnosing Fungal Infection in Horses: A Veterinarian’s Guide to Specialized Laboratory Testing

Fungal diseases in horses include a range of conditions that can affect the skin, respiratory tract, eyes, and internal organs. While less common than bacterial or viral infections, fungal infections are often more insidious and challenging to diagnose.

Because clinical signs can be subtle or mimic other diseases, accurate diagnosis of fungal infections relies on clinical assessment supported by diagnostic testing. Diagnosis typically combines microscopic examination, culture, and molecular testing.

Direct microscopic examination of affected tissues can reveal fungal elements that confirm infection, while fungal culture allows for species identification and antifungal susceptibility testing. Molecular techniques, including polymerase chain reaction (PCR), provide rapid and sensitive confirmation, especially for organisms that are slow-growing or difficult to culture.

Timely and accurate identification of fungal pathogens is critical for guiding treatment and improving outcomes. Because antifungal therapy can be costly and prolonged, confirming the diagnosis before treatment ensures both efficacy and responsible antimicrobial use.

Read on to learn more about the process for diagnosing fungal infection in horses, the reasons why your veterinarian might recommend specialized testing, and how to interpret fungal test results.

Diagnosing Fungal Infections in Horses

Fungi are complex organisms found in the environment as yeasts, mushrooms, or molds. ^[1] They are a hardy class of organism due to their resilient cell wall, which can make treatment of fungal infections challenging.

They reproduce through budding (splitting into two organisms) or through producing fungal hyphae, long filamentous (string-like) structures that can invade deep into tissues. ^[1] These hyphae produce fruiting bodies or fungal spores that spread the fungus to new locations.

Horses are constantly exposed to fungi in their hay, bedding, pastures, and paddocks. Despite this, fungal diseases are considered rare in horses. ^[2]

Most fungal pathogens are opportunistic invaders, meaning they only affect horses with underlying disease or those who are immunocompromised ^[1]. Common scenarios that may be more likely to develop fungal infection include:

• Skin wounds
• Corneal abrasions or ulcerations
• Vulval anatomical abnormalities in broodmares, resulting in uterine infection
• Immunocompromise secondary to Cushing’s Disease (PPID)

Common Fungal Infections

Common equine fungal infections include: ^[3]

• Yeast infections, such as Candida or Malassezia species
• Dermatophytosis (ringworm, also known as girth itch)
• Pythiosis
• Phaeohyphomycosis
• Sporotrichosis
• Aspergillosis

Truly infectious fungi typically cause systemic (whole body) infections that are difficult to treat and may be life-threatening. Fortunately, systemic fungal infections are uncommon in horses.

Prompt diagnosis is key to treating these conditions and improving prognosis.

Potentially life-threatening equine fungal infections include: ^[3]

• Histoplasmosis
• Cryptococcosis
• Coccidioidomycosis
• Blastomycosis

Clinical Signs

Clinical signs of opportunistic fungal infections in horses depend on the location of the infection.

In some cases, no clinical signs are evident at all.

Possible signs of opportunistic fungal infections include:

• Signs of corneal ulcers: Tearing, squinting, corneal cloudiness, mucopurulent discharge, visible corneal defects, or excessive sensitivity to light
• Signs of skin wounds or infection: Crusting, hair loss, ulcerated or non-healing lesions, swelling, heat, discharge, or localized pain
• Signs of endometritis or placentitis: Vulvar discharge, premature udder development, abdominal discomfort, shortened gestation, or changes in fetal activity
• Signs of guttural pouch disease: Unilateral nasal discharge, difficulty swallowing, coughing, nosebleeds, head shaking, or abnormal respiratory noise

Clinical signs of systemic fungal infections in horses include: ^[3]

• Fever
• Cough
• Abnormal lung sounds or difficulty breathing
• Nasal discharge
• Loss of appetite
• Weight loss
• Enlarged lymph nodes
• Neurologic signs, such as seizures or uncoordinated movements

Fungal infection is also responsible for guttural pouch mycosis, a condition where Aspergillus fungi invade the large arteries running through the guttural pouches. If the fungi damage the artery walls significantly, they can cause profound nosebleeds that may lead to death. ^[1]

Sample Collection

If a veterinarian suspects a fungal infection, they will collect diagnostic samples from the affected area to test for the presence of fungal organisms. The type of sample collected depends on the location and nature of the infection.

Common samples for diagnosing fungal disease in horses are: ^[1]

• Tissue sample, such as biopsy or corneal scraping
• Hair samples
• Blood
• Fluid samples, such as uterine or respiratory fluid
• Respiratory swabs

When collecting samples, the veterinarian is careful to avoid contamination of the sample. Introducing fungal spores from the environment into the submitted sample may lead to a false positive, or identification of a fungus when there is no fungal infection present.

For this reason, veterinarians use aseptic techniques such as cleaning the area surrounding the collection site and using sterile equipment when taking samples for fungal testing. ^[1]

Appropriate handling of the sample is necessary to prevent bacterial overgrowth, which may kill off any fungus present in the sample. Most samples are transferred to a fungal growth medium shortly after collection or shipped to the diagnostic laboratory immediately. This ensures that any fungal organisms in the sample are preserved. ^[1]

Diagnostic Tests

There are several methods for diagnosing fungal infections from an equine sample. The most common methods are: ^[1]

• Microscopic examination
• Fungal culture
• Polymerase chain reaction
• Antigen testing
• Serology

Some laboratories may also offer antifungal susceptibility testing, which allows veterinarians to select the most effective antifungal for treating the fungus identified. ^[1]

Microscopic Examination

Diagnosticians can identify fungal organisms under the microscope, allowing them to characterize them by their shape and other characteristics. This can help narrow down a list of potential species causing the infection, allowing the veterinarian to choose appropriate antifungal therapies. ^[1]

Samples suitable for microscopic examination include: ^[1]

• Impression smears
• Aspirates
• Tissue biopsies
• Fluid sediments

The two main shapes of fungal organisms visible under the microscope are yeasts and hyphae. ^[1]

Yeasts appear as circular or budding shapes. Candida species are classic examples of yeast-forming fungi. Molds, such as Aspergillus, produce hyphae that form long filaments extending through the sample.

The size of the hyphae, branching angle, and appearance can help diagnosticians narrow down the species. Both yeasts and hyphae can be highlighted using special stains that bind to the fungal cell walls and improve their visibility. ^[1]

In addition to confirming the presence of fungal elements, microscopic examination of biopsy samples allows assessment of the surrounding tissue reaction.

The presence of inflammation or tissue death can support the diagnosis of a true infection rather than contamination. It can also determine the extent of tissue damage, which may help veterinarians determine a prognosis.

Fungal Culture

The diagnostic laboratory can grow the fungus on special growth media to help identify the species. Certain fungi grow best on particular growth media, allowing the diagnosticians to narrow down potential species. ^[1]

Based on the type of fungal growth, color changes, and other features, the laboratory can make a final diagnosis. ^[1] They can also take samples of the grown fungal organisms for analysis under the microscope or using polymerase chain reaction. ^[1]

Although fungal culture is considered the gold standard for diagnosis, it has several limitations. Many fungi grow slowly, sometimes requiring days to weeks before colonies are visible, which can delay treatment decisions.

Some fungi may fail to grow in culture, leading to false-negative results. Contamination from environmental spores is another challenge, particularly if samples are not collected or handled aseptically. For these reasons, culture results should always be interpreted in conjunction with microscopic examination and clinical findings.

Polymerase Chain Reaction

The polymerase chain reaction (PCR) is a laboratory technique used to rapidly multiply specific DNA sequences present in a sample. During this process, a primer, short DNA fragment designed to recognize a unique sequence from a particular fungal species, is added.

If the target fungal DNA is present, the primer binds to it, and the PCR process amplifies that region, producing millions of identical copies. The resulting amplified DNA can then be detected and used to confirm the presence of the organism.

PCR is one of the most common methods for diagnosing fungal infections. Since many diagnostic samples only contain a few fungal organisms, PCR is able to detect fungal infections in samples where fungal culture failed to grow organisms. ^[1]

The test method is also quick, allowing for results within days of sample submission, compared to weeks for fungal culture and identification.

Fungal infections commonly diagnosed through PCR include: ^[1]

• Aspergillosis
• Cryptococcosis
• Yeast infections
• Pythiosis

Antigen Detection

Antigen detection involves introducing a dyed antibody against a fungus into the sample. If the fungus is present, the antibody binds to the fungus, allowing the diagnosticians to identify the dyed antibodies under the microscope.

Antigen testing is available for: ^[1]

• Aspergillosis
• Cryptococcosis
• Candidiasis

Serology

Serologic testing identifies whether there are antibodies against the fungus in the horse’s bloodstream. The presence of antibodies indicates the horse was previously exposed to the fungus, which triggers its immune system to produce antibodies.

Although this type of testing is more common for viral and bacterial diseases, it can help identify fungal infections such as coccidioidomycosis and aspergillosis. ^[1]

Antifungal Susceptibility Testing

Antifungal susceptibility testing may be available at some laboratories. The procedure for susceptibility testing involves exposing the fungus cultured from a sample to increasing concentrations of antifungal drugs. ^[4]

By identifying which drugs are most likely to inhibit or kill the fungus, susceptibility testing helps veterinarians select the most effective treatment while minimizing unnecessary exposure to ineffective medications.

The fungal organisms grown from the sample are either suspended in a nutritious broth or transferred to a new growth medium. If using broth, the diagnosticians add increasing concentrations of antifungal medications and monitor for fungal growth.

The concentration where the fungus stops growing is considered the minimum inhibitory concentration, or the amount of drug necessary to prevent fungal growth. ^[4] Veterinarians can use the minimum inhibitory concentration to determine effective drug doses.

For susceptibility testing using growth media, the diagnosticians place a paper disk impregnated with antifungal medication directly onto the growth medium.

As the medication diffuses into the growth medium, it kills off fungal colonies. Diagnosticians measure the distance between the disk and the first successfully growing fungal colony to determine the effectiveness of the drug. ^[4]

This method does not produce a specific minimum inhibitory concentration, but can give veterinarians an indication of which antifungals are most effective.

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Interpreting Results

Interpreting fungal testing can be challenging, as horses are exposed to numerous fungal organisms daily. Many fungal organisms can be found on healthy skin, in the respiratory tract, or within the gastrointestinal system without causing disease. ^[1]

As a result, the presence of fungal elements in a sample does not always confirm an active infection. These organisms may produce a false positive result on testing, requiring careful assessment by the veterinarian to determine if they are truly causing an infection.

Veterinarians must assess whether the detected fungal organism is acting as a true pathogen or simply an incidental contaminant. Factors such as the location of the organism within tissues, the degree of associated inflammation, and the consistency of findings across multiple diagnostic modalities (i.e. microscopic examination, culture, or PCR) all help in determining clinical relevance.

For example, identification of fungal hyphae invading tissue on histopathology provides stronger evidence of infection than a positive culture result alone.

Additionally, very low numbers of fungal organisms can cause an infection that leads to clinical signs in the affected horse. This means the chances of collecting a fungal organism in the diagnostic sample are low, which may lead to a false negative.

This happens when there is a fungal infection present but a fungal organism is not present in the sample submitted for analysis.

In these cases, veterinarians with a strong suspicion of a fungal infection may prescribe antifungal medications even with a negative result. ^[1] They may also perform repeat sampling or change sampling methods to help improve the chances of a positive result.

 

Frequently Asked Questions

Here are some frequently asked questions about diagnosing fungal diseases in horses:

Summary

Fungal diseases in horses can cause conditions ranging from skin infections to serious, life-threatening diseases in horses.

• Common equine fungal infections include Aspergillosis, Candidiasis, Cryptococcosis, and dermatophytosis (ringworm)
• Clinical signs are often nonspecific and may resemble bacterial infections
• Diagnosis involves microscopic examination, fungal culture, and molecular testing such as PCR
• Proper sample collection and handling are critical to avoid contamination and false negatives
• Early detection enables prompt antifungal treatment and improves prognosis