Fungal diagnostics update: faster tests, better identification, and the challenge of making results clinically useful

Audience: patients, carers, non-specialist clinicians and laboratory colleagues interested in fungal disease diagnostics.

Last reviewed: 18 May 2026

Key points

• Several recent papers show that fungal diagnostics are becoming more advanced, but the main challenge is often not the technology itself — it is how to interpret and implement the tests safely.
• For fungal infection in tissue samples, molecular tests can help identify fungi when microscopy or culture are not enough, but formalin-fixed paraffin-embedded tissue can be difficult to analyse because fungal DNA may be damaged or present in very small amounts.
• Surveys of diagnostic capacity suggest that access to specialist fungal testing remains uneven, which may contribute to delayed diagnosis.
• Biomarker tests such as beta-D-glucan can support diagnosis of invasive fungal disease, but results are especially difficult to interpret in critically ill patients.
• Whole genome sequencing is becoming increasingly important for investigating Candida auris outbreaks and understanding transmission.
• Cryptococcal antigen lateral flow tests remain one of the clearest examples of a rapid fungal diagnostic test with strong real-world value, particularly for cryptococcal meningitis and advanced HIV care.

Contents

• Overview
• Fungal testing in tissue samples
• Diagnostic capacity and access to specialist testing
• Candida biomarkers and beta-D-glucan
• Whole genome sequencing for Candida auris
• Cryptococcal antigen lateral flow testing
• Overall message
• Common questions
• When to seek medical advice
• References

Overview

Fungal infections can be difficult to diagnose. Many fungi grow slowly in culture, some infections occur deep inside the body, and symptoms often overlap with bacterial infection, cancer, inflammation, or other lung conditions. This is especially important in people who are immunocompromised, critically ill, or living with chronic lung disease.

A group of recent fungal diagnostics papers highlights a clear direction of travel: laboratories are moving beyond traditional microscopy and culture alone. Newer tools include molecular testing, sequencing, biomarkers, rapid lateral flow tests and genomic surveillance. These methods can provide faster or more precise answers, but they also introduce new questions: which test is best, how reliable is the result, and how should clinicians act on it?

The most important message is that no single fungal test solves every problem. Good fungal diagnosis usually depends on combining the right sample, the right test, expert interpretation, and the clinical picture.

1. Fungal testing in tissue samples: useful, but technically difficult

Paper: FFPE fungal diagnostics comparison
PMID: 42133463
DOI: 10.1093/mmy/myag049

One recent paper compares molecular approaches for detecting fungi in formalin-fixed paraffin-embedded tissue. These are tissue samples that have been preserved for pathology. They are extremely valuable because they may contain visible fungal elements, but they can also be hard to analyse because the preservation process can damage DNA.

Traditional histology can show that fungal elements are present, but it often cannot identify the exact species. This matters because different fungi may require different antifungal treatment, and some fungi have predictable resistance patterns.

Molecular methods can help. These may include:

• Internal transcribed spacer sequencing, often called ITS sequencing, which targets a fungal DNA region commonly used for fungal identification.
• Droplet digital polymerase chain reaction, or ddPCR, which can be very sensitive when looking for a specific fungal target.
• Metagenomic next-generation sequencing, or mNGS, which attempts to detect genetic material from many possible organisms in a sample.

Each approach has strengths and weaknesses. ITS sequencing is more established for fungal identification and can often help with genus-level or species-level identification. ddPCR may be highly sensitive, but it is usually targeted: the laboratory needs to know what it is looking for. mNGS is attractive because it is broad and does not require the same level of pre-selection, but it can be affected by contamination, large amounts of human DNA, low fungal burden, and differences in bioinformatics pipelines.

Practical interpretation: for preserved tissue samples, the field does not yet appear to have a single perfect method. ITS sequencing remains an important and relatively established approach for species-level fungal identification. ddPCR may be useful as a sensitive targeted test. mNGS is promising, especially when the diagnosis is uncertain, but it still needs careful validation, quality control and expert interpretation before it can be treated as a routine answer in every setting.

2. Diagnostic capacity: access to specialist fungal testing remains uneven

Paper: French fungal diagnostics capacity survey
PMID: 42133464
DOI: 10.1093/mmy/myag050

A second paper looks at fungal diagnostics capacity in France. Although this is a national survey, the issues are relevant internationally. Fungal diagnostic capacity is often unevenly distributed. Some hospitals and laboratories have access to specialist fungal tests and expert mycology support, while others may rely on sending samples away or may not have access to the full range of tests.

This matters because delayed diagnosis is a major problem in fungal disease. Invasive fungal infections can progress quickly, and chronic fungal infections may be missed for months or years if clinicians do not suspect them or if appropriate tests are unavailable.

Important diagnostic capacity gaps may include:

• limited access to fungal polymerase chain reaction testing;
• limited availability of fungal biomarkers such as galactomannan or beta-D-glucan;
• delays in fungal culture and species identification;
• limited antifungal susceptibility testing;
• lack of access to molecular identification or sequencing;
• limited specialist interpretation by experienced medical mycology teams.

The emerging model is not simply “everything local” or “everything centralised”. A more realistic model is a hub-and-spoke approach. Local hospitals need access to rapid tests that can guide urgent care. Specialist centres and reference laboratories are still needed for complex identification, antifungal resistance testing, outbreak investigation, rare fungi, sequencing and expert advice.

Practical interpretation: better fungal diagnostics are not only about inventing new tests. They also require investment in laboratory networks, training, sample pathways, referral routes and expert interpretation.

3. Candida biomarkers: useful, but cutoffs may not fit every patient group

Paper: CandiSep biomarker trial
PMID: 42023876
DOI: 10.1128/jcm.01500-25

The CandiSep biomarker trial focuses on invasive candidiasis and biomarker testing. Invasive candidiasis is a serious infection caused by Candida species entering the bloodstream or deep tissues. It is particularly important in critically ill patients, including those in intensive care.

One widely used fungal biomarker is beta-D-glucan. This is a component of the cell wall of many fungi, including Candida. A positive result can support the possibility of invasive fungal infection, but it is not specific to Candida and it is not always straightforward to interpret.

In intensive care patients, beta-D-glucan can be especially complicated. Results may be affected by many factors, including:

• major surgery;
• renal replacement therapy;
• some antibiotics or medical products;
• blood products;
• severe bacterial sepsis;
• gut barrier damage;
• colonisation with Candida without invasive disease;
• previous or current antifungal treatment.

This means beta-D-glucan is often more useful as part of a diagnostic pathway than as a stand-alone yes-or-no test. Repeated negative results may help reduce suspicion in some settings, but a positive result usually needs to be interpreted alongside cultures, imaging, clinical risk factors, and the patient’s overall condition.

Practical interpretation: the field appears to be moving toward more careful, population-specific interpretation of fungal biomarkers. A single cutoff may not perform equally well in all patient groups. In intensive care, fungal biomarkers may need recalibration, repeated testing, or combination with clinical risk scores and other diagnostic methods.

4. Candida auris: whole genome sequencing is becoming central to outbreak investigation

Paper: Candida auris whole genome sequencing transmission study
PMID: 41879325
DOI: 10.1128/jcm.01348-25

Candida auris is an emerging fungal pathogen of major concern. It can cause outbreaks in healthcare settings, survive in the environment, spread between patients, and may be resistant to multiple antifungal drugs.

Whole genome sequencing, often abbreviated to WGS, allows laboratories to compare isolates in great genetic detail. This can help answer important outbreak questions:

• Are cases likely to be linked?
• Is there evidence of transmission within a ward, hospital or region?
• Are there multiple separate introductions?
• How does the local outbreak relate to national or international strains?

Sequencing can provide much more detail than routine species identification alone. However, interpretation still requires caution. Single nucleotide polymorphism thresholds, often called SNP thresholds, are not always universally standardised. A threshold that suggests transmission in one setting may not automatically apply in another.

Important limitations include:

• not all cases may have been sampled;
• transmission may occur through unsampled patients, staff, equipment or environments;
• different sequencing platforms and bioinformatics pipelines may produce slightly different results;
• within-host variation can complicate interpretation;
• genomic data must be interpreted alongside epidemiology and infection prevention information.

Practical interpretation: whole genome sequencing is becoming an essential tool for Candida auris outbreak investigation in specialist and reference laboratories. However, it should not be interpreted in isolation. The strongest approach combines genomic data with careful epidemiological investigation.

5. Cryptococcal antigen lateral flow testing: a strong example of rapid fungal diagnosis

Paper: Cryptococcal antigen lateral flow assay study
PMID: 42017896
DOI: 10.1128/jcm.01438-25

Cryptococcal disease is a serious fungal infection, especially in people with advanced HIV or other forms of immune suppression. Cryptococcal meningitis can be life-threatening, so rapid diagnosis is vital.

Cryptococcal antigen lateral flow assays are among the most successful examples of rapid fungal diagnostics. They detect cryptococcal antigen in samples such as serum, plasma, whole blood or cerebrospinal fluid. These tests can often provide results quickly and can be used in settings where access to complex laboratory infrastructure is limited.

Performance is generally strong, especially for diagnosis of cryptococcal meningitis and screening in people with advanced HIV. However, interpretation still depends on the clinical context. Screening an at-risk person is different from diagnosing meningitis in someone who is already unwell. Use in non-HIV immunocompromised patients may also require careful interpretation.

Practical interpretation: compared with many other fungal tests, cryptococcal antigen lateral flow testing is already relatively well established. It shows what rapid fungal diagnostics can achieve when a test is accurate, simple, affordable and connected to a clear treatment pathway.

Overall message: fungal diagnostics are improving, but pathways matter

These papers show a field moving in several directions at once. Some tests are becoming faster. Some are becoming more precise. Some are helping laboratories identify outbreaks. Others are improving access to diagnosis in settings where laboratory infrastructure is limited.

However, the same lesson appears repeatedly: a fungal diagnostic test is only as useful as the pathway around it.

Good fungal diagnostics require:

• the right sample taken at the right time;
• access to suitable laboratory tests;
• clear quality control;
• clinicians who understand when to request fungal tests;
• laboratory specialists who can interpret complex results;
• systems that allow urgent results to change patient care quickly.

The field seems to be moving toward combined diagnostic workflows. Local laboratories may provide rapid screening and first-line tests. Specialist and reference laboratories provide advanced molecular testing, sequencing, antifungal susceptibility testing, outbreak investigation and expert advice.

For patients, this is encouraging. Fungal infections have often been diagnosed late or missed altogether. Better diagnostics should mean earlier recognition, more targeted treatment, and improved monitoring. But it is also important not to overstate what any single test can do. Results must always be interpreted by clinicians in the context of the patient’s symptoms, scans, immune status, microbiology and overall health.

Common questions

Does a positive fungal test always mean active infection?

No. Some tests may detect colonisation, contamination, past exposure or non-invasive presence of fungi. The result must be interpreted alongside symptoms, imaging, immune status and other test results.

Does a negative fungal test rule out fungal disease?

Not always. Fungal disease can be patchy, samples may miss the infected area, and some tests are less sensitive in certain settings. A negative test may reduce suspicion, but it does not always exclude disease.

Why are fungal infections hard to diagnose?

Fungi may grow slowly, may be difficult to sample, and may cause symptoms that look similar to other conditions. Some patients also have complex underlying illness, which makes interpretation harder.

Why are specialist fungal laboratories important?

Specialist laboratories can provide advanced identification, antifungal susceptibility testing, molecular methods, genomic sequencing and expert interpretation. This is especially important for rare fungi, resistant infections, outbreaks and complex cases.

Are molecular tests replacing culture and microscopy?

No. Molecular tests are increasingly important, but culture, microscopy, histology, imaging, biomarkers and clinical assessment all remain valuable. The best approach is usually a combined diagnostic pathway.

When to seek medical advice

This article is for general education and should not be used to interpret individual test results without clinical support.

Patients should seek medical advice urgently if they have symptoms such as:

• worsening breathlessness;
• persistent fever or chills;
• coughing up blood;
• new confusion, severe headache or neck stiffness;
• rapid deterioration while immunocompromised;
• significant worsening after chemotherapy, transplant treatment or intensive care admission.

Anyone concerned about fungal infection should speak to their clinical team. Test results need to be interpreted in the full clinical context.

References

1. FFPE fungal diagnostics comparison. PMID: 42133463. DOI: 10.1093/mmy/myag049
2. French fungal diagnostics capacity survey. PMID: 42133464. DOI: 10.1093/mmy/myag050
3. CandiSep biomarker trial. PMID: 42023876. DOI: 10.1128/jcm.01500-25
4. Candida auris whole genome sequencing transmission study. PMID: 41879325. DOI: 10.1128/jcm.01348-25
5. Cryptococcal antigen lateral flow assay study. PMID: 42017896. DOI: 10.1128/jcm.01438-25