Fungal Infections

Clinical diagnosis

Most fungal infections are not distinctive in their clinical features, although a few are (Table). The clinical features of each are described in each section for each fungal disease.

A video teaching retinal examinatiom of the eye by direct ophthalmoscopy is available here,  useful to assist in diagnosis, with kind permission of  Prof Liu ( Published in NEJM 2015) , with notes.

Highly distinctive fungal infections that may require confirmation by laboratory testing




Oral thrush

Candida albicans

May be fluconazole resistant, if previously treated

Seborrheic dermatitis and dandruff

Malassezia furfur

Highly distinctive clinical appearance



Diagnosis clearcut but different fungi involved



Appearance not always distinctive, especially if steroid cream used, and some fungi are un-responsive to terbinafine and acquired from infected pets.

Athlete’s foot 

Trichophyton rubrum or interdigitale

If limited to the toewebs, really distinctive, May be co-infected with bacteria.

Of the 5 groups of fungal infections, the most difficult to diagnose are the serious infections.  These same infections usually have no symptoms or non-specific features (ie mimicking a bacterial chest infection), and it only when the fungal disease worsens that testing is initiated. As many as 40% of fatal life-threatening fungal infections are not even considered before death, with testing or treatment given. Corticosteroids mask fever and symptoms and topical steroids mask rash features. 

Fungal infections that can be diagnosed with one test with or without imaging;


Key test


Vaginal thrush

Microscopy showing yeasts and hyphae or chromogenic 

Commonest misdiagnosis in bacterial vaginosis, but several others

Eosophageal candidiasis

Upper GI endoscopy or barium swallow

Endoscopy preferable, culture taken through scope confirms species and antifungal sensitivity

Candida bloodstream infection

Blood culture

Several species involved; not more than 75% sensitive and dependent on how much blood is cultured

Onychomycosis (nail infection)

Microscopy showing hyphae 

In toenail infection, the causative fungus important to determine therapy. Cultures desirable.

Tinea capitis  

Hair microscopy showing hyphae

The causative fungus important to optimise therapy. Cultures desirable.

Otitis externa

Microscopy or culture showing Aspergillus (usually A. niger)

Main differential diagnosis is bacterial infection, Pseudomonas especially

Allergic bronchopulmonary aspergillosis (video)

Serum IgE >1,000 KIU/L in context of asthma or cystic fibrosis

Specific fungal skin or IgE tests useful, as are eosinophil count and chest CT scan.

Severe asthma with fungal sensitization (SAFS) (video)

Specific anti fungal IgE levels, and raised total IgE

Anti fungal IgE as tested by specific skin testing.

Fungus ball of the sinus

CT or MR scan of the sinuses

Highly characteristic appearance, culture and histopathology follow surgical cure.

Chronic pulmonary aspergillosis (video)

Aspergillus IgG in context of upper lobe cavitation on chest Xray or CT scan

Presence of fungal ball in a cavity very typical, but only present in 25%. Most caused by Aspergillus fumigatus.

Pneumocystis pneumonia

Positive microscopy or PCR test in context of AIDS or other immunocompromised patient

Low level positive PCR can be problematic to interpret.

Cryptococcal meningitis

CSF showing yeasts with a capsule or cryptococcal antigen test

Blood cryptococcal antigen test an excellent screen, but some false negatives. 


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