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Laboratory Diagnosis of Fungal Infections mltgeeks

The laboratory diagnosis of fungal infection begins with the appropriate sample collection and transportation.In most fungal infections, identifications are primarily based on the assessment of colony morphology and microscopic characteristics.Key biochemistry tests may be required to distinguish genes and species.In some cases, serological studies using lateral flow assay  are needed to establish a differential diagnosis,cytospin method and molecular techniques such as Nucleic acid probe tests with increased frequency are also used to provide early confirmation in suspected cases of deep – seated mycoses.Non – cultural methods & automated system are also available for diagnosing fungal infections.


For the laboratory diagnosis of fungal infections such as fungi nail infections,foot fungal infection,yeast infection prevention and fungal infection treatment,different samples can be received in the laboratory.Doctors, nurses, ward staff and laboratory technicians must work together to develop protocols that ensure proper  and prompt collection of samples and the selection of appropriate collection devices,transport containers, specimen labeling and complete application forms are important considerations to ensure the correct diagnosis of fungal infections

Specimen collection container
Specimen collection container

Transport conditions for fungal infection diagnosis

SpecimenCondition of Transport
Tissue biopsyThe sample should not be frozen or dehydrated before culture
UrineIf a delay of more than 2 hours is expected, refrigerate at 4 ° C.
BloodBiphasic agar broth bottles specifically designed for fungal cultures
CSFIf the delay is anticipated, the sample must be left at room temperature.
Bronchoscopy FluidSterile Screw capped container
SputumSterile Screw capped container

The specimen should be transported to the laboratory as soon as possible.In general, specimens that are not processed immediately are held at room temperature (for urine if delays exceed 2 hrs at the specimen should be refrigerated at a temperature of 4 ° C).Cryptococcus neoformans, Histoplasma capsulatum and Blastomyces dermatitidis do not survive in ice or frozen specimens.


For common fungal infections,specimens  should be processed immediately after reception of the sample. The direct wet mount or swabs are prepared and the sample is inoculated on specific culture media for culture.

Direct Examination of Fungal specimen

Almost all samples are processed by direct macroscopic and  microscopic examination. This provides the presumed diagnosis for the physician and also helps in the selection of appropriate culture media.

The following are various methods for direct examinations of fungal specimen

Direct Microscopic Observations Presumptive Identification
Hyphae with irregular size (6-50 μm),Ribbon Like and without septa Zygomycetes (Phycomycetes) rhizopus-Mucor
Hyphae relatively small (3 – 6 μm) and regular in size, dichotomous branching at  an angle of 45 ° with distinct cross septaAspergillus spp
Small hyphae (2 – 3 μm) and regular, sometimes seen branching with rectangular arthrospores found only in skin, nail scraping and hairMicrosporum spp
Trichophyton spp
Dermatophyte group
Epidermophyton spp
Regular hyphae with  diameter (3-6 µm), parallel walls, irregular branching, septate, dark yellow, brown or hyaline.Phaeohyphomycosis spp
Hyalohyphomycosis spp
Hyphae,distinct points of constriction simulating link sausages (pseudohyphae), with budding yeast forms (blastospores) often seenCandida spp
Yeast forms, cell are spherical and irregular in size (5-20 µm) classically with a thick polysaccharide capsule (not all cells are encapsulated), with one or more buds attached by a narrow constrictionCryptococcus spp
Cryptococcus neoformans
Small budding yeast, which are relatively uniform in size (3-5 µm) with a single bud attached by a narrow base, extracellular or within macrophages Histoplasma capsulatum
Yeast forms with large cells (8-20 µm) appearing to have a thick, double contoured wall, with a single bud attached by a broad baseBlastomyces dermatitidis
Large and irregularly sized (10-50 µm) thick walled spherules, many of which contain small (2-4 µm) round endosporesCoccidioides immitis
Also read  Acid Fast organisms not Always Mycobacterium species

Wet Mounts Preparation

The microslide techniques and tease mount, transparency tape method are commonly used methods for fungal microscopic examination.

As for the mold colony,It is mounted in a drop of Lactophenol cotton blue stain on a glass slide and microscopically examined.

The specimen are directly mounted in 10% and 40% Potassium Hydroxide for nail and skin specimens respectively. Skin and nail samples are mounted on a glass slide to which two drops of Potassium hydroxide preparation is added and kept for sometime. KOH helps in dissolving the epithelial cells giving a clear  fungal visibility.

KOH wet mount showing budded yeast cells
KOH wet mount showing budded yeast cells

India Ink

This can be added to the  specimens such as exudates or spinal fluids which provide a dark background that highlights hyalines and capsular material (halo effect).It should therefore be used to examine specimens suspected of containing Cryptococcus neoformans.White blood cells may differ from Cryptococcus neoformansdue to the irregular edge of the halo and pale cell wash.Some laboratory don’t routinely offer India ink preparation but instead offer the Cryptococcus Antigen Test which is serological test.

India Ink showing Cryptococcus neoformans
India Ink showing Cryptococcus neoformans

Fungi Gram stain

Gram staining is usually  poor when used to stain fungal specimen.Gram staining  method may be used when smears of Malassezia,Candida species and Sporothrix are examined but should not be used to detect yeast from other dimorphic fungi.Also Gram stain can be used to detect the filaments of Nocardia and Actinomyces, which causes clinical symptoms similar to mycotic infections.

Candi albicans in gram stain
Candi albicans in gram stain

Modified staging Stain for Nocardia

This method is used to identify Nocardia species


  • Start by Making a thin smear of the specimen to be stained
  • Fix it  in methanol. You can use a positive control smear organism of Nocardia asteroides and a negative control smear of Streptomyces species.
  • Flood the smear with Kinyoun carbolfuchsin for  5 minutes (Do not heat)
  • Rinse the smear with water
  • Decolorize the smear with 50% ethanol until excess carbolfuchsin is removed.
  • Rinse the smear with water
  • Decolorize with 0.5% (aqueous) Sulphuric acid for 3 minutes
  • Rinse with water
  • Flood the slide with 1% (aqueous) methylene blue for 1 minute.
  • Rinse with water and examined microscopically
Also read  Listeria Oxford Agar Principle, Composition, Preparation and Colonies Characteristics

Selection and Inoculation of fungal culture media

Usually two types of culture media are used that is  non – selective growth media such as brain heart infusion which allows the growth of all clinically relevant fungi.The use of sabouraud’s dextrose agaras the primary recovery medium is discouraged because it is insufficiently rich to recover certain fastidious pathogenic species, especially those dimorphic fungi.It is recommended to use growth media like Potato flake agar (PFA), inhibitory mold agar (IMA) or a combination of sabouraud dextrose agar with Brain heart infusion (SABHI) agar.

Sabouraud’s dextrose agar is sufficient for the recovery of dermatophytes from cutaneous samples or vaginal culture yeasts.Czepak ‘s agar can be used for subculture of aspergillus species if colony morphology is an important criteria for identifying any given unknown isolate.

For more fastidious dimorphic fungi such as Blastomyces dermatitidis and  histoplasma capsulatum, an enrich agar like IMA or SABHI is used and in particular for Histoplasma capsulatum media with the addition of 5 – 10 percent  sheep blood is recommended.

Aspergillus fumigatus and Cryptococcus neoformans can be partially or completely inhibited with antibiotic cycloheximide, so a non – selective media should always be used in parallel.

Incubation of fungal culture

Fungal sample are cultured each in two set of culture media and incubated at two different temperatures at 30 °C (Room temperature) and at 35°C

All fungal cultures are incubated for a minimum of 30 days before being discard as negative or no growth.The choice between the use of culture tubes or plate is optional. For tube, the media is poured in thick slants which prevent dehydration during prolonged incubation period. After the medium is inoculated, do not screw down the cap too tightly because fungi require breathing.

Culture media in tubes have the advantage of easy transport, while limitation is difficult to prepare stained mounts for microscopic examination and petri dishes have the advantages of providing a larger surface for growth that leads to better separation of the colony and makes cultures easier to examine and subculture.Also tease mounts or tape preparations for transparency are made from plate cultures.

The disadvantage with petri dishes is that the plates can be dehydrated during prolonged incubation period.In order to prevent the drying of the plates,They are placed in a sealed, moisturized polyester or the edges are sealed with oxygen permeable tape.


After the culture plates have shown fungal growth of possible fungi, the colonies are identified by colony characteristic and morphology. A Lactophenol cotton blue mount is also prepared from growth culture and examined microscopically.

Preparation of Sabouraud dextrose agar
Preparation of Sabouraud dextrose agar

Colonies with a creamy,smooth,viscous or pasty look, could probably be yeast hence should be  considered.Dematiaceous molds produce dark colonies.Gray to black mycelium growth and the colony reverse is black.For molds that grow within 3 – 5 days have a distinct border and on the surface are white or patel.One dimorphic species should be considered for molds growing in 7 – 14 days or having a cobweb aerial mycelium.



The only commercially available current system is the applied Biosystems, the Microseq OZ large subunit r DNA sequencing kit. Micro scan also offers the identification kit for Candida species and candida albicans test such as threelac candida but not for other fungi isolates.


Nucleic acid probe assays are used with increasing frequency to confirm early culture, especially in deep mycoses.

For the future, it should be mentioned that nucleic acid sequencing has become the standard method for fungal identification, especially in reference laboratories.


Hyaline Fungi

Growth in lesser than 3 DaysGrowth 3- 5 days
Hyphae are broad and aseptate
Hyphae hyaline and septate
Suspect Zygomycetes

Suspect agents of Hyalohyphomycosis Conidia in Chains
Conidia in Clusters
Gliocladium Conidia Borne Singly
Scedosporium apiospermum


Growth 3-5 daysGrowth > 5 days
Colonies often granular and pigmented, hyphae septate, hyalineHyphae
Suspect Dermatophyte Genus Microsporidia common
Microsporum adnum
Genus Trichophyton common
Trichophyton rubrum
Trichophyton mentogrophytes
Trichophyton tonsurans
Trichophyton Verrucosum
Trichophyton Violaceum
Trichophyton Schoenleinii
Genus Epidermophyton
Epidermophyton Floccosum
Suspect Dimorphic fungi


Growth 3-5 daysGrowth > 5 days
Dark colony, black reverse, hyphae yellow-pigmented and septateSmooth, pasty or mucoid colonies
Suspect Agent of Phaeohyphomycosis Conidia Muriform

Shermaria Ulocladium

Steaphylium Epicoccum

Conidia divided by Transverse Septa only


Exserohilum Pycnidia produced
Suspect Agent of Chromomycosis or mycetoma Caldosprium-Type Sporulation Cladophialophora carrunil
Cladophialophora bantiana
Phialophora – type Sporulation
Phialophora verrucosa
Phialophora richardsiae
Exophiala jeanselmei
Acrotheca-Type sporulation
Fonsecaea pedrosoi
Fonsecaea compacta


Growth 2-5 daysGrowth 2-5 days
Smooth, pasty or mucoid coloniesYeast-like colonies with low aerial mycelium
Suspect Yeast Common
Candida albicans
Cryptococcus neoformans
Cryptococcus Rhodotorula
Hansenula anomala
Malassezia furfur
Saccharomyces cerevisiae
Basidiobolus species
Conidiobolus species
Black yeasts
Pullalaria pullalans
Phaeococcomyces species
Yeast forms of dimorphic fungi
Arthroconidia Produced Suspect
Geotrichum candidum
Trichosporon beigeliicoraplex Blastoschizomyces capitis

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About the Author: Arthur Westmann

DEFFE ARTHUR (AMOEBAMANN) is the founder and author of MLTGEEKS and MLTEXPO.He’s from Cameroon and is currently a Final year State Medical Laboratory Technician (MLT MA). Beyond lab works, he’s a passionate internet user with a keen interest in web design and blogging. Furthermore He likes traveling, hanging around with friends and social networking to do in his spare time.

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