Microbiology Laboratory


Written by MicroDok

Mycology is defined as the study fungi. The mycology unit of the clinical microbiology laboratory is largely responsible for handling, examining, and processing of patient’s specimens suspected to contain fungal organisms. Our concern here is on fungi that are of medical importance i.e. fungi that cause infections in humans. Fungi reside in nature, with the soil accounting for a large amount of their dwelling place. They play important role in our ecosystem, such as breaking down of organic matter and recycling of organic matter in the environment, thus getting rid of organic wastes from the environment. Their saprophytic nature has gained them this advantage over other group/category of microorganisms. Fungi like some bacteria have proved worthy in the manufacture/production of a wide variety of antibiotics which are used today in clinical medicine to treat infectious disease caused by microbes/pathogens. Example is the fungus Penicillium notatum from which the first antibiotic (penicillin) was produced from in late 1920’s.

Fungi unlike bacteria are eukaryotes/eukaryotic organisms and they grow in two basic forms viz: the mould form and the yeast form. The moulds grow by the production of multicellular filamentous colonies which consists of branching cylindrical tubules known as hyphae. Rhizopus nigricans is an example of a mould.  Yeasts are single celled, and they are usually spherical to ellipsoid in shape with varying diameters. Most yeasts reproduce by budding. Saccharomyces cerevisiae is a typical example of yeast.

Fungal infections are called mycoses. Candidiasis caused by Candida albicans, and dermatophytosis caused by dermatophytes like Trichophyton spp and other species of Candida are the common mycoses with the highest incidence in humans. These mycoses are caused by fungi that are part of the body’s normal microbial flora, fungi that are highly adapted to survival on the human body. Fungal infections (mycoses) are classified as: Superficial, Systemic, Opportunistic, Cutaneous, and Subcutaneous mycoses depending on the part of the body that is infected and the site via which they gain entrance into their human host.

Fungi are usually larger than bacteria, and most occur in nature and grow readily on simple sources of nitrogen and carbohydrates. Sabouraud’s dextrose agar (SDA) which contains glucose and modified peptone has been used to grow fungi because it does not readily support the growth of bacteria. Antibiotics can also be added to SDA during its preparation, when culturing medical fungi from non-sterile patient’s specimens. The essence of adding antibiotics is to prevent/inhibit the growth of bacteria and saprophytic moulds that might affect fungal growth. Gentamicin & chloramphenicol are used for the bacteria while cycloheximide is used against the saprophytic mould.

Two other very important reagents/stains which aid and help the easy identification of fungal organisms in the mycology unit are: potassium hydroxide (KOH) and lactophenol cotton blue.

Potassium hydroxide (KOH) is used to the KOH mount in the mycology unit. Fungal specimens (skin scrapings, hair, or nails) are softened and cleared first in KOH solution prior to their direct microscopy. The KOH helps to digest the keratinized tissues (portions) surrounding the specimen so that the fungal spores (conidia) and hyphae can be exposed and seen under the microscope.

Lactophenol cotton blue is used to mount fungal cultures in the mycology unit. It helps in giving good contrast that is required during viewing with the microscope so that fungal structures can be easily seen and identified.

Specimens encountered in the mycology unit include:

  • Skin scrapings
  • Cornea clippings
  • Hair
  • Nail clippings
  • Collection of specimens that cannot be scraped, using sterile swab stick
  • Other specimens handled here are biopsy, sputum, aspirate, pleural fluid, pus & CSF


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