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Chapter 112 : Specimen Collection, Transport, and Processing: Mycology

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Abstract:

This chapter offers guidelines for specimen collection and transport, specimen handling, specimen pretreatment and processing in the laboratory, medium selection, and incubation of cultures. Abscess specimens should be collected from the active peripheral edge of open abscesses or aspirated from closed abscesses by use of a syringe. Fungemia is a major cause of morbidity and mortality in hospitalized patients, with species being the major cause. Early detection of organisms in the bloodstream is incredibly important because it is an indicator of disseminated disease. As in bacteriology, the volume of blood, the blood-to-broth ratio, and the number of blood cultures are all critical factors, with the volume of blood being the most important variable. Bone marrow is most useful for the diagnosis of disseminated candidiasis, cryptococcosis, and histoplasmosis. Subcutaneous tissue should be examined for the presence of granules. The chapter contains a table listing various media used for the recovery of fungi from clinical specimens, including primary media, selective and/or differential media, and specialized media. A wide variety of media are available for primary isolation, and in many laboratories, the choice is based on personal experience and the technologist's preferences. Mycology laboratories that are responsible for culturing and aerobic actinomycetes must include other media for these pathogens, such as Sabouraud agar.

Citation: McGowan K. 2011. Specimen Collection, Transport, and Processing: Mycology, p 1756-1766. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch112

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References

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Tables

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TABLE 1

Specimen collection and transport guidelines

Abbreviations: BAL, bronchoalveolar lavage fluid; CSF, cerebrospinal fluid; RT, room temperature.

Citation: McGowan K. 2011. Specimen Collection, Transport, and Processing: Mycology, p 1756-1766. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch112
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TABLE 2

Common clinical sites for laboratory recovery of pathogenic fungi

X, recovery of fungus from indicated tissue.

Includes skin and mucous membranes.

Citation: McGowan K. 2011. Specimen Collection, Transport, and Processing: Mycology, p 1756-1766. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch112
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TABLE 3

Pretreatment of clinical specimens prior to plating

-Acetyl-l-cysteine, 5% oxalic acid, or dithiothreitol (Sputolysin).

Citation: McGowan K. 2011. Specimen Collection, Transport, and Processing: Mycology, p 1756-1766. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch112
Generic image for table
TABLE 4

Media suggested for the recovery of fungi from clinical specimens

Abbreviations: BHI, brain heart infusion agar; SDA, Sabouraud dextrose agar; Sabhi medium, Sabouraud dextrose and brain heart infusion agar; IMA, inhibitory mold agar; DTM, dermatophyte test medium; DIM, dermatophyte identification medium; CMA, cornmeal agar; PDA, potato dextrose agar; PFA, potato flake agar; RSA, rapid sporulation agar; EBM, esculin base medium.

Citation: McGowan K. 2011. Specimen Collection, Transport, and Processing: Mycology, p 1756-1766. In Versalovic J, Carroll K, Funke G, Jorgensen J, Landry M, Warnock D (ed), Manual of Clinical Microbiology, 10th Edition. ASM Press, Washington, DC. doi: 10.1128/9781555816728.ch112

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