Basic Mycology

  • Deanna A. SuttonEmail author
Part of the Infectious Disease book series (ID)


The mycology laboratory plays a vital role in the diagnosis of fungal infections through the recovery and identification of the etiologic agent. Specimen collection from appropriate sites is critical, as is the proper transport, storage, and processing of samples. Fungal elements seen by direct microscopy often provide the first clues to a fungal infection, and are the basis upon which empiric therapy is initiated. To ensure recovery of the fungus, a sufficient number and types of media should be utilized for primary isolation based upon the clinical history and the possible organisms expected. Accurate fungal identification, in combination with antifungal susceptibility testing, provides the basis for appropriate organism-directed antifungal therapy and is essential for conducting epidemiologic investigations.

Human and/or animal pathogens historically considered to be fungal are now placed in three kingdoms: Fungi, Straminipila (Stramenopila), containing the Oomycete Pythium, and Protoctista, with the bulk of the human pathogens in the kingdom Fungi. Organisms within this kingdom are eukaryotic (have cells containing a membrane-bound nucleus), heterotrophic (lack chlorophyll or other pigments capable of photosynthesis for making food, therefore must obtain nourishment from an external food source), may be unicellular or filamentous, and have cells surrounded by cell walls containing glucan, chitin, or both. Unlike animals, fungi possess cell walls, but unlike plants, the major cell wall component is not cellulose. In the past, medical problems attributed to these organisms, in comparison to those caused by the bacteria, viruses, and parasites, have been relatively few, and included allergic symptoms, mushroom poisoning, mycotoxicoses from the ingested fungal toxins, and occasional fungal infections. However, with the advent of modern medical advances utilizing immunosuppressive regimens, and with an increase in diseases/underlying conditions significantly altering the human immune system, fungal infections (mycoses) have increased significantly over the past couple decades. The recovery of these organisms from host tissue and their identification is often critical to the diagnosis and treatment of mycotic disease and is the classic method for documentation of pathogenicity. Histopathology and other adjunctive tools, such as antigen or antibody assays and molecular techniques, addressed elsewhere in this text, may also be relied upon for empiric/preemptive therapeutic decisions, when cultures are either not available or fail to provide unequivocal information. The proper collection, transport, and processing of specimens; selection of fungal stains and preliminary direct microscopy techniques; and use of appropriate media and incubation conditions are all important to the accurate identification of fungal infection. This chapter provides a cursory review of the laboratory fundamentals as they relate to medical mycology. It also reviews basic taxonomy, classification, and nomenclature regarding the kingdom Fungi and changes resulting from the Melbourne Code implemented in January 2013. Also included are descriptions of mycologic terms/features common to the most frequently recovered etiologic agents in the teleomorphic (sexual) phyla Ascomycota, Basidiomycota, and Glomeromycota (formerly Zygomycota) as well as those seen in the anamorphic (asexual) fungi. Fungi without known sexual states are referred to as “mitosporic” (based upon their reproductive mitotic processes). The mitosporic fungi are the most common etiologic agents of human and animal disease.


Fungal specimens Specimen collection Processing fungal specimens Direct microscopy Fungal taxonomy Fungal media Fungal identification 


  1. 1.
    Mendoza L, Vilela R. The mammalian pathogenic Oomycetes. Curr Fungal Infect Rep. 2013; DOI 10.1007/s12281-013-0144-z.Google Scholar
  2. 2.
    Howard DH. An introduction to the taxonomy of zoopathogenic fungi. In: Howard DH, editor. Pathogenic fungi in humans and animals. vol. 16, 2nd Ed. New York: Marcel Dekker, Inc.; 2003. pp. 1–16.Google Scholar
  3. 3.
    International Code of Nomenclature for algae, fungi, and plants (Melbourne Code). Adopted by the Eighteenth International Botanical Congress, Melbourne, Australia, July 2011. Prepared and edited by McNeill J et al. Regnum Vegetabile 154. Koeltz Scientific Books; 2012. (ISBN 978-3-87429-425–6)Google Scholar
  4. 4.
    Hibbert DS, Binder M, Fischoff JF, Blackwell M, et al. A higher-level classification of the Fungi. Mycol Res. 2007;111:509–47.CrossRefGoogle Scholar
  5. 5.
    CLSI. Principles and procedures for detection of fungi in clinical specimens—direct examination and culture: approved guideline. Wayne: Clinical and Laboratory Standards Institute; 2012. (CLSI document M54-A)Google Scholar
  6. 6.
    Bartlett JG, Ryan KJ, Smith TF, Wilson WR. Cumitech 7A. Laboratory diagnosis of lower respiratory tract infections. Washington II JA, Coordinating ed. Washington: American Society of Microbiology; 1987.Google Scholar
  7. 7.
    Clarridge J, Pezzlo MT, Vosti KL. Cumitech 2A. Laboratory diagnosis of urinary tract infections. Weissfeld AW, coordinating ed. Washington: American Society for Microbiology; 1987.Google Scholar
  8. 8.
    Eschenbach D, Pollock HM, Schacter J Cumitech 17. Laboratory diagnosis of female genital tracts infections. Rubin SJ, coordinating ed. Washington: American Society for Microbiology; 1983.Google Scholar
  9. 9.
    Jones DB, Liesegang TJ, Robinson NM. Cumitech 13. Laboratory diagnosis of ocular infections. Washington JA, coordinating ed. Washington: American Society for Microbiology; 1981.Google Scholar
  10. 10.
    Maki DG, Weise CD, Sarafin HW. A semiquantitative culture method for identifying intravenous-catheter-related infection. N Engl J Med. 1977;296:1303–9.CrossRefGoogle Scholar
  11. 11.
    McGowan KL. Specimen collection, transport, and processing: mycology. In: Versalovic J, Carroll KC, Funke G, Jorgensen JH, Landry ML, Warnock DW, editors. Manual of clinical microbiology. 10th Ed. Washington: ASM Press; 2011. pp. 1756–66.Google Scholar
  12. 12.
    CLSI. Principles and Procedures for Blood Cultures; Approved Guideline. CLSI document M47-A. Wayne, PA: Clinical and Laboratory Standards Institute; 2007Google Scholar
  13. 13.
    Jorgensen JH, Mirrett S, McDonald LC, et al. Controlled clinical laboratory comparison of BACTEC plus aerobic/F resin medium with BacT/Alert aerobic FAM medium for detection of bacteremia and fungemia. J Clin Microbiol. 1997;35:53–8.PubMedCentralPubMedGoogle Scholar
  14. 14.
    Mattia AR. FDA review criteria for blood culture systems. Clin Microbiol Newsl. 1993;15:132–6.CrossRefGoogle Scholar
  15. 15.
    Horvath LL, George BJ, Murray CK, Harrison LS, Hospenthal DR. Direct comparison of the BACTEC 9240 and BacT/ALERT 3D automated blood culture systems for Candida growth detection. J Clin Microbiol. 2004;42:115–8.CrossRefPubMedCentralPubMedGoogle Scholar
  16. 16.
    Horvath LL, Hospenthal DR, Murray CK, Dooley DP. Detection of simulated candidemia by the BACTEC 9240 system with plus aerobic/F and anaerobic/F blood culture bottles. J Clin Microbiol. 2003;41:4714–7.CrossRefPubMedCentralPubMedGoogle Scholar
  17. 17.
    Horvath LL, Hospenthal DR, Murray CK, Dooley DP. Direct isolation of Candida spp. from blood cultures on the chromogenic medium CHROMagar Candida. J Clin Microbiol. 2003;41:2629–32.CrossRefPubMedCentralPubMedGoogle Scholar
  18. 18.
    McDonald LC, Weinstein MP, Fune J, Mirrett S, Reimer LG, Reller LB. Controlled comparison of BacT/ALERT FAN aerobic medium and BACTEC fungal blood culture medium for detection of fungemia. J Clin Microbiol. 2004;39:622–4.CrossRefGoogle Scholar
  19. 19.
    Meyer M-H, Letscher-Bru V, Jaulhac B, Waller J, Candolfi E. Comparison of Mycosis IC/F and plus aerobic/F media for diagnosis of fungemia by the BACTEC 9240 system. J Clin Microbiol. 2004;42:773–7.CrossRefPubMedCentralPubMedGoogle Scholar
  20. 20.
    Auckenthaler R, Ilstrup DM, Washington JA II. Comparison of recovery of organisms from blood cultures diluted 10 % (volume/volume) and 20 % (volume/volume). J Clin Microbiol. 1982;15:860–4.PubMedCentralPubMedGoogle Scholar
  21. 21.
    Billi J, Stockman L, Roberts GD, Horstmeier CD, Istrup DM. Evaluation of a lysis-centrifugation system for recovery of yeasts and filamentous fungi from blood. J Clin Microbiol. 1983;18:469–71.Google Scholar
  22. 22.
    Bille J, Edson RS, Roberts GD. Clinical evaluation of the lysis-centrifugation blood culture system for detection of fungemia and comparison with a conventional biphasic broth blood culture system. J Clin Microbiol. 1984;19:126–8.PubMedCentralPubMedGoogle Scholar
  23. 23.
    Guerra-Romero L, Edson RC, Dockerill FR, Horstmeier CD, Roberts GD. Comparison of Du Pont Isolator and Roche Septi-check for detection of fungemia. J Clin Microbial. 1987;25:1623–5.Google Scholar
  24. 24.
    Lyon R, Woods G. Comparison of the BacT/Alert and ISOLATOR blood culture systems for recovery of fungi. Am J Clin Pathol. 1995;103:660–2.PubMedGoogle Scholar
  25. 25.
    Hazen KC. Mycology and aerobic actinomycetes. In: Isenberg HD, ed. Essential procedures for clinical microbiology. Washington: American Society for Microbiology; 1998. pp. 255–283.Google Scholar
  26. 26.
    Miller JM. A guide to specimen management in clinical microbiology. 2nd Ed. Washington: American Society for Microbiology Press; 1999.CrossRefGoogle Scholar
  27. 27.
    Labarca JAI, Wagar EA, Grasmick AE, Kokkinos HM, Bruckner DA. Critical evaluation of a 4-week incubation for fungal cultures: is the fourth week useful? J Clin Microbiol. 1998;36:3683–5.PubMedCentralPubMedGoogle Scholar
  28. 28.
    Sutton DA. Coelomycetous fungi in human disease. A review: clinical entities, pathogenesis, identification and therapy. Rev Iberoam Micol. 1999;16:171–9.PubMedGoogle Scholar
  29. 29.
    Stchigel AM, Sutton DA. Coleomycete fungi in the clinical lab. Curr Fungal Infect Rep. 2013;7:171–91.CrossRefGoogle Scholar
  30. 30.
    McGinnis MR. Laboratory handbook of medical mycology. New York: Academic Press; 1980.Google Scholar
  31. 31.
    Samson RA, Yilmaz N, Houbraken J, Spierenburg H, Seifert K, Peterson SW, Varga J, Frisvad JC. Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium. Stud Mycol. 2011;70:159–83.CrossRefPubMedCentralPubMedGoogle Scholar
  32. 32.
    Marimon R, Cano J, Gené J, Sutton DA, Kawasaki M, Guarro J. Sporothrix brasiliensis, S. globosa, and S. mexicana, three new Sporothrix species of clinical interest. J Clin Microbiol. 2007;45:3198–206.CrossRefPubMedCentralPubMedGoogle Scholar
  33. 33.
    Chen YC, Eisner JD, Kattar MM, Rassoulian-Barrett SL, Lafe K, Bui U, Limaye AP, Cookson BT. Polymorphic internal transcribed spacer region 1 DNA sequences identify medically important yeasts. J Clin Microbiol. 2001;39:4042–51.CrossRefPubMedCentralPubMedGoogle Scholar
  34. 34.
    Kurtzman CP, Robnett CJ. Identification of clinically important ascomycetous yeasts based on nucleotide divergence in the 5′ end of the large-subunit (26S) ribosomal DNA gene. J Clin Microbiol. 1997;35:1216–23.PubMedCentralPubMedGoogle Scholar
  35. 35.
    Glass NL, Donaldson GC. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol. 1995;61:1323–30.PubMedCentralPubMedGoogle Scholar
  36. 36.
    Sutton DA, Thompson EH, Fothergill AW, Wiederhold NP. Mould identification by ITS rDNA sequencing: ready for prime time in the routine lab? Abstract M-1381 of the 53rd Interscience Conference on antimicrobial agents and chemotherapy, Sept 19, 2013, Denver, CO.Google Scholar
  37. 37.
    O’Donnell K, Sutton DA, Rinaldi MG, Sarver BAJ, et al. Internet-accessible DNA sequence database for identifying fusaria from human and animal infections. J Clin Microbiol. 2010;48:3708–18.CrossRefPubMedCentralPubMedGoogle Scholar
  38. 38.
    Hawksworth DL, Crous PW, Redhead SA, et al. The Amsterdam Declaration on fungal nomenclature. IMA Fungus. 2011;2:105–12.CrossRefPubMedCentralPubMedGoogle Scholar
  39. 39.
    Sandoval-Denis M, Sutton DA, Fothergill AW, Cano-Lira J, Decock CA, de Hoog GS, Guarro J. Scopulariopsis, a poorly known opportunistic fungus: spectrum of species in clinical samples and in vitro responses to antifungal drugs. J Clin Microbiol. 2013;51:3937–43.CrossRefPubMedCentralPubMedGoogle Scholar
  40. 40.
    Geiser DM, Aoki T, Bacon CW, Baker SE, et al. One fungus, one name: defining the genus Fusarium in a scientifically robust way that preserves longstanding use. Phytopathology. 2013;103:400–8.CrossRefPubMedGoogle Scholar
  41. 41.
    Gilgado F, Cano J, Gené J, Sutton DA, Guarro J. Molecular and phenotypic data supporting distinct species statuses for Scedosporium apiospermum and Pseudallescheria boydii and the proposed new species Scedosporium dehoogii. J Clin Microbiol. 2008;46:766–71.CrossRefPubMedCentralPubMedGoogle Scholar
  42. 42.
    Hoffman K, Pawlowska J, Walther G, Wrzosek M, de Hoog GS, Benny GL, Kirk PM, Voigt K. The family structure of the Mucorales: a synoptic revision based on comprehensive multigene-genealogies. Persoonia. 2013;30:57–76.CrossRefGoogle Scholar
  43. 43.
    Alastruey-Izquierdo A, Hoffman K, de Hoog GS, Ridriguez-Tudela JL, Voight K, Bibashi E, Walther G. Species recognition and clinical relevance of the zygomycetous genus Lichtheimia (syn. Absidia pro parte, Mycocladus). J Clin Microbiol. 2010;48:2154–70.CrossRefPubMedCentralPubMedGoogle Scholar
  44. 44.
    Manamgoda DS, Cai L, McKenzie EHC, Crous PW, Madrid H, Chukeatirote E, Shivas RG, Tan YP, Hyde KD. A phylogenetic and taxonomic re-evaluation of the BipolarisCochliobolusCurvularia complex. Fungal Diversity. 2012;56:131–44.CrossRefGoogle Scholar
  45. 45.
    Crous PW, Slippers B, Wingfield MJ, Rheeder J, Marasas WFO, Philips AJL, Alves A, Burgess T, Barber P, Groenewald JZ. Phylogenetic lineages in the Botryosphaeriaceae. Stud Mycol. 2006;55:235–53.CrossRefPubMedCentralPubMedGoogle Scholar

Suggested Reading

  1. Chandler FW, Watts JC. Pathologic diagnosis of fungal infections. Chicago: American Society of Clinical Pathologists Press; 1987.Google Scholar
  2. deHoog GS, Guarro J, Gene J, Figueras MJ. Atlas of clinical fungi, 2nd Ed. Utrecht: Centraalbureau voor Schimmelcultures; 2000.Google Scholar
  3. Larone DH. Medically important fungi: a guide to identification, 5th Ed. Washington, DC: American Society for Microbiology Press; 2011.Google Scholar
  4. Mandell GL, Diamond RD (eds). Atlas of fungal infections, (Atlas of infectious diseases). Philadelphia: Current Medicine; 2000.Google Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  1. 1.Fungus Testing Laboratory, Pathology DepartmentUniversity of Texas Health Science Center at San AntonioSan AntonioUSA

Personalised recommendations