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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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1. Bain, B. J.,, D. M. Clark,, I. A. Lampert,, and B. S. Wilkins. 2001. Bone Marrow Pathology, 3rd ed., p. 99. Wiley-Blackwell, New York, NY.
2. Barenfanger, J.,, C. Drake,, J. Lawhorn,, and S. J. Verhulst. 2004. Comparison of chlorhexidine and tincture of iodine for skin antisepsis in preparation for blood culture collection. J. Clin. Microbiol. 42: 2216 2217.
3. Baron, E. J.,, M. P. Weinstein,, W. M. Dunne, Jr.,, P. Yagupsky,, D. F. Welch,, and D. M. Wilson. 2005. Cumitech 1C, Blood cultures IV. Coordinating ed., E. J. Baron. ASM Press, Washington, DC.
4. Carrol, K.,, and L. Reimer. 1996. Microbiology and laboratory diagnosis of upper respiratory tract infections. Clin. Infect. Dis. 23: 442 448.
5. Chapin-Robertson, K.,, S. E. Dahlberg,, and S. C. Edberg. 1992. Clinical and laboratory analyses of cytospin-prepared Gram stains for recovery and diagnosis of bacteria from sterile body fluids. J. Clin. Microbiol. 30: 377 380.
6. Chern, K. C.,, D. M. Meisler,, K. R. Wilhelmus,, D. B. Jones,, G. A. Stern,, and C. Y. Lowder. 1996. Corneal anesthetic abuse and Candida keratitis. Ophthalmology 103: 37 40.
7. Chiarini, A.,, A. Palmeri,, T. Amato,, R. Immordino,, S. Distefano,, and A. Giammanco. 2008. Detection of bacterial and yeast species with the Bactec 9120 automated system with routine use of aerobic, anaerobic, and fungal media. J. Clin. Microbiol. 46: 4029 4033.
8. Cimbaluk, D.,, J. Scudiere,, J. Butsch,, and S. Jakate. 2005. Invasive candidal enterocolitis followed shortly by fatal cerebral hemorrhage in immuno-compromised patients. J. Clin. Gastroenterol. 39: 795 797.
9. Cockerill, F. R., III,, J. W. Wilson,, E. A. Vetter,, K. M. Goodman,, C. A. Torgerson,, W. S. Harmsen,, C. D. Schleck,, D. M. Illstrup,, J. A. Washington III,, and W. R. Wilson. 2004. Optimal testing parameters for blood cultures. Clin. Infect. Dis. 38: 1724 1730.
10. Cockerill, F. R., III,, C. A. Torgerson,, G. S. Reed,, E. A. Vetter,, A. L. Weaver,, J. C. Dale,, G. D. Roberts,, N. K. Henry,, D. M. Illstrup,, and J. E. Rosenblatt. 1996. Clinical comparison of Difco ESP, Wampole Isolator, and Becton Dickinson Septi-Chek aerobic blood culturing systems. J. Clin. Microbiol. 34: 20 24.
11. Creger, R. J.,, K. E. Weeman,, M. R. Jacobs,, A. Morrisey,, P. Parker,, R. M. Fox,, and H. M. Lazarus. 1998. Lack of utility of the lysis-centrifugation blood culture method for detection of fungemia in immunocompromised cancer patients. J. Clin. Microbiol. 36: 290 293.
12. Duong, S.,, B. J. Dezube,, G. Desai,, K. Eichelberger,, Q. Qian,, and J. E. Kirby. 2009. Limited utility of bone marrow culture: a ten-year retrospective analysis. Lab. Med. 40: 37 38.
13. Ellis, M. E.,, H. Al-Abdely,, A. Sandridge,, W. Greer,, and W. Ventura. 2001. Fungal endocarditis: evidence in the world literature. Clin. Infect. Dis. 32: 50 62.
14. Fisher, J. E.,, C. L. Newman,, and J. D. Sobel. 1995. Yeast in the urine: solutions for a budding problem. Clin. Infect. Dis. 20: 183 189.
15. Forbes, B. A.,, D. F. Sahm,, and A. S. Weissfeld. 2007. Bailey & Scott’s Diagnostic Microbiology, 12th ed., p. 778 797. Mosby Elsevier, St. Louis, MO.
16. Forbes, B. A.,, D. F. Sahm,, and A. S. Weissfeld. 2007. Bailey & Scott’s Diagnostic Microbiology, 12th ed., p. 629 713. Mosby Elsevier, St. Louis, MO.
17. Fraser, V. J.,, M. Jones,, and J. Dunkel. 1992. Candidemia in a tertiary care hospital: epidemiology, risk factors, and predictors of mortality. Clin. Infect. Dis. 15: 414 421.
18. Fricker-Hidalgo, H.,, B. Lebeau,, H. Pelloux,, and R. Grillot. 2004. Use of the BACTEC 9240 system with mycosis-IC/F blood culture bottles for detection of fungemia. J. Clin. Microbiol. 42: 1855 1856.
19. Gaur, A. H.,, M. A. Giannini,, P. M. Flynn,, J. W. Boudreaux,, M. A. Mestemacher,, J. L. Shenep,, and T. Hayden. 2003. Optimizing blood culture practices in pediatric immunocompromised patients: evaluation of media types and blood culture volume. Pediatr. Infect. Dis. J. 22: 545 552.
20. Hazen, K. C., 1998. Section 6. Mycology and aerobic actinomycetes, p. 255 283. In H. D. Isenberg (ed.), Essential Procedures for Clinical Microbiology. American Society for Microbiology, Washington, DC.
21. Hellinger, W. C.,, J. J. Cawley,, S. Alvarez,, S. F. Hogan,, W. S. Harmsen,, D. M. Ilstrup,, and F. R. Cockerill III. 1995. Clinical comparison of the Isolator and BacT/Alert aerobic blood culture systems. J. Clin. Microbiol. 33: 1787 1790.
22. Hubbard, T. W.,, and J. M. de Triquet. 1992. Brush-culture method for diagnosing tinea capitis. Pediatrics 90: 416 418.
23. Joint Commission (JCAHO). 2009. IM.6.240. Clinical Laboratory Improvement Act Subpart K Sec. 493.1232, Sec. 493.1242, and Sec. 493.1249. Joint Commission, Oakbrook Terrace, IL.
24. Kellogg, J. A.,, J. P. Manzella,, and D. A. Bankert. 2000. Frequency of low-level bacteremia in children from birth to fifteen years of age. J. Clin. Microbiol. 38: 2181 2185.
25. Kosmin, A. R.,, and T. Fekete. 2008. Use of fungal blood cultures in an academic medical center. J. Clin. Microbiol. 46: 3800 3801.
26. Kouklakis, G.,, S. Dokas,, E. Molyvas,, P. Vakianis,, and A. Efthymiou. 2001. Candida colitis in a middle-aged male receiving permanent haemodialysis. Eur. J. Gastroenterol. Hepatol. 13: 735 736.
27. Kwon-Chung, K. J.,, and J. Bennett. 1992. Medical Mycology, p. 45 46. Lea & Febiger, Philadelphia, PA.
28. Labarca, J. A.,, E. A. Wagar,, A. E. Grasmick,, H. M. Kokkinos,, and D. A. Bruckner. 1998. Critical evaluation of 4-week incubation for fungal cultures: is the fourth week useful? J. Clin. Microbiol. 35: 3683 3685.
29. Larone, D. H. Medically Important Fungi: a Guide to Identification, 4th ed. ASM Press, Washington, DC.
30. Lee, A.,, S. Mirrett,, L. B. Reller,, and M. P. Weinstein. 2007. Detection of bloodstream infections in adults: how many blood cultures are needed? J. Clin. Microbiol. 45: 3546 3548.
31. Maki, D. G.,, C. D. Weise,, and H. W. Sarafin. 1977. A semiquantitative culture method for identifying intravenouscatheter- related infection. N. Engl. J. Med. 296: 1305 1309.
32. Mawhorter, S. D.,, G. V. Curley,, E. D. Kursh,, and C. E. Farver. 2000. Prostatic and central nervous system histoplasmosis in an immunocompetent host: case report and review of the prostatic histoplasmosis literature. Clin. Infect. Dis. 30: 595 598.
33. McGinnis, M. R. 1980. Laboratory Handbook of Medical Mycology. Academic Press, New York, NY.
34. Merz, W. G.,, and G. D. Roberts,. 1999. Detection and recovery of fungi from clinical specimens, p. 709 722. In P. R. Murray et al. (ed.), Manual of Clinical Microbiology, 7th ed. American Society for Microbiology, Washington, DC.
35. Mess, T.,, and E. S. Daar. 1997. Utility of fungal blood cultures for patients with AIDS. Clin. Infect. Dis. 25: 1350 1353.
36. Mirrett, S.,, L. B. Reller,, C. A. Petti,, C. W. Woods,, B. Vazirani,, R. Sivadas,, and M. P. Weinstein. 2003. Controlled clinical comparison of BacT/ALERT standard aerobic medium with BACTEC standard aerobic medium for culturing blood. J. Clin. Microbiol. 41: 2391 2394.
37. Mirrett, S.,, K. E. Hanson,, and L. B. Reller. 2007. Controlled clinical comparison of VersaTREK and BacT/ALERT blood culture systems. J. Clin. Microbiol. 45: 299 302.
38. Morello, J. A.,, S. M. Matushek,, W. M. Dunne,, and D. B. Hinds. 1991. Performance of a BACTEC nonradiometric medium for pediatric blood cultures. J. Clin. Microbiol. 29: 359 362.
39. Morrell, R. M.,, B. L. Wasilauskas,, and C. H. Steffe. 1996. Performance of fungal blood cultures by using the Isolator collection system: is it cost effective? J. Clin. Microbiol. 34: 3040 3043.
40. Musial, C. E.,, F. R. Cockerill III,, and G. D. Roberts. 1988. Fungal infections of the immunocompromised host: clinical and laboratory aspects. Clin. Microbiol. Rev. 1: 349 364.
41. Neal, P. M.,, and A. Nikolai. 2008. Systemic blastomycosis diagnosed by prostate needle biopsy. Clin. Med. Res. 6: 24 28.
42. Petti, C. A.,, A. K. M. Zaidi,, S. Mirrett,, and L. B. Reller. 1996. Comparison of Isolator 1.5 and BACTEC NR660 aerobic 6A blood culture systems for detection of fungemia in children. J. Clin. Microbiol. 34: 1877 1879.
43. Procop, G. W.,, F. R. Cockerill III,, E. A. Vetter,, W. S. Harmsen,, J. G. Hughes,, and G. D. Roberts. 2000. Performance of five agar media for recovery of fungi from Isolator blood cultures. J. Clin. Microbiol. 38: 3827 3829.
44. Reimer, L. G.,, M. L. Wilson,, and M. P. Weinstein. 1997. Update on detection of bacteremia and fungemia. Clin. Microbiol. Rev. 10: 444 465.
45. Reimer, L. G.,, and K. C. Carroll. 1998. Role of the microbiology laboratory in the diagnosis of lower respiratory tract infections. Clin. Infect. Dis. 26: 742 748.
46. Richardson, M.,, and C. Lass-Flörl. 2008. Changing epidemiology of systemic fungal infections. Clin. Microbiol. Infect. 4(Suppl.): 5 24.
46a. Scognamiglio, T.,, R. Zinchuk,, P. Gumpeni,, and D. H. Larone. 2010. Comparison of inhibitory mold agar to Sabouraud dextrose agar as a primary medium for isolation of fungi. J. Clin. Microbiol. 48: 1924 1925.
47. Shanholtzer, C. J.,, P. J. Schaper,, and L. R. Peterson. 1982. Concentrated Gram stain smears prepared with a cytospin centrifuge. J. Clin. Microbiol. 16: 1052 1056.
48. Sohail, M. R.,, P. E. Andrews,, and J. E. Blair 2005. Coccidioidomycosis of the male genital tract. J. Urol. 173: 1978 1982.
49. Sonntag, H. G. 2002. Sampling and transport of specimens for microbial diagnosis of ocular infections. Dev. Ophthalmol. 33: 362 367.
50. Sutton, D. A., 2007. Specimen collection, transport, and processing: mycology, p. 1728 1736. In P. R. Murray,, E. J. Baron,, J. H. Jorgensen,, M. L. Landry,, and M. A. Pfaller (ed.), Manual of Clinical Microbiology, 9th ed. American Society for Microbiology, Washington, DC.
51. Szymzcak, E. G.,, J. T. Barr,, W. A. Durbin,, and D. A. Goldman. 1979. Evaluation of blood culture procedures in a paediatric hospital. J. Clin. Microbiol. 9: 88 92.
52. Tanure, M. A.,, E. J. Cohen,, S. Sudesh,, C. J. Rapuano,, and P. R. Laibson. 2000. Spectrum of fungal keratitis at Wills Eye Hospital, Philadelphia, Pennsylvania. Cornea 19: 307 312.
53. Telenti, A.,, and G. D. Roberts. 1989. Fungal blood cultures. Eur. J. Clin. Microbiol. Infect. Dis. 8: 825 831.
54. Washington, J. A., II,, and D. M. Illstrup. 1986. Blood cultures: issues and controversies. Rev. Infect. Dis. 8: 792 802.
55. Watts, B.,, P. Argekar,, S. Saint,, and C. A. Kauffman. 2007. Clinical problem-solving. Building a diagnosis from the ground up—a 49-year-old man came to the clinic with a 1-week history of suprapubic pain and fever. N. Engl. J. Med. 356: 1456 1462.
56. Witebsky, F. G.,, and V. J. Gill. 1995. Fungal blood culture systems: which ones and when to use them. Clin. Microbiol. Newsl. 17: 161 163.
57. Wolf, J.,, and A. Daley. 2007. Microbiological aspects of bacterial lower respiratory tract illness in children: typical pathogens. Paediatr. Respir. Rev. 8: 204 211.
58. Yurkanin, J. P.,, F. Ahmann,, and B. L. Dalkin. 2006. Coccidioidomycosis of the prostate: a determination of incidence, report of 4 cases, and treatment recommendations. J. Infect. 52: e19 e25.

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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