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Chapter 116 : General Approaches for Direct Detection and Identification of Fungi*

Author: H. Ruth Ashbee
Content Type: Reference
Publication Year: 2015

Category: Clinical Microbiology

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Abstract:

This chapter summarizes general approaches to the direct detection and identification of fungi in clinical samples. Techniques such as direct microscopy, histopathology, antigen and antibody detection, mass spectrometry, and nucleic acid detection are reviewed. The availability of commercial kits and the sensitivity and specificity of the various methods are detailed. Applications and limitations for each area are reviewed.

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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General Approaches for Direct Detection and Identification of Fungi*
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Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
/content/10.1128/9781555817381.mcm11.ch116.ch116.fig001
FIGURE 1

(Row 1, left) Gram stain of BAL specimen showing Gram-negative branching septate hyphae of Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f1

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Image of FIGURE 1
FIGURE 1

(Row 1, left) Gram stain of BAL specimen showing Gram-negative branching septate hyphae of Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f1

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 2

(Row 1, right) Gram stain of skin biopsy with Gram-variable branching hyphae of . Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f2

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Image of FIGURE 2
FIGURE 2

(Row 1, right) Gram stain of skin biopsy with Gram-variable branching hyphae of . Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f2

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 3

(Row 2, left) Gram stain of skin biopsy with Gram-negative aseptate hyphae of the group. Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f3

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Image of FIGURE 3
FIGURE 3

(Row 2, left) Gram stain of skin biopsy with Gram-negative aseptate hyphae of the group. Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f3

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 4

(Row 2, right) Gram stain of sputum with showing Gram-positive budding yeast cells with pseudohyphae. doi:10.1128/9781555817381.ch116.f4

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Image of FIGURE 4
FIGURE 4

(Row 2, right) Gram stain of sputum with showing Gram-positive budding yeast cells with pseudohyphae. doi:10.1128/9781555817381.ch116.f4

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 5

(Row 3, left) Gram stain of spleen demonstrating ghost-like budding yeastlike cells with pseudohyphae. Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f5

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Image of FIGURE 5
FIGURE 5

(Row 3, left) Gram stain of spleen demonstrating ghost-like budding yeastlike cells with pseudohyphae. Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f5

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 6

(Row 3, right) Gram stain of vaginal secretions with Gram-positive budding yeast cells of . doi:10.1128/9781555817381.ch116.f6

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Image of FIGURE 6
FIGURE 6

(Row 3, right) Gram stain of vaginal secretions with Gram-positive budding yeast cells of . doi:10.1128/9781555817381.ch116.f6

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 7

(Row 4, left) Gram stain of skin abscess with showing Gram-positive and Gram-variable budding yeast cells of variable size surrounded by amorphous orange halos. doi:10.1128/9781555817381.ch116.f7

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Image of FIGURE 7
FIGURE 7

(Row 4, left) Gram stain of skin abscess with showing Gram-positive and Gram-variable budding yeast cells of variable size surrounded by amorphous orange halos. doi:10.1128/9781555817381.ch116.f7

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 8

(Row 4, right) Parker ink stain of skin lesion showing typical yeast cells and short, stubby hyphae of spp. Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f8

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Image of FIGURE 8
FIGURE 8

(Row 4, right) Parker ink stain of skin lesion showing typical yeast cells and short, stubby hyphae of spp. Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f8

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 9

(Row 1, left) Gomori methenamine silver (GMS) stain of BAL specimen showing dichotomously branching septate hyphae. Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f9

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Image of FIGURE 9
FIGURE 9

(Row 1, left) Gomori methenamine silver (GMS) stain of BAL specimen showing dichotomously branching septate hyphae. Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f9

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 10

(Row 1, right) Calcofluor white stain of BAL specimen showing dichotomously branching septate hyphae. Magnification, approximately ×500. doi:10.1128/9781555817381.ch116.f10

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Image of FIGURE 10
FIGURE 10

(Row 1, right) Calcofluor white stain of BAL specimen showing dichotomously branching septate hyphae. Magnification, approximately ×500. doi:10.1128/9781555817381.ch116.f10

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 11

(Row 2, left) GMS stain of skin biopsy with spp. showing ribbonlike hyphae. Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f11

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Image of FIGURE 11
FIGURE 11

(Row 2, left) GMS stain of skin biopsy with spp. showing ribbonlike hyphae. Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f11

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 12

(Row 2, right) Calcofluor white stain of spp. showing ribbonlike hyphae. Magnification, approximately ×500. doi:10.1128/9781555817381.ch116.f12

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Image of FIGURE 12
FIGURE 12

(Row 2, right) Calcofluor white stain of spp. showing ribbonlike hyphae. Magnification, approximately ×500. doi:10.1128/9781555817381.ch116.f12

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 13

(Row 3, left) GMS stain of lung biopsy specimen showing with bulb formation at hyphal tip. Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f13

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Image of FIGURE 13
FIGURE 13

(Row 3, left) GMS stain of lung biopsy specimen showing with bulb formation at hyphal tip. Magnification, approximately ×1,000. doi:10.1128/9781555817381.ch116.f13

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 14

(Row 3, right) H&E stain of lung biopsy specimen showing dichotomously branching septate hyphae (shown at arrow). Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f14

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Image of FIGURE 14
FIGURE 14

(Row 3, right) H&E stain of lung biopsy specimen showing dichotomously branching septate hyphae (shown at arrow). Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f14

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 15

(Row 1, left) Diff-Quik stain of CSF with . Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f15

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Image of FIGURE 15
FIGURE 15

(Row 1, left) Diff-Quik stain of CSF with . Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f15

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 16

(Row 1, right) India ink preparation of CSF showing encapsulated budding yeast cell of . Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f16

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Image of FIGURE 16
FIGURE 16

(Row 1, right) India ink preparation of CSF showing encapsulated budding yeast cell of . Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f16

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 17

(Row 2, left) H&E stain of eumycotic mycetoma granule of . Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f17

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Image of FIGURE 17
FIGURE 17

(Row 2, left) H&E stain of eumycotic mycetoma granule of . Magnification, approximately ×400. doi:10.1128/9781555817381.ch116.f17

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 18

(Row 2, right) Toluidine blue stain of BAL specimen showing cysts of . doi:10.1128/9781555817381.ch116.f18

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Image of FIGURE 18
FIGURE 18

(Row 2, right) Toluidine blue stain of BAL specimen showing cysts of . doi:10.1128/9781555817381.ch116.f18

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 19

(Row 3, left) Calcofluor white stain of toenail specimen showing arthroconidia and hyphae of . Magnification, approximately ×200. doi:10.1128/9781555817381.ch116.f19

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Image of FIGURE 19
FIGURE 19

(Row 3, left) Calcofluor white stain of toenail specimen showing arthroconidia and hyphae of . Magnification, approximately ×200. doi:10.1128/9781555817381.ch116.f19

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 20

(Row 3, right) Muriform (sclerotic) cells (copper penny) in tissue of chromoblastomycosis. Magnification, ×1,000. doi:10.1128/9781555817381.ch116.f20

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Image of FIGURE 20
FIGURE 20

(Row 3, right) Muriform (sclerotic) cells (copper penny) in tissue of chromoblastomycosis. Magnification, ×1,000. doi:10.1128/9781555817381.ch116.f20

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 21

(Row 1, left) GMS stain of lymph node showing characteristic cigar-shaped yeast cells of . doi:10.1128/9781555817381.ch116.f21

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Image of FIGURE 21
FIGURE 21

(Row 1, left) GMS stain of lymph node showing characteristic cigar-shaped yeast cells of . doi:10.1128/9781555817381.ch116.f21

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 22

(Row 1, right) Gram stain of abscess material showing large, broad-based, budding yeast cell with thick refractile wall characteristic of doi:10.1128/9781555817381.ch116.f22

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Image of FIGURE 22
FIGURE 22

(Row 1, right) Gram stain of abscess material showing large, broad-based, budding yeast cell with thick refractile wall characteristic of doi:10.1128/9781555817381.ch116.f22

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 23

(Row 2, left) GMS stain of lymph node showing blastoconidia of . Magnification, ×625. doi:10.1128/9781555817381.ch116.f23

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Image of FIGURE 23
FIGURE 23

(Row 2, left) GMS stain of lymph node showing blastoconidia of . Magnification, ×625. doi:10.1128/9781555817381.ch116.f23

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 24

(Row 2, right) H&E stain of . Large, round, thick-walled spherules (10 to 80 µm in diameter) filled with endospores (2 to 5 µm in diameter). Young spherules have a clear center with peripheral cytoplasm and a prominent thick wall. doi:10.1128/9781555817381.ch116.f24

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Image of FIGURE 24
FIGURE 24

(Row 2, right) H&E stain of . Large, round, thick-walled spherules (10 to 80 µm in diameter) filled with endospores (2 to 5 µm in diameter). Young spherules have a clear center with peripheral cytoplasm and a prominent thick wall. doi:10.1128/9781555817381.ch116.f24

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 25

(Row 3, left) Bright-field photomicrograph of showing multiple budding yeast cells resembling mariner’s wheels. Magnification, ×1,590. doi:10.1128/9781555817381.ch116.f25

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10.1128/9781555817381/9781555817381.ch116.f25.gif
Image of FIGURE 25
FIGURE 25

(Row 3, left) Bright-field photomicrograph of showing multiple budding yeast cells resembling mariner’s wheels. Magnification, ×1,590. doi:10.1128/9781555817381.ch116.f25

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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FIGURE 26

(Row 3, right) Wright-Giemsa stain of BAL specimen showing characteristic fission yeast cells of doi:10.1128/9781555817381.ch116.f26

10.1128/9781555817381/9781555817381.ch116.f26_thmb.gif
10.1128/9781555817381/9781555817381.ch116.f26.gif
Image of FIGURE 26
FIGURE 26

(Row 3, right) Wright-Giemsa stain of BAL specimen showing characteristic fission yeast cells of doi:10.1128/9781555817381.ch116.f26

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
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Tables

General Approaches for Direct Detection and Identification of Fungi*
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Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
/content/10.1128/9781555817381.mcm11.ch116.ch116.tab001
TABLE 1

Characteristic fungal morphology seen by direct examination of clinical specimens

Generic image for table
TABLE 1

Characteristic fungal morphology seen by direct examination of clinical specimens

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116
/content/10.1128/9781555817381.mcm11.ch116.ch116.tab002
TABLE 2

Methods and stains available for direct microscopic and histological detection of fungi in clinical specimens

Generic image for table
TABLE 2

Methods and stains available for direct microscopic and histological detection of fungi in clinical specimens

Citation: Ashbee H. 2015. General Approaches for Direct Detection and Identification of Fungi*, p 1965-1983. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch116

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