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Chapter 18 : Specimen Collection, Transport, and Processing: Bacteriology*

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Specimen Collection, Transport, and Processing: Bacteriology*, Page 1 of 2

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Abstract:

This chapter provides a detailed description of collection, transport, and initial handling of all sample types submitted for bacteriological studies. It includes guidance on specimen rejection, choice of specimen based on syndrome, media, molecular tests available, and Gram stain interpretations.

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
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Image of FIGURE 1
FIGURE 1

(row 1, left) Gram stain (×100) of surgical wound showing elastin fibers. doi:10.1128/9781555817381.ch18.f1.

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
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Image of FIGURE 2
FIGURE 2

(row 1, right) Gram stain (×1,000) of sputum showing Curschmann’s spirals. doi:10.1128/9781555817381.ch18.f2.

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
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Image of FIGURE 3
FIGURE 3

(row 2, left) Gram stain (×1,000) of vaginal secretions showing clue cells. doi:10.1128/9781555817381.ch18.f3.

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
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Image of FIGURE 4
FIGURE 4

(row 2, right) Gram stain (×100) of unacceptable sputum specimen (grossly contaminated with members of the oropharyngeal microbiota) showing >10 SECs per low-power field. doi:10.1128/9781555817381.ch18.f4.

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
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Image of FIGURE 5
FIGURE 5

(row 3, left) Gram stain (×100) of acceptable sputum specimen showing <10 SECs per low-power field. doi:10.1128/9781555817381.ch18.f5.

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
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Image of FIGURE 6
FIGURE 6

(row 3, right) Gram stain (×100) of urine showing 4+ SECs, indicating gross contamination with vaginal or periurethral secretions and bacteria. doi:10.1128/9781555817381.ch18.f6.

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
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Image of FIGURE 7
FIGURE 7

(row 4, left) Gram stain (×1,000) of urine showing PMNs and 4+ Gram-negative bacilli. doi:10.1128/9781555817381.ch18.f7.

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
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Image of FIGURE 8
FIGURE 8

(row 4, right) Gram stain (×1,000) of a wound showing PMNs, mixed bacterial morphotypes suggesting aerobic and anaerobic bacteria, and both intra- and extracellular bacteria. This appearance suggests a mixed aerobic and anaerobic abscess or closed-space infection. doi:10.1128/9781555817381.ch18.f8.

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
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Tables

Generic image for table
TABLE 1

Selection of common clinical specimens for bacterial culture

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 2

Collection, transport, and storage guidelines for microbiological laboratory diagnostic studies

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 3

Suitability of various specimens for anaerobic culture

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 4

Specimen management for infrequently encountered organisms

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 5

Screening specimens requested for routine bacterial culture to ensure quality

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 6

Suggested priority list for accessioning samples received for bacteriology studies

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 7a

Recommendations for Gram stain and plating media for bacteriology specimens or organisms

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 8

Usual etiologies of selected infectious disease syndromes

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 9

Recommended blood volumes to obtain for blood cultures

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 10

Diagnosis of BV using a Gram-stained smear of vaginal secretions, by the Vaginal Infection and Prematurity Study Group criteria

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 11

Interpretation of bacterial lower respiratory tract culture results

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18
Generic image for table
TABLE 12

Interpretation of urine culture results

Citation: Baron E. 2015. Specimen Collection, Transport, and Processing: Bacteriology*, p 270-315. 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.ch18