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Chapter 16 : Specimen Collection, Transport, and Processing: Bacteriology

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Abstract:

One of the key principles of good specimen collection is to avoid introduction of colonizing bacteria surrounding the site of infection or on the skin or mucous membranes near the infectious site. A relatively recently introduced type of swab, the flocked swab, has proved to be superior to fiber swabs for collection of nasopharyngeal samples for detection of respiratory viruses, but there were no significant differences between flocked and rayon swabs when throat cultures were evaluated. For abscess contents, body fluids, and other fluid collections below the skin, aspirates obtained through disinfected intact skin are preferred over swabs. Expectorated sputum is the best sample for diagnosis of pneumonia, a disease of the distal lung alveolar spaces. Urine can be collected by midstream collection, catheterization, cystoscopic collection, or suprapubic aspiration. Urine specimens should be transported to the laboratory immediately and processed within 2 h of collection. Testing more than one stool for bacterial pathogens is usually not productive. Fresh stool should be examined visually, and the areas showing blood, pus, or mucus should be sampled preferentially. In spite of acceptable labeling, some specimen collection sites, transport containers, or transport conditions render the specimen unacceptable for processing. Although blood has not yet been used widely for detection of bacteria using nucleic acid amplification (NAA) tests or hybridization, such tests are in development. Swabs should be transported to the laboratory in special media.

Citation: Baron E, Thomson R. 2011. Specimen Collection, Transport, and Processing: Bacteriology, p 228-271. 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.ch16

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Bacterial Diseases
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Upper Respiratory Tract Infections
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Severe Acute Respiratory Syndrome
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Image of FIGURE 1
FIGURE 1

(row 1, left) Gram stain (×100) of surgical wound showing elastin fibers.

Citation: Baron E, Thomson R. 2011. Specimen Collection, Transport, and Processing: Bacteriology, p 228-271. 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.ch16
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Image of FIGURE 2
FIGURE 2

(row 1, right) Gram stain (×1,000) of sputum showing Curschman's spirals.

Citation: Baron E, Thomson R. 2011. Specimen Collection, Transport, and Processing: Bacteriology, p 228-271. 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.ch16
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Image of FIGURE 3
FIGURE 3

(row 2, left) Gram stain (×1,000) of vaginal secretions showing clue cells.

Citation: Baron E, Thomson R. 2011. Specimen Collection, Transport, and Processing: Bacteriology, p 228-271. 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.ch16
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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 squamous epithelial cells per low-power field.

Citation: Baron E, Thomson R. 2011. Specimen Collection, Transport, and Processing: Bacteriology, p 228-271. 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.ch16
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Image of FIGURE 5
FIGURE 5

(row 3, left) Gram stain (×100) of acceptable sputum specimen showing <10 squamous epithelial cells per low-power field.

Citation: Baron E, Thomson R. 2011. Specimen Collection, Transport, and Processing: Bacteriology, p 228-271. 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.ch16
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Image of FIGURE 6
FIGURE 6

(row 3, right) Gram stain (×100) of urine showing 4+ squamous epithelial cells, indicating gross contamination with vaginal or periurethral secretions and bacteria.

Citation: Baron E, Thomson R. 2011. Specimen Collection, Transport, and Processing: Bacteriology, p 228-271. 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.ch16
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Image of FIGURE 7
FIGURE 7

(row 4, left) Gram stain (×1,000) of urine showing polymorphonuclear leukocytes and 4+ gram-negative bacilli.

Citation: Baron E, Thomson R. 2011. Specimen Collection, Transport, and Processing: Bacteriology, p 228-271. 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.ch16
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Image of FIGURE 8
FIGURE 8

(row 4, right) Gram stain (×1,000) of a wound showing polymorphonuclear leukocytes, mixed bacterial morphotypes suggesting aerobic and anaerobic bacteria, and both intra- and extracellular bacteria. This appearance suggests a mixed aerobic and anaerobic abscess or closedspace infection.

Citation: Baron E, Thomson R. 2011. Specimen Collection, Transport, and Processing: Bacteriology, p 228-271. 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.ch16
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