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Section 3 : Specimen Collection and Processing

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Specimen Collection and Processing, Page 1 of 2

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Abstract:

This section serves two purposes; to assist medical staff in the details of selection, collection, and transport of clinical specimens for microbiologic analysis, and provide a model for use in writing the specimen management portion of the laboratory procedures manual. It deals with the selection, collection and processing of body fluid specimens such as abdominal-peritoneal fluid (paracentesis, ascites), blood specimens and cerebrospinal fluids. Subsequently procedures for gastrointestinal specimens such as duodenal contents, gastric-antral biopsy samples for Helicobacter pylori and gastric contents are discussed in the chapter. The chapter talks about collection and processing of respiratory specimens including bronchoscopy-bronchial washing, nasal specimens and nasopharyngeal specimens. Throat specimens, urine specimens and cystoscopic specimens are also discussed in the section. Specimens and collection methods for Chlamydia testing are tabulated in the chapter. Specimens for the detection of Mycoplasma spp. are usually of respiratory or urogenital origin, although other specimens such as blood can be submitted. Specimens and collection methods for viral testing have also been discussed in the chapter.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figures

Image of Figure 5
Figure 5

Drawing of an Entero-Test capsule. In comparison to intubation, this capsule allows a less invasive examination of duodenum contents for parasitic infection.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 6

Diagram of the stomach, showing the antral region.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Image of Figure 7
Figure 7

Plastic collection device for obtaining specimen for pinworm analysis.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 8

Alternative method for pinworm collection when a paddle device is unavailable. Adapted from reference 34.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 9

Disposable sanitary device for collection of stool specimens. Oral and written directions for specimen timing, preservation, and transport to the laboratory should be provided to the patient.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 10

For parasitology studies, patients must be given one or two special transport vials and directions for their use.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 11

Illustrated instructions on how to use the parasitology transport and preservative vial(s) may be helpful to patients. A non-mercury-containing fixative may be used in place of polyvinyl alcohol (PVA). Adapted from reference 34.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 12

Specimen quality is judged microscopically. The presence of epithelial cells usually signals the presence of commensal floras.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Image of Figure 13
Figure 13

A Lukens trap is used for collecting many respiratory aspirates.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 14

Diagram of the nose and nasopharyngeal region. While nasal and nasopharyngeal specimens may be obtained by swab, a needle aspirate is the only specimen of choice for determining the etiologic agent(s) of sinusitis.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Image of Figure 15
Figure 15

Sterile, prepackaged sputum collection containers are provided to patients along with oral and written instructions on how to collect an appropriate specimen. In this system, sputum is collected in the funnel-shaped device. The tube that contains the specimen is removed, and the cap is firmly applied.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 16

Proper technique for obtaining throat specimens. Firmly sampling only the inflamed areas of the throat and tonsils and avoiding other oral sites will enhance detection of etiologic agents.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 17

Sterile, prepackaged urine collection cups, some with special transport tubes, are made available to patients along with oral and written instructions.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Figure 18

Wound specimens should, at the least, be labeled as “surface wound” or “deep wound.” The laboratory depends on this information for selecting appropriate culture media and interpreting results.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Image of Figure 19
Figure 19

Diagram of the ear. A swab is not the specimen of choice for laboratory diagnosis of otitis media because it obviously will not reach the infected area. Preparing the ear for specimen collection is a critical step in obtaining an appropriate specimen.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Image of Figure 20
Figure 20

Diagram of the eye. The nature and potential severity of infections of the eye dictate special attention to the details of specimen management and an accurate description of the specimen submitted for analysis.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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References

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Tables

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Table 7

Specimen management of sterile body fluids a

a Adapted from reference 4.

b WBC, white blood cell. Any cytocentrifuged sediment can be cultured or stained.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Table 8

Conditions and protocols for collecting blood specimens

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Table 9

Characteristics of preservatives used to transport feces for parasite examination a

a Data from L. S. Garcia and D. A. Bruckner, 1993, Diagnostic Medical Parasitology, 2nd ed., American Society for Microbiology, Washington, D.C.

b MIF, merthiolate–iodine–formalin; SAF, sodium acetate–acetic acid–formalin; PVA, polyvinyl alcohol.

c Formalin (5 or 10%) is often selected by manufacturers as an all-purpose fixative.

d The iodine in MIF allows observation of protozoa (cysts), eggs, and larvae without further staining.

e A good choice if a single preservative is preferred, but albumin-coated slides are required.

f Iron hematoxylin stain provides a better view of organism morphology.

g Trichuris eggs and giardia cysts are not concentrated as easily as from formalin. Isospora oocysts may not be seen. Strongyloides larval morphology is poor.

h Many of these fixatives use a zinc sulfate base rather than a mercuric chloride base.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Table 10

Genital specimens for culture

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
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Table 11

Agents of genital infection in women

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
Generic image for table
Table 12

Specimens and collection methods for Chlamydia testing

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
Generic image for table
Table 13

Specimens and collection methods for viral testing

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3
Generic image for table
Table 14

Methods of collecting specimens from the eye

a CAT, computed axial tomography.

Citation: Miller J. 1999. Specimen Collection and Processing, p 51-140. In A Guide to Specimen Management in Clinical Microbiology, Second Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818234.ch3

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