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Chapter 2.1 : Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns

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Abstract:

The tables in this section address the initial events that lead to the accurate, rapid identification of microorganisms and viruses. Remember that results can only be as good as the original specimen. All the long-established precautions must be observed, keeping in mind that many specimens are obtained from anatomic sites that encourage specimen contamination with indigenous microbiota and results must be evaluated accordingly ( ).

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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References

/content/book/10.1128/9781555817435.chap2.1
1. Amies, C. R. 1967. A modified formula for the preparation of Stuart's transport medium. Am. J. Public Health 58:296299.
2. Carey, S. G.,, and E. B. Blair. 1964. New transport medium for shipment of clinical specimens. I. Fecal specimens. J. Bacteriol. 88:9698.
3. Forbes, B. A.,, D. F. Sahm,, and A. S. Weissfeld. 2007. Bailey and Scott's Diagnostic Microbiology, 12th ed. Mosby, Inc., St. Louis, MO.
4. Garcia, L. S. 2007. Diagnostic Medical Parasitology, 5th ed. ASM Press, Washington, DC.
5. Garcia, L. S. 2009. Practical Guide to Diagnostic Parasitology, 2nd ed. ASM Press, Washington, DC.
6. Gorbach, S. L.,, J. G. Barlett,, and N. R. Blacklow. 1992. Infectious Diseases. The W. B. Saunders Co., Philadelphia, PA.
7. Heymann, D. L. 2008. Control of Communicable Diseases Manual, 19th ed. American Public Health Association, Washington, DC.
8. Jousimies-Somer, H. R.,, P. Summanen,, D. M. Citron,, E. J. Barron,, H. W. Wexler,, and S. M. Finegold. 2002. Wadsworth—KTL Anaerobic Bacteriology Manual, 6th ed. Star Publishing Co., Belmont, CA.
9. Mandell, G. L.,, J. E. Bennett,, and R. Dolin. 2005. Principles and Practices of Infectious Diseases, 6th ed. Elsevier Inc., Philadelphia, PA.
10. Miller, J. M. 1999. A Guide to Specimen Management in Clinical Microbiology, 2nd ed. ASM Press, Washington, DC.
11. Murray, P. R.,, and T. R. Shea. 2004. Pocket Guide to Clinical Microbiology, 3rd ed. ASM Press, Washington, DC.
12. Stuart, R. D.,, S. R. Tosach,, and T. M. Patsula. 1954. The problem of transport for gonococci. Am. J. Public Health 45:7377.

Tables

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Table 2.1-1a

“Rule-out” clinical impressions and potential etiological agents

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-1b

“Rule-out” clinical impressions and potential etiological agents

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-1c

“Rule-out” clinical impressions and potential etiological agents

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-1d

“Rule-out” clinical impressions and potential etiological agents

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-1e

“Rule-out” clinical impressions and potential etiological agents

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-1f

“Rule-out” clinical impressions and potential etiological agents

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-1g

“Rule-out” clinical impressions and potential etiological agents

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-2

Collection of specimens for bacteriological analysis

NOTE: Standard precautions must be observed at all times. When the “Container” column indicates the specimen may be submitted in a syringe, the caveats of standard precautions must be followed, i.e., the syringe must be capped with a sterile closure; syringes with needles in place are unacceptable. Many specimens may contain important yeasts, moulds, or viruses. Follow the instructions of the director of the laboratory in concert with Infectious Disease Advisory Committee which designate such examinations as routine procedures with select specimens or follow the request of the physician of record based on the patient's history and clinical impression. Perform smears whenever possible.

Abbreviations: TM, transport medium; TB, tuberculosis; SPS, sodium polyanethole sulfonate; GC, gonorrhea; AFB, acid-fast bacillus; STD, sexually transmitted disease; UTI, urinary tract infection; GN, gram negative; DFA, direct fluorescent-antibody assay; Fuo, fever of unknown origin; HSV, herpes simplex virus; lpf, low-power field.

If copious amounts are available, fill sterile tube.

Preparation of smears for Gram (and other) stains at time of autopsy is helpful.

Culture for viruses based on clinical impression; inoculate virus transport vial if intended for reference laboratory.

Culture for yeasts and moulds if suspected from clinical history or premortem findings.

Cultures for mycobacteria and fungus require special attention. See the appropriate sections.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-2b

Collection of specimens for bacteriological analysis

NOTE: Standard precautions must be observed at all times. When the “Container” column indicates the specimen may be submitted in a syringe, the caveats of standard precautions must be followed, i.e., the syringe must be capped with a sterile closure; syringes with needles in place are unacceptable. Many specimens may contain important yeasts, moulds, or viruses. Follow the instructions of the director of the laboratory in concert with Infectious Disease Advisory Committee which designate such examinations as routine procedures with select specimens or follow the request of the physician of record based on the patient's history and clinical impression. Perform smears whenever possible.

Abbreviations: TM, transport medium; TB, tuberculosis; SPS, sodium polyanethole sulfonate; GC, gonorrhea; AFB, acid-fast bacillus; STD, sexually transmitted disease; UTI, urinary tract infection; GN, gram negative; DFA, direct fluorescent-antibody assay; Fuo, fever of unknown origin; HSV, herpes simplex virus; lpf, low-power field.

If copious amounts are available, fill sterile tube.

Preparation of smears for Gram (and other) stains at time of autopsy is helpful.

Culture for viruses based on clinical impression; inoculate virus transport vial if intended for reference laboratory.

Culture for yeasts and moulds if suspected from clinical history or premortem findings.

Cultures for mycobacteria and fungus require special attention. See the appropriate sections.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-2c

Collection of specimens for bacteriological analysis

NOTE: Standard precautions must be observed at all times. When the “Container” column indicates the specimen may be submitted in a syringe, the caveats of standard precautions must be followed, i.e., the syringe must be capped with a sterile closure; syringes with needles in place are unacceptable. Many specimens may contain important yeasts, moulds, or viruses. Follow the instructions of the director of the laboratory in concert with Infectious Disease Advisory Committee which designate such examinations as routine procedures with select specimens or follow the request of the physician of record based on the patient's history and clinical impression. Perform smears whenever possible.

Abbreviations: TM, transport medium; TB, tuberculosis; SPS, sodium polyanethole sulfonate; GC, gonorrhea; AFB, acid-fast bacillus; STD, sexually transmitted disease; UTI, urinary tract infection; GN, gram negative; DFA, direct fluorescent-antibody assay; Fuo, fever of unknown origin; HSV, herpes simplex virus; lpf, low-power field.

If copious amounts are available, fill sterile tube.

Preparation of smears for Gram (and other) stains at time of autopsy is helpful.

Culture for viruses based on clinical impression; inoculate virus transport vial if intended for reference laboratory.

Culture for yeasts and moulds if suspected from clinical history or premortem findings.

Cultures for mycobacteria and fungus require special attention. See the appropriate sections.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
Generic image for table
Table 2.1-2b

Collection of specimens for bacteriological analysis

NOTE: Standard precautions must be observed at all times. When the “Container” column indicates the specimen may be submitted in a syringe, the caveats of standard precautions must be followed, i.e., the syringe must be capped with a sterile closure; syringes with needles in place are unacceptable. Many specimens may contain important yeasts, moulds, or viruses. Follow the instructions of the director of the laboratory in concert with Infectious Disease Advisory Committee which designate such examinations as routine procedures with select specimens or follow the request of the physician of record based on the patient's history and clinical impression. Perform smears whenever possible.

Abbreviations: TM, transport medium; TB, tuberculosis; SPS, sodium polyanethole sulfonate; GC, gonorrhea; AFB, acid-fast bacillus; STD, sexually transmitted disease; UTI, urinary tract infection; GN, gram negative; DFA, direct fluorescent-antibody assay; Fuo, fever of unknown origin; HSV, herpes simplex virus; lpf, low-power field.

If copious amounts are available, fill sterile tube.

Preparation of smears for Gram (and other) stains at time of autopsy is helpful.

Culture for viruses based on clinical impression; inoculate virus transport vial if intended for reference laboratory.

Culture for yeasts and moulds if suspected from clinical history or premortem findings.

Cultures for mycobacteria and fungus require special attention. See the appropriate sections.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-2e

Collection of specimens for bacteriological analysis

NOTE: Standard precautions must be observed at all times. When the “Container” column indicates the specimen may be submitted in a syringe, the caveats of standard precautions must be followed, i.e., the syringe must be capped with a sterile closure; syringes with needles in place are unacceptable. Many specimens may contain important yeasts, moulds, or viruses. Follow the instructions of the director of the laboratory in concert with Infectious Disease Advisory Committee which designate such examinations as routine procedures with select specimens or follow the request of the physician of record based on the patient's history and clinical impression. Perform smears whenever possible.

Abbreviations: TM, transport medium; TB, tuberculosis; SPS, sodium polyanethole sulfonate; GC, gonorrhea; AFB, acid-fast bacillus; STD, sexually transmitted disease; UTI, urinary tract infection; GN, gram negative; DFA, direct fluorescent-antibody assay; Fuo, fever of unknown origin; HSV, herpes simplex virus; lpf, low-power field.

If copious amounts are available, fill sterile tube.

Preparation of smears for Gram (and other) stains at time of autopsy is helpful.

Culture for viruses based on clinical impression; inoculate virus transport vial if intended for reference laboratory.

Culture for yeasts and moulds if suspected from clinical history or premortem findings.

Cultures for mycobacteria and fungus require special attention. See the appropriate sections.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
Generic image for table
Table 2.1-2f

Collection of specimens for bacteriological analysis

NOTE: Standard precautions must be observed at all times. When the “Container” column indicates the specimen may be submitted in a syringe, the caveats of standard precautions must be followed, i.e., the syringe must be capped with a sterile closure; syringes with needles in place are unacceptable. Many specimens may contain important yeasts, moulds, or viruses. Follow the instructions of the director of the laboratory in concert with Infectious Disease Advisory Committee which designate such examinations as routine procedures with select specimens or follow the request of the physician of record based on the patient's history and clinical impression. Perform smears whenever possible.

Abbreviations: TM, transport medium; TB, tuberculosis; SPS, sodium polyanethole sulfonate; GC, gonorrhea; AFB, acid-fast bacillus; STD, sexually transmitted disease; UTI, urinary tract infection; GN, gram negative; DFA, direct fluorescent-antibody assay; Fuo, fever of unknown origin; HSV, herpes simplex virus; lpf, low-power field.

If copious amounts are available, fill sterile tube.

Preparation of smears for Gram (and other) stains at time of autopsy is helpful.

Culture for viruses based on clinical impression; inoculate virus transport vial if intended for reference laboratory.

Culture for yeasts and moulds if suspected from clinical history or premortem findings.

Cultures for mycobacteria and fungus require special attention. See the appropriate sections.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
Generic image for table
Table 2.1-2g

Collection of specimens for bacteriological analysis

NOTE: Standard precautions must be observed at all times. When the “Container” column indicates the specimen may be submitted in a syringe, the caveats of standard precautions must be followed, i.e., the syringe must be capped with a sterile closure; syringes with needles in place are unacceptable. Many specimens may contain important yeasts, moulds, or viruses. Follow the instructions of the director of the laboratory in concert with Infectious Disease Advisory Committee which designate such examinations as routine procedures with select specimens or follow the request of the physician of record based on the patient's history and clinical impression. Perform smears whenever possible.

Abbreviations: TM, transport medium; TB, tuberculosis; SPS, sodium polyanethole sulfonate; GC, gonorrhea; AFB, acid-fast bacillus; STD, sexually transmitted disease; UTI, urinary tract infection; GN, gram negative; DFA, direct fluorescent-antibody assay; Fuo, fever of unknown origin; HSV, herpes simplex virus; lpf, low-power field.

If copious amounts are available, fill sterile tube.

Preparation of smears for Gram (and other) stains at time of autopsy is helpful.

Culture for viruses based on clinical impression; inoculate virus transport vial if intended for reference laboratory.

Culture for yeasts and moulds if suspected from clinical history or premortem findings.

Cultures for mycobacteria and fungus require special attention. See the appropriate sections.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-3

Collection of specimens to detect infrequently encountered organisms

Adapted from references and .

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-4

Laboratory approaches to suspected fungal infections

SAB, Sabouraud's agar; SAB-SPEC, Sabouraud's agar with chloramphenicol and cycloheximide; SAB-SPEC C, Sabouraud's agar with chloramphenicol only; DTM, dermatophyte test medium (presumptive); BHIA, BHI agar; blood culture, any approach extant in laboratory is acceptable—however, lysiscentrifugation (Isolator-Wampole) is preferred. All media required are available commercially (see Appendix A at the end of this handbook). For selected commercial suppliers, see the mycology section.

BW, bronchial wash.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-5

Collection of specimens to detect parasites

Abbreviations: FA, fluorescent antibody; BAL, bronchoalveolar lavage.

Immediate delivery to laboratory desirable; if request is for organisms other than spp., request it be indicated on label and on requisition for parasites such as filariae ( ).

Immediate delivery to laboratory desirable; requires prompt processing.

Examinations of fresh stool specimens require special attention. Liquid stool specimens for protozoan trophozoites must be examined within 30 min of passage (not 30 min after arriving at laboratory); soft stools should be examined within 1 h of being passed, although protozoan cysts survive and can be detected in firm stools within 24 h of being passed. The preserved stool specimens are suitable for examination for spp., spp., and related coccidia. NOTE: Stool examinations for ova, parasites, and enteropathogenic bacteria should not be requested if patients have been hospitalized for 3 days or more.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-6

Commercially available transport media

Various commercial suppliers have these transport vials, tubes, and devices available, often packaged with polyester or flocked nylon fiber tips and plastic shanks (to avoid toxic effects of cotton and wood). Consult section 9 for names of suppliers. Z-PVA, zinc-polyvinyl alcohol.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-7a

Rejection criteria for microbiological specimens

Abbreviations: GC, gonococcus; AFB, acid-fast bacillus; lpf, low-power field; DFA, direct fluorescent antibody assay; PVA, polyvinyl alcohol.

A record for all rejections or discrepancies must be maintained (book, card file, or computer). Note patient demographic information; physician of record; date and time specimen received; type and source of specimen; examination requested; reason for rejection or discrepancy noted; person contacted by phone; date, time, and manner of contact (phone, computer, or FAX); and final disposition or resolution. Records should be reviewed by supervisory personnel at regular intervals.

Specimens unsuitable for routine anaerobic cultures: throat swabs; nasopharyngeal swabs; gingival and other internal mouth surface swabs; expectorated sputum; sputum obtained by nasotracheal or orotracheal suction; bronchial washings or other specimens obtained with bronchoscopy unless procured with a protected double-lumen catheter or by properly executed bronchoalveolar lavage; gastric and small-bowel contents; large-bowel contents except for Clostridium difficile, Clostridiumbotulinum, Anaerobiospirillum succiniciproducens, and other specific causative agents; ileostomy and colostomy effluents; feces, except for large-bowel contents (as directed above); voided or catheterized urine; vaginal or cervical swabs; female genital tract cultures collected via vagina, except for suction curettings or other specimens collected with a double-lumen catheter; surface swabs from decubitus ulcers, perirectal abscesses, foot ulcers, exposed wounds, eschars, or pilonidal and other sinus tracts; any material adjacent to a mucous membrane that has not been adequately decontaminated.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
Generic image for table
Table 2.1-7b

Rejection criteria for microbiological specimens

Abbreviations: GC, gonococcus; AFB, acid-fast bacillus; lpf, low-power field; DFA, direct fluorescent antibody assay; PVA, polyvinyl alcohol.

A record for all rejections or discrepancies must be maintained (book, card file, or computer). Note patient demographic information; physician of record; date and time specimen received; type and source of specimen; examination requested; reason for rejection or discrepancy noted; person contacted by phone; date, time, and manner of contact (phone, computer, or FAX); and final disposition or resolution. Records should be reviewed by supervisory personnel at regular intervals.

Specimens unsuitable for routine anaerobic cultures: throat swabs; nasopharyngeal swabs; gingival and other internal mouth surface swabs; expectorated sputum; sputum obtained by nasotracheal or orotracheal suction; bronchial washings or other specimens obtained with bronchoscopy unless procured with a protected double-lumen catheter or by properly executed bronchoalveolar lavage; gastric and small-bowel contents; large-bowel contents except for Clostridium difficile, Clostridiumbotulinum, Anaerobiospirillum succiniciproducens, and other specific causative agents; ileostomy and colostomy effluents; feces, except for large-bowel contents (as directed above); voided or catheterized urine; vaginal or cervical swabs; female genital tract cultures collected via vagina, except for suction curettings or other specimens collected with a double-lumen catheter; surface swabs from decubitus ulcers, perirectal abscesses, foot ulcers, exposed wounds, eschars, or pilonidal and other sinus tracts; any material adjacent to a mucous membrane that has not been adequately decontaminated.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-8a

Procedure for processing clinical specimens in microbiology

Abbreviations: MS, mitis salivarius agar; SEA, selective enterococcus agar; TM, transport medium; PEA, phenyl ethanol agar; CAMPY, campylobacter agar; HE, Hektoen enteric agar; GN, gram-negative; SABSEL, Sabouraud's selective agar; BRU, brucella agar; BBE/LKV, bacteroides bile esculin agar/lakedblood-kanamycin-vancomycin agar.

Special instructions for processing urine specimens:

1. Do not centrifuge urine before culturing.

2. Mix urine well before culturing.

3. Use 0.001-ml calibrated loop for inoculating media for routine urine.

4. Transfer 1 loopful of urine to BAP.

5. Pull the loop down the surface of the agar to form a single streak in the center of the first quadrant.

6. Spread the inoculum over the first quadrant by streaking the loop back and forth.

7. Streak for isolation in the other quadrants.

8. Transfer 1 loopful of urine to MAC or EMB plate. Repeat procedure using SEA or colistin-nalidixic acid (CNA) agar.

9. Pull loop down surface of agar to form a single streak that crosses the center of the plate.

10. Cross streak through the initial inoculum streak by moving the loop back and forth at perpendicular angles to initial streak.

11. To inoculate media for special-collection urines, i.e., suprapubic tap, high and low counts, or nephrostomy, inoculate two sets of plates:

a. 0.001 loop: BAP and MAC (EMB) and SEA (CNA) agars.

b. 0.01 loop: BAP and MAC (EMB) and SEA (CNA) agars.

c. Use the same inoculation procedure outlined above for both the 0.001 loop and the 0.01 loop.

12. If a urine Gram stain is ordered, use a ringed microscope slide.

NOTE: Biplates, commercially available, consisting of MAC and CNA or MAC and SEA may be used instead of single-agar plates of each.

NOTE: bioMérieux-Vitek AMS has urine cards that can be substituted for culture analysis.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
Generic image for table
Table 2.1-8b

Procedure for processing clinical specimens in microbiology

Abbreviations: MS, mitis salivarius agar; SEA, selective enterococcus agar; TM, transport medium; PEA, phenyl ethanol agar; CAMPY, campylobacter agar; HE, Hektoen enteric agar; GN, gram-negative; SABSEL, Sabouraud's selective agar; BRU, brucella agar; BBE/LKV, bacteroides bile esculin agar/lakedblood-kanamycin-vancomycin agar.

Special instructions for processing urine specimens:

1. Do not centrifuge urine before culturing.

2. Mix urine well before culturing.

3. Use 0.001-ml calibrated loop for inoculating media for routine urine.

4. Transfer 1 loopful of urine to BAP.

5. Pull the loop down the surface of the agar to form a single streak in the center of the first quadrant.

6. Spread the inoculum over the first quadrant by streaking the loop back and forth.

7. Streak for isolation in the other quadrants.

8. Transfer 1 loopful of urine to MAC or EMB plate. Repeat procedure using SEA or colistin-nalidixic acid (CNA) agar.

9. Pull loop down surface of agar to form a single streak that crosses the center of the plate.

10. Cross streak through the initial inoculum streak by moving the loop back and forth at perpendicular angles to initial streak.

11. To inoculate media for special-collection urines, i.e., suprapubic tap, high and low counts, or nephrostomy, inoculate two sets of plates:

a. 0.001 loop: BAP and MAC (EMB) and SEA (CNA) agars.

b. 0.01 loop: BAP and MAC (EMB) and SEA (CNA) agars.

c. Use the same inoculation procedure outlined above for both the 0.001 loop and the 0.01 loop.

12. If a urine Gram stain is ordered, use a ringed microscope slide.

NOTE: Biplates, commercially available, consisting of MAC and CNA or MAC and SEA may be used instead of single-agar plates of each.

NOTE: bioMérieux-Vitek AMS has urine cards that can be substituted for culture analysis.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-9

Panic values in microbiology

Panic values in microbiology encompass the detection of clinically important microorganisms and viruses that require notification, immediate action by the physician of record or his/her designate, action by hospital personnel and visitors, and notification of governmental agencies (this may differ from state to state). AFB, acid-fast bacterium.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-10

Alert request

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
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Table 2.1-11a

Serodiagnostic tests

Tests can be performed in the laboratory or sent to a reference laboratory. Abbreviations: IgG, immunoglobulin G; LGV, lymphogranuloma venereum; MHA-TP, microhemagglutination; CMV, cytomegalovirus; HIV-1, human immunodeficiency virus type 1; HTLV-1, human T-cell leukemia virus type 1.

ACIF, anticomplement immunofluorescence; CF, complement fixation; DA, direct agglutination; IB, immunoblot; EIA, enzyme immunoassay; EN, enzyme neutralization; ID, immunodiffusion; IFA, indirect fluorescent antibody; IHA, indirect hemagglutination; LPA, latex particle agglutination; MAT, microagglutination titer; MIF, micro-indirect fluorescence; MC, mucin clot technique; NT, neutralization; PHA, passive hemagglutination; RPR, rapid plasma reagintest; SA, slide agglutination; VDRL, venereal disease research laboratory; IDTP, immunodiffusion tube precipitin test; IDCF, immune diffusion complement fixing antigen F test; TA, tube agglutinin.

Draw blood in red-top tube except when otherwise indicated.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
Generic image for table
Table 2.1-11b

Serodiagnostic tests

Tests can be performed in the laboratory or sent to a reference laboratory. Abbreviations: IgG, immunoglobulin G; LGV, lymphogranuloma venereum; MHA-TP, microhemagglutination; CMV, cytomegalovirus; HIV-1, human immunodeficiency virus type 1; HTLV-1, human T-cell leukemia virus type 1.

ACIF, anticomplement immunofluorescence; CF, complement fixation; DA, direct agglutination; IB, immunoblot; EIA, enzyme immunoassay; EN, enzyme neutralization; ID, immunodiffusion; IFA, indirect fluorescent antibody; IHA, indirect hemagglutination; LPA, latex particle agglutination; MAT, microagglutination titer; MIF, micro-indirect fluorescence; MC, mucin clot technique; NT, neutralization; PHA, passive hemagglutination; RPR, rapid plasma reagintest; SA, slide agglutination; VDRL, venereal disease research laboratory; IDTP, immunodiffusion tube precipitin test; IDCF, immune diffusion complement fixing antigen F test; TA, tube agglutinin.

Draw blood in red-top tube except when otherwise indicated.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
Generic image for table
Table 2.1-11c

Serodiagnostic tests

Tests can be performed in the laboratory or sent to a reference laboratory. Abbreviations: IgG, immunoglobulin G; LGV, lymphogranuloma venereum; MHA-TP, microhemagglutination; CMV, cytomegalovirus; HIV-1, human immunodeficiency virus type 1; HTLV-1, human T-cell leukemia virus type 1.

ACIF, anticomplement immunofluorescence; CF, complement fixation; DA, direct agglutination; IB, immunoblot; EIA, enzyme immunoassay; EN, enzyme neutralization; ID, immunodiffusion; IFA, indirect fluorescent antibody; IHA, indirect hemagglutination; LPA, latex particle agglutination; MAT, microagglutination titer; MIF, micro-indirect fluorescence; MC, mucin clot technique; NT, neutralization; PHA, passive hemagglutination; RPR, rapid plasma reagintest; SA, slide agglutination; VDRL, venereal disease research laboratory; IDTP, immunodiffusion tube precipitin test; IDCF, immune diffusion complement fixing antigen F test; TA, tube agglutinin.

Draw blood in red-top tube except when otherwise indicated.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1
Generic image for table
Table 2.1-11

Serodiagnostic tests

Tests can be performed in the laboratory or sent to a reference laboratory. Abbreviations: IgG, immunoglobulin G; LGV, lymphogranuloma venereum; MHA-TP, microhemagglutination; CMV, cytomegalovirus; HIV-1, human immunodeficiency virus type 1; HTLV-1, human T-cell leukemia virus type 1.

ACIF, anticomplement immunofluorescence; CF, complement fixation; DA, direct agglutination; IB, immunoblot; EIA, enzyme immunoassay; EN, enzyme neutralization; ID, immunodiffusion; IFA, indirect fluorescent antibody; IHA, indirect hemagglutination; LPA, latex particle agglutination; MAT, microagglutination titer; MIF, micro-indirect fluorescence; MC, mucin clot technique; NT, neutralization; PHA, passive hemagglutination; RPR, rapid plasma reagintest; SA, slide agglutination; VDRL, venereal disease research laboratory; IDTP, immunodiffusion tube precipitin test; IDCF, immune diffusion complement fixing antigen F test; TA, tube agglutinin.

Draw blood in red-top tube except when otherwise indicated.

Citation: Garcia L. 2010. Collection, Transport, and Manipulation of Clinical Specimens and Initial Laboratory Concerns, p 52-81. In Clinical Microbiology Procedures Handbook, 3rd Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817435.ch2.1

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