Prescott's Microbiology,4/e

		Microbiology, 4/e Prescott, Harley, Klein
		Instructor Resources

34 Clinical Microbiology

CHAPTER OVERVIEW

This chapter presents important information for understanding the field of clinical microbiology, which involves the detection and identification of pathogens that are the etiological agents of infectious disease. Identification may be based on the results of some combination of morphological, physiological, biochemical, and immunological procedures. Time may be critical in life-threatening situations; therefore, rapid identification systems and computers can be used to greatly speed up the process. Procedures that are useful for determining microorganism sensitivity to various antimicrobial agents are also discussed.

CHAPTER OBJECTIVES

After reading this chapter you should be able to:

! describe the functions and/or services performed by clinical microbiology laboratories

! discuss the need for proper specimen selection, collection, handling, and processing

! discuss the various procedures used to identify microorganisms in specimens

! explain the methods used for testing the sensitivity of microorganisms to antimicrobial agents

! discuss the use and advantage of computers in clinical microbiology

CHAPTER OUTLINE

I. SpecimensCportions of human material that are tested, examined, or studied to determine the presence or absence of specific microorganisms; universal safety precautions have been recommended by the CDC to address safety issues in specimen handling

A. Specimens should be:

1. Representative of the diseased area

2. Adequate in quantity for a variety of diagnostic tests

3. Devoid of contamination, particularly by microorganisms indigenous to the skin and mucous membranes

4. Forwarded promptly to the clinical laboratory

5. Obtained prior to the administration of any antimicrobials

B. Collection

1. Sterile swabCskin and mucous membranes

2. Needle aspirationCblood and cerebrospinal fluidCskin surface microorganisms must be excluded by the use of stringent antiseptic techniques

3. IntubationCstomach

4. CatheterizationCurine

5. Clean-catch midstream urineCfirst urine voided is not collected, because it is likely to be contaminated with surface organisms

6. SputumCmucous secretion expectorated from the lungs, bronchi, and/or trachea

C. HandlingCincludes any special additives (e.g., anticoagulants) and proper labeling

D. TransportCshould be timely; temperature control may be needed; special treatment may be needed for anaerobes

II. Identification of Microorganisms from Specimens

A. MicroscopyCdirect examination of specimen, or examination of specimen after various staining procedures

B. Growth and Biochemical characteristics

1. VirusesCidentified by isolation in living cells, immunoassays, or nucleic acid technology

a. Host organisms for culture

(1) Embryonated hen=s eggs

(2) Laboratory animals

(3) Cell or tissue cultures

(4) Transgenic cell lines from transgenic animals

b. Detection of virus growth

(1) Cytopathic effects, lesions, plaques

(2) HemadsorptionCthe binding of red blood cells to the surface of infected cells

(3) Interference with subsequent infection by another virus

2. FungiCidentified by direct microscopic examination; immunofluorescence; yeast can be identified by the use of rapid ID methods (e.g., API 20C; Microring YT)

3. ParasitesCidentified by examining specimens for eggs, cysts, larvae, or vegetative cells; immunofluorescence is often used

4. BacteriaCidentified by growth on selective and differential media; hemolytic, metabolic, and fermentative properties are also used

5. RickettsiasCidentified by isolation (hazardous) or by immunoassays

6. ChlamydiaeCidentified by immunofluorescence and growth in cell culture

7. MycoplasmasCidentified immunologically or by the use of DNA probes

C. Rapid methods of identification

1. Manual biochemical techniquesCAPI 20E system for enterobacteria

a. Consists of 20 microtube inoculation tests

b. Results are converted to a seven- or nine-digit profile number

c. The number is compared to the API Profile Index to determine the name of the bacterium

2. Mechanized/automated techniques (e.g., BIOLOG)Cbased on substrate catabolism

3. Immunological techniquesCquick test kits that usually do not require growing the organism

D. Immunological techniquesCdetection of antigens or serum antibodies in specimens by the various procedures discussed in chapter 32

E. Bacteriophage typingCthe host range specificities of bacteriophages are dependent upon surface receptors on the particular bacteria; therefore, this can be a reliable method of identification

F. Molecular methods (some have been previously discussed)

1. Enzyme kinetic comparisons

2. Nucleic Acid-based detection methodsCssDNA molecules that have been cloned from organism or prepare by PCR technology can be used in hybridization procedures; rRNA genes can be used to identify bacterial strains (ribotyping)

3. Gas-liquid chromatography (GLC)Cused to identify specific microbial metabolites, cellular fatty acids, and products of pyrolysis; usually for nonpolar substances that are extractable in ether

4. Plasmid fingerprintingCseparation and detection of the number and molecular weight of different plasmids, which are often consistently present in a strain of bacteria

III. Susceptibility TestingCused to help physician decide which drug(s) and which dosage(s) to use

IV. Computers in Clinical Microbiology

A. Test orderingCspecific requests, patient data, and accession number

B. Result entry

C. Report printingCflexible format to meet the needs of physician

D. Laboratory management

E. Interfaced with automated instruments

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