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Diagnostic medical microbiology is concerned with the etiologic diagnosis of infection. Laboratory procedures used in the diagnosis of infectious disease in humans include the following:


  1. Morphologic identification of the agent in stains of specimens or sections of tissues (light and electron microscopy).

  2. Culture isolation and identification of the agent.

  3. Detection of antigen from the agent by immunologic assay (latex agglutination, enzyme immunoassay [EIA], etc) or by fluorescein-labeled (or peroxidase-labeled) antibody stains.

  4. DNA-DNA or DNA-RNA hybridization to detect pathogen- specific genes in patients'specimens.

  5. Detection and amplification of organism nucleic acid in patients'specimens.

  6. Demonstration of meaningful antibody or cell-mediated immune responses to an infectious agent.


In the field of infectious diseases, laboratory test results depend largely on the quality of the specimen, the timing and the care with which it is collected, and the technical proficiency and experience of laboratory personnel. Although physicians should be competent to perform a few simple, crucial microbiologic tests—make and stain a smear, examine it microscopically, and streak a culture plate—technical details of the more involved procedures are usually left to the bacteriologist or virologist and the technicians on the staff. Physicians who deal with infectious processes must know when and how to take specimens, what laboratory examinations to request, and how to interpret the results.


This chapter discusses diagnostic microbiology for bacterial, fungal, chlamydial, and viral diseases. The diagnosis of parasitic infections is discussed in Chapter 46.


Diagnostic microbiology encompasses the characterization of thousands of agents that cause or are associated with infectious diseases. The techniques used to characterize infectious agents vary greatly depending on the clinical syndrome and the type of agent being considered, be it virus, bacterium, fungus, or parasite. Because no single test will permit isolation or characterization of all potential pathogens, clinical information is much more important for diagnostic microbiology than it is for clinical chemistry or hematology. The clinician must make a tentative diagnosis rather than wait until laboratory results are available. When tests are requested, the physician should inform the laboratory staff of the tentative diagnosis (type of infection or infectious agent suspected). Proper labeling of specimens includes such clinical data as well as the patient's identifying data (at least two methods of definitive identification) and the requesting physician's name and pertinent contact information.


Many pathogenic microorganisms grow slowly, and days or even weeks may elapse before they are isolated and identified. Treatment cannot be deferred until this process is complete. After obtaining the proper specimens and informing the laboratory of the tentative clinical diagnosis, the clinician should begin treatment with drugs aimed at the organism thought to be responsible for the patient's illness. As the laboratory staff begins to obtain results, they inform health care providers, who can then reevaluate the diagnosis and clinical course of the patient and perhaps make changes in the therapeutic program. This "feedback" information from the laboratory consists of preliminary reports of the results of ...

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