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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. Detection of the agent in patient specimens by antigen testing (latex agglutination, enzyme immunoassay, etc) or nucleic acid testing (nucleic acid hybridization, polymerase chain reaction [PCR], sequencing, etc).

  3. Culture isolation and identification of the agent. Susceptibility testing of the agent by culture or nucleic acid methods, where appropriate.

  4. 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 transported, and the technical proficiency and experience of laboratory personnel. Although physicians should be competent to perform a few simple, crucial microbiologic tests (perform direct wet mounts of certain specimens, make a Gram-stained smear and examine it microscopically, and streak a culture plate), the technical details of the more involved procedures are usually left to trained microbiologists. 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, and viral diseases. The diagnosis of parasitic infections is discussed in Chapter 46.


Diagnostic microbiology encompasses the detection and 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, whether virus, bacterium, fungus, or parasite. Due to the wide variety of available tests for diagnosis of infectious diseases and need for their interpretation, 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(s) 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(s) thought to be responsible for the patient’s illness. As the laboratory staff begins to obtain results, they will inform health care providers, who can then reevaluate the diagnosis and clinical course ...

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