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The diagnosis of a microbial infection begins with an assessment of clinical and epidemiologic features, leading to the formulation of a diagnostic hypothesis. Anatomic localization of the infection with the aid of physical and radiologic findings (eg, right lower lobe pneumonia, subphrenic abscess) is usually included. This clinical diagnosis suggests a number of possible etiologic agents based on knowledge of infectious syndromes and their courses. The specific cause is then established by the application of methods described in this chapter. A combination of science and art on the part of both the clinician and laboratory worker is required: The clinician must select the appropriate tests and specimens to be processed and, where appropriate, suggest the suspected etiologic agents to the laboratory. The laboratory worker must use the methods that will demonstrate the probable agents, and be prepared to explore other possibilities suggested by the clinical situation or by the findings of the laboratory examinations. The best results are obtained when communication between the clinician and laboratory is maximal.

The general approaches to laboratory diagnosis vary with different microorganisms and infectious diseases. However, the types of methods are usually some combination of direct microscopic examinations, culture, antigen detection, and antibody detection (serology). Nucleic acid amplification (NAA) assays that allow direct detection of genomic components of pathogens are now numerous, and are becoming more routinely conducted in many clinical microbiology laboratories as they have become more automated and less expensive. This chapter considers the principles of infectious disease laboratory diagnosis. Details with regard to particular agents are discussed in their chapters and with regard to clinical situations in the clinical tables at the back of the book. All diagnostic approaches begin with some kind of specimen collected from the patient.

Microscopic, culture, antigen, and antibody detection are classic methods

Genomic approaches are becoming the new gold standard for specific types of microorganisms and are continuing to expand in applications.


The primary connection between the clinical encounter and the diagnostic laboratory is the specimen submitted for processing. If it is not appropriately chosen and/or collected, no degree of laboratory skill can rectify the error. Failure at the level of specimen collection is the most common reason for failing to establish an etiologic diagnosis, or worse, for suggesting a wrong diagnosis. In the case of bacterial infections, the primary problem lies in distinguishing resident or contaminating normal floral organisms from those causing the infection. The three specimen categories illustrated in Figure 4–1A-C are discussed in the text that follows.


Specimens for the diagnosis of infection. A. Direct specimen. The pathogen is localized in an otherwise sterile site, and a barrier such as the skin must be passed to sample it. This may be done surgically or by needle aspiration as shown. The specimen collected contains only the pathogen. Examples are deep abscess and cerebrospinal fluid. ...

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