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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 or etiologic diagnosis 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 scientist 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 being used in many clinical microbiology laboratories. Particularly promising are newer multiplexed polymerase chain reaction (PCR) platforms that enable rapid detection of multiple potential pathogens in a single test reaction. Panels are available for respiratory, gastrointestinal, and central nervous system pathogens directly on appropriate specimens and identification of positive blood cultures. Despite such progress, however, traditional methods remain important and complementary, since isolation of microorganisms by culture is needed for most antimicrobial susceptibility testing. Not all pathogens are detected in these panels, and only known pathogens are sought. Therefore, this chapter considers the principles of infectious disease laboratory diagnosis and the methods available. Details about particular agents are discussed in the relevant chapters and in the section about infectious disease syndromes and etiologies at the back of the book. All diagnostic approaches begin with some kind of specimen collected from the patient.

Clinical diagnosis or question precedes and guides approach to etiologic diagnosis

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 ...

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