Introduction to Laboratory Diagnosis of Infectious Disease

Laboratory tests may identify organisms directly (eg, visually, using a microscope, growing the organism in culture) or indirectly (eg, identifying antibodies to the organism). General types of tests include

• Microscopy

• Culture

• Immunologic tests (agglutination tests such as latex agglutination, enzyme immunoassays, Western blot, precipitation tests, and complement fixation tests)

• Genotypic nucleic acid–based identification methods or NAATs (eg, polymerase chain reaction [PCR])

• Phenotypic non-nucleic acid–based identification methods (eg, serologic assays, mass spectrometry [MALDI-TOF MS], nuclear magnetic resonance [NMR] spectrometry)

Culture is normally the gold standard for identification of organisms, but results may not be available for days or weeks, and not all pathogens can be cultured, making alternative tests useful. When a pathogen is cultured and identified, the laboratory can also assess its susceptibility to antimicrobials. The introduction of both genotypic and phenotypic rapid diagnostic tests (RDTs) has allowed for a more rapid and targeted approach to antimicrobial therapy. Sometimes molecular methods can be used to detect specific resistance genes.

Some tests (eg, Gram stain, routine aerobic culture) can detect a large variety of pathogens and are commonly done for many suspected infectious illnesses. However, because some pathogens are missed on these tests, clinicians must be aware of the limitations of each test for each suspected pathogen. In such cases, clinicians should request tests specific for the suspected pathogen (eg, special stains or culture media) or advise the laboratory of the suspected organism or organisms so that more specific tests may be selected (1).