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
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Immunologic tests (agglutination tests such as latex agglutination, enzyme immunoassays, Western blot, precipitation tests, and complement fixation tests)
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 antimicrobial drugs. 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(s) so that it may select more specific tests. (See table Diagnostic Tests for Common Pathogens.)
Diagnostic Tests for Common Pathogens
Microorganism |
Microscopy |
Culture |
Nucleic Acid Amplification Test (NAAT) |
Antigen Detection |
Antibody Detection |
Bacteria |
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✓ |
✓ |
✓ |
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|
✓ |
|
✓ |
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|
✓ |
✓ |
|
✓ |
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|
✓ |
✓ |
|
✓ |
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|
✓ |
✓ |
✓ |
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|
|
✓ |
✓ |
|
✓ |
✓ |
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|
✓ |
✓ |
✓ |
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|
✓ |
✓ |
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|
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|
✓ |
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|
Erysipelothrix species |
✓ |
✓ |
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|
✓ |
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✓ |
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|
✓ |
✓ |
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✓ |
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✓ |
✓ |
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✓ |
✓ |
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✓ |
✓ |
✓ |
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✓ |
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✓ |
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✓ |
✓ |
✓ |
✓ |
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✓ |
✓ |
✓ |
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✓ |
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✓ |
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✓ |
✓ |
✓ |
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✓ |
✓ |
✓ |
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Rhodococcus equus |
✓ |
✓ |
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|
✓ |
✓ |
✓ |
✓ |
✓ |
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|
✓ |
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✓ |
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X |
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|
✓ |
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✓ |
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✓ |
✓ |
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✓ |
✓ |
✓ |
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✓ |
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Mycobacteria |
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✓ |
✓ |
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Tuberculosis and ulcerans |
✓ |
✓ |
✓ |
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Intracellular Organisms |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
✓ |
✓ |
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✓ |
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✓ |
✓ |
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✓ |
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✓ |
✓ |
✓ |
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✓ |
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Fungi |
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✓ |
✓ |
✓ |
✓ |
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✓ |
✓ |
✓ |
✓ |
✓ |
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✓ |
✓ |
✓ |
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✓ |
✓ |
✓ |
✓ |
✓ |
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✓ |
✓ |
✓ |
✓ |
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✓ |
✓ |
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✓ |
✓ |
✓ |
✓ |
✓ |
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✓ |
✓ |
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✓ |
✓ |
✓ |
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✓ |
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✓ |
✓ |
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✓ |
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✓ |
✓ |
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Viruses |
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✓ |
✓ |
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BK virus |
✓ |
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✓ |
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✓ |
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✓ |
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✓ |
✓ |
✓ |
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✓ |
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✓ |
✓ |
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✓ |
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✓ |
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✓ |
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Hepatitis A, B, C, D and E |
|
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✓ |
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✓ |
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✓ |
✓ |
✓ |
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✓ |
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✓ |
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✓ |
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✓ |
✓ |
✓ |
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✓ |
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✓ |
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✓ |
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✓ |
✓ |
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JC virus |
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✓ |
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✓ |
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LaCrosse virus |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
✓ |
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✓ |
✓ |
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✓ |
✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
✓ |
✓ |
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✓ |
✓ |
✓ |
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✓ |
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St Louis encephalitis virus |
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✓ |
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Tickborne encephalitis virus |
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✓ |
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✓ |
✓ |
✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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Protozoa and Parasites |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
✓ |
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✓ |
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✓ |
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✓ |
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✓ |
✓ |
✓ |
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✓ |
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✓ |
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✓ |
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Intestinal nematodes |
✓ |
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✓ |
✓ |
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✓ |
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✓ |
✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
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✓ |
✓ |
✓ |
✓ |
✓ |
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Adapted from Bennett JE, Dolin R, Blaser MJ: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 9th Edition. Elsevier, 2020. |
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