Molecular genetics - microbial


Blood, urine, swabs, sputum, nasopharyngeal aspirate, CSF, pleural/pericardial fluid, peritoneal fluid - as appropriate.


Detection of specific bacterial, viral, fungal, protozoal, parasitic or plasmid DNA, viral or ribosomal DNA or viral RNA, using nucleic acid probes with or without preceding PCR amplification.

See Molecular genetics.


Diagnosis of infection in circumstances where other approaches involve significant difficulty or delay:

  1. Presence of few or no free organisms (eg, CSF in herpes simplex encephalitis).

  2. Prolonged time required for culture of Mycobacterium tuberculosis, with results required for initial therapy of tuberculous infection.

  3. Limited sensitivity and specificity of serology; a positive result may only indicate past infection eg for with hepatitis C, serology is less informative than identification of viral RNA in serum; in enterovirus meningitis or encephalitis, detection of enterovirus RNA in CSF provides a more rapid and reliable diagnosis than serology.

  4. Organisms which cannot be cultured can be identified by molecular genetics eg, hepatitis C virus, Tropheryma whippelii in suspected Whipple’s disease.

  5. Difficulties with storage or transport may render conventional techniques impractical or insensitive eg, in genital Chlamydia trachomatis infection or infection with Neisseria gonorrhoeae. Even with delays in specimen processing chlamydial ribosomal RNA or plasmid DNA can be identified by molecular genetics techniques.

Molecular genetics techniques are also used for typing organisms for epidemiological purposes and may be used to provide quantitative results to monitor the progress of therapy eg, in HIV and hepatitis C.


Both false positive and negative results occur. A knowledge of the specificity and sensitivity of the tests in individual laboratories is required.

There are now a plethora of nucleic acid tests for a variety of conditions available, but for many of these the sensitivity and specificity have not yet been determined and the clinical utility is thus undefined.

Although a positive test indicates the presence of the organism, the diagnosis of the actual infection requires the presence of consistent clinical findings.

See also RCPA Catalogue of Genetic Tests and Laboratories.


Padzorski R and Persing D. In: Murray PR et al eds. Manual of Clinical Microbiology. 6th ed. 1995. ASM Press.

Schirm J et al. J Clin Microbiol 1995; 33: 3221-3224.

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