Once delegated only to research, molecular methods are now finding application in many branches of clinical microbiology:
- Virology
- Bacteriology
- Mycology
- Mycobacteriology
- Parasitology
In vitro molecular assays of interest evolve constantly, depending on the presence of newly emerging infectious diseases and the need to streamline or improve current test methods. Tests have been developed for use in portable molecular diagnostics instrumentation (eg., field work - as in tuberculosis assays used all over the world, and point-of-care scenarios), as well as in very large, complex, high-throughput instrumentation located in public health and reference laboratories. Many clinical laboratories utilize benchtop models, and some have designated entire rooms to large instrumentation. Assays (and the platforms on which they are run) may be one of three types:
- Lab-developed tests (LDT) - where the tests have been developed by medical professionals and researchers and may be used for diagnostic testing (some using CDC primer sets) as long as all additional required and applicable quality controls, verifications, and validations have been performed;
- Approved for use as research use only (RUO) or investigational use only (IUO) - tests should not be used in diagnostic procedures because they are still under development; or
- Commercial tests, referred to as "kits", developed by industry professionals and FDA-approved -- or approved for use under emergency use authorization (EUA) designation. (The most recent example of an EUA kit has been the SARS-CoV-2 molecular test kit.) Clinical laboratories must still provide their own evidence of method verification as required by the Clinical Laboratory Improvement Act (CLIA).
In molecular testing, the particular assay (primer or probe) patent may be owned by one company, while a license to use it is sold to several different manufacturers for development and use on their own instrumentation platform. It is not uncommon to see software patented by one company in use by another.
Always refer to manufacturer instructions before use, as well as the expressed wording of any package insert or method validation before choosing or implementing a system for the laboratory.
In the subtopic sections that follow, examples of assays for commonly encountered infectious diseases are presented. See if you can pick out the method(s) of amplification (target or signal), using knowledge gained from review of the table (on page 21). (This practice will prove useful when performing future package insert/method reviews.) It is well beyond the scope of this course to discuss all assays; however, a good article for understanding the scope of this topic across microbiology molecular laboratories (see Tables within the reference below) may be found here:
Vira H, Bhat V, Chavan P. Diagnostic molecular microbiology and its applications: current and future perspectives.
Open Access Text. 2016. Accessed May 31, 2022.
https://oatext.com/pdf/CMID-1-105.pdf.
