Principles of molecular microbiology testing methods

Application of rapid-cycle real-time polymerase chain reaction for diagnostic testing in the clinical microbiology laboratory

CONTEXT

Rapid-cycle real-time polymerase chain reaction (PCR) technology combines rapid thermocycling with real-time fluorescent probe detection of amplified target nucleic acids.

OBJECTIVES

To review and compare the method of rapid-cycle real-time PCR to conventional PCR methods. To describe the application of rapid-cycle real-time PCR for diagnostic testing in the microbiology laboratory.

DATA SELECTION

Information is presented from published literature as well as from personal experience at the Mayo Clinical Microbiology Laboratory (Rochester, Minn).

CONCLUSIONS

Compared to conventional PCR methods, rapid-cycle real-time PCR diagnostics are much faster and easier to perform, and, because both PCR and probe detection occur in the same reaction vessel, the possibility of amplified product (amplicon) contamination is lessened. Furthermore, compared to conventional culture-based or direct antigen detection methods, rapid-cycle real-time PCR assays are frequently more sensitive and much more rapid techniques for detecting or quantifying microorganisms in human samples and for identifying genes or mutations in pathogens associated with antimicrobial resistance.

Applications of polymerase chain reaction in rheumatology

Polymerase chain reaction (PCR) is a highly sensitive and specific method for detection and quantification of specific nucleic acids from a clinical sample. With its use, genetic, infectious, neoplastic, and autoimmune diseases can be diagnosed and managed with a high level of sensitivity, accuracy, and rapidity. This technique exactly reproduces unlimited copies of DNA, even if only a small amount are present initially. PCR assays can detect presence of fastidious and slow-growing microorganisms, such as chlamydia, mycoplasmas, mycobacterias, and viruses directly from clinical specimens and also can detect antimicrobial resistance. The value of viral load measurement by nucleic acid amplification in the management of patients with HIV infection or hepatitis C has also been well established. From the point of view of a clinician, the applications of PCR are focused mainly in the amplification and detection of diagnostic DNA segments from the genomes of both pathogens and patients.

Susceptibility testing. Phenotypic and genotypic tests for bacteria and mycobacteria

Genotypic-based methods hold promise for the rapid and accurate detection or confirmation of antimicrobial resistance; however, phenotypic methods will continue to have an advantage when resistance to the same antimicrobial agent may be caused by several different mechanisms. The diversity of genetic mechanisms may exceed the capabilities of current molecular technology. Genotypic assays have the ability to detect resistance but not susceptibility. Although resutls can be obtained rapidly, many molecular methods are labor-intensive, expensive, and lack standardization. Clinical studies will be required to validate the genotypic approach to detection of antimicrobial resistance. Molecular assays are also at risk for false-positive results because of contamination of specimens by other specimens that carry the DNA targeted for the assay, or carryover of amplified target DNA (amplicons) from a previous PCR assay during sample preparation. Detection of certain genetic resistance loci in clinical specimens must be interpreted with caution, because organisms in normal flora may also harbor the same loci. All these factors must be taken into consideration when introducing a genotypic method in the clinical laboratory. Other considerations include cost, turnaround time, and assay performance. It must be emphasized that the bedside assessment of the patient should always be considered in addition to the results of antimicrobial susceptibility tests (whether phenotypic or genotypic) so that the best outcome is assured for the patient.