Molecular techniques for clinical diagnostic bacteriology

Abstract

Molecular methods have contributed tremendously to the understanding of the pathogenesis and epidemiology of infectious diseases. The polymerase chain reaction (PCR) is the most widely used target nucleic acid amplification method. By this method, a single copy of a nucleic acid is multiplied to more than 107 times within a very short period. New technologies such as real-time PCR, sequencing and mass spectrophotometry have been described and have many applications in a clinical microbiology laboratory. The greatest impact of real-time assays was in the field of virology where they have been used to detect rapidly a range of viruses in human specimens and to monitor quantitatively viral loads and response to antiviral therapy. In bacteriology they are used for rapid detection of bacterial pathogens and/or antibiotic resistance genes can help to ensure the appropriate use of antibiotics, reduce the duration of hospital stay and minimize the potential for resistant strains of bacteria to emerge. Commercial kits employing PCR technology for detection of Neisseria gonorrhoeae and Chlamydia trachomatis have been developed. Nucleic acid amplification tests can be used directly to identify Mycobacterium tuberculosis complex in clinical specimens. Some clinical laboratories have developed their in-house assays based on PCR assays to detect M. tuberculosis in clinical specimens. Some studies have compared the kits and "in-house" methods and have found similar results. In addition to in-house developed assays, there are commercial amplification tests some of them that are widely used. This chapter describes the basic principles and applications of recently DNA-based molecular techniques for the clinical bacteriology.