The principles of bacterial cultivation and identification discussed in Chapter 7 focus on pheno-typic methods. These methods analyze readily observable bacterial traits and "behavior." Although these strategies are the mainstay of diagnostic bacteriology, notable limitations are associated with the use of phenotypic methods. These limitations are as follows:
The explosion in molecular biology over the past 20 years has provided alternatives to phenotype-based strategies used in clinical microbiology. These alternatives have the potential to avert some of the aforementioned limitations. The detection and manipulation of nucleic acids (DNA and RNA) allows microbial genes to be examined directly (i.e., genotypic methods) rather than by analysis of their products such as enzymes (Le., phenotypic methods). Additionally, nonnucleic acid-based analytic methods that detect phenotypic traits not detectable by conventional strategies (e.g., cell wall components) have been developed to enhance bacterial detection, identification, and characterization. For the laboratory diagnosis of infectious diseases to remain timely and effective, strategies that integrate conventional, nucleic acid-based, and analytic techniques must continue to evolve.
Several methods that analyze microbial DNA or RNA can detect, identify, and characterize infectious etiologies. Although technical aspects may differ, all molecular procedures involve the direct manipulation and analysis of genes, in whole or in part, rather than the analysis of gene products. Furthermore, because nucleic acids are common to all living entities, most methods are adaptable for the diagnosis of viral, fungal, parasitic, or bacterial infections. This chapter discusses the general principles and applications of molecular diagnostics.
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