Bacterial identification based on 16S ribosomal RNA gene sequence analysis

Clinical microbiology laboratory is responsible for the isolation or detection of microorganisms to establish the diagnosis of infection. Rapid and accurate identification of these organisms and subsequent antibacterial drug susceptibility tests also guide antibiotic therapy. Although these goals can be fulfilled most of the time, some bacteria may be difficult to be identified due to fastidious growth, morphological variations, unusual biochemical reactions, lack of previous recognition, or a combination of these. Subculture failure, though it rarely happens, virtually makes routine identification impossible. Fortunately, technological advances have largely overcome these limitations for bacterial identification. One of the advances realized in the past decade or so has been the analysis of the nucleotide sequences of the 16S ribosomal RNA gene (16S rDNA), which has emerged as the single best method to identify bacteria (Kolbert and Persing, 1999; Drancourt et al., 2000). This chapter reviews its theoretical basis, methodology, clinical application, and limitations. A thorough and in-depth review with many practical points has just been published elsewhere (Clarridge, 2004).