Systems for detection and identification of bacteria and yeasts

Traditionally, the detection and identification of bacteria were based on conventional tube-based biochemical reactions, and their results were compared to historical charts of expected biochemical reactions. Automation in microbiology first occurred in the early 1970s with the introduction of semiautomated blood culture instruments, followed by instrumented systems for identification and susceptibility testing of bacteria. This chapter reviews the systems used for the detection of bacteria and yeasts from blood and provides an overview of technologies for microorganism identification. The volume of blood obtained for culture is one of the most important variables in the detection of bloodstream infections (BSIs). The chapter describes the identification of microorganisms by nonphenotypic methods from instrument-flagged blood culture bottles, and from pure culture. The approximate turnaround time of the fluorescence in situ hybridization (FISH) procedure is 2.5 to 3 h (without batch testing), compared with <18 to 24 h for identification of bacteria and yeasts by conventional methods. The selection of DNA targets to identify bacteria and fungi relies on the concept that some genes have conserved segments flanked by variable regions. The technology is based on analyzing the protein composition of a bacterial cell, with ribosomal proteins comprising most bacterial proteins being detected. Another technique to characterize bacteria is the application of electrospray ionization-mass spectrometry to analyze products of multilocus, broad-range PCR (PCR/ESI-MS).