Chapter 3.16 : Guidelines for Biochemical Identification of Aerobic Bacteria

Abstract:

Clinical microbiology practice is rapidly moving away from the primary use of conventional biochemical tests for the identification of aerobic bacteria and towards the use of nonphenotypic identification methods. Analysis of the protein composition of a bacterial cell using matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry is being widely implemented into routine practice worldwide. MALDI-TOF mass spectrometry rapidly identifies a wide range of bacterial pathogens, including nonfermenting Gram-negative bacilli, staphylococci, corynebacteria, and anaerobes ( 1 , 2 , 3 , 4 , 5 , 6 ). Molecular methods are also being implemented either as laboratory-developed assays or as part of a commercial platform for rapid identification of specific pathogens by various methods, including real-time PCR, partial DNA target sequencing, or microarrays ( 7 ). Referral or reference laboratories may also routinely perform in-house partial 16S rRNA gene sequencing of fastidious or unusual bacterial isolates that cannot be definitively identified by other means ( 8 ).