title: Detection and identification of microorganisms by gene amplification and sequencing.
abstract: Gene amplification and sequencing have led to the discovery of new pathogens as agents of disease and have enabled us to better classify microorganisms from culture. Sequence-based identification of bacteria and fungi using culture is more objective and accurate than conventional methods, especially for classifying unusual microorganisms that are emerging pathogens in immunocompromised hosts. Although a powerful tool, the interpretation of sequence-based classification can be challenging as microbial taxonomy grows more complex, without known clinical correlatives. Additionally, broad-range gene polymerase chain reaction and sequencing have emerged as alternative, culture-independent methods for detecting pathogens from clinical material. The promise of this technique has remained strong, limited mainly by contamination and inadequate sensitivity issues. This review explains sequence-based microbial classification, with emphasis on relating the complex world of microbial taxonomy to a clinical context. Additionally, this review discusses a rational approach to broad-range bacterial polymerase chain reaction and gene sequencing when applied directly to clinical samples.
authors: Department of Medicine, University of Utah School of Medicine, and Associated Regional University Pathologists Laboratories, Salt Lake City, UT 84132, USA. cathy.petti@aruplab.com
authors: Cathy A
authors: CA
authors: Petti
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification*; D015373:Bacterial Typing Techniques; D017931:DNA Primers; D005784:Gene Amplification; D021141:Nucleic Acid Amplification Techniques; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000032:analysis* / Q000235:genetics
chemical_list: D017931:DNA Primers; D012336:RNA, Ribosomal, 16S