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Clin Infect Dis. 2007 Apr 15;44(8):1108-14. Epub 2007 Mar 2.

Detection and identification of microorganisms by gene amplification and sequencing.

Author information

1
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

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.

PMID:
17366460
DOI:
10.1086/512818
[Indexed for MEDLINE]

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