Recent advances in DNA sequencing technology have allowed the rapid sequencing of pathogen genomes for detection and forensic purposes. DNA sequencing emerged in 1977 with the chemical method of Maxam and Gilbert, followed by the biochemical dideoxy method of Sanger, Nicken, and Coulson. The Sanger method revitalized the sequencing industry with the completion of the sequence of the first draft of the human genome published in 2001, but the refinement and analysis of the human genome sequence and understanding the biology of different aspects of the human genome will continue for the unforeseeable future. During the past 5 years, new "massively parallel" sequencing methods coupled with automation are greatly increasing sequencing capacity and making it possible to collect large amounts of data in a day or two to be analyzed for functional significance for detection, diagnostic, and forensic use. This review article will focus on how to analyze the different sequencing methodologies available in the market and their application in the clinical microbiology laboratory for detection, diagnostic, and forensic use and, therefore, the management of infectious disease outbreaks.
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