Bioinformatic Analyses of Whole-Genome Sequence Data in a Public Health Laboratory

Details

• Alternative Title:
  Emerg Infect Dis
• Personal Author:
  Oakeson, Kelly F. ; Wagner, Jennifer Marie ; Mendenhall, Michelle ; Rohrwasser, Andreas ; Atkinson-Dunn, Robyn
• Description:
  The ability to generate high-quality sequence data in a public health laboratory enables the identification of pathogenic strains, the determination of relatedness among outbreak strains, and the analysis of genetic information regarding virulence and antimicrobial-resistance genes. However, the analysis of whole-genome sequence data depends on bioinformatic analysis tools and processes. Many public health laboratories do not have the bioinformatic capabilities to analyze the data generated from sequencing and therefore are unable to take full advantage of the power of whole-genome sequencing. The goal of this perspective is to provide a guide for laboratories to understand the bioinformatic analyses that are needed to interpret whole-genome sequence data and how these in silico analyses can be implemented in a public health laboratory setting easily, affordably, and, in some cases, without the need for intensive computing resources and infrastructure.
• Subjects:
  Bacteria/classification Bacteria/genetics Bacteria/isolation & Purification Bacteria/pathogenicity Bacterial Infections/diagnosis Bacterial Infections/epidemiology Computational Biology/methods Computers Genome, Bacterial High-Throughput Nucleotide Sequencing/instrumentation High-Throughput Nucleotide Sequencing/methods Humans Laboratories Perspective Phylogeny Public Health/instrumentation Public Health/methods Public Health Surveillance Software Virulence Whole Genome Sequencing

  More +
• Source:
  Emerg Infect Dis. 23(9):1441-1445.
• Pubmed ID:
  28820135
• Pubmed Central ID:
  PMC5572866
• Document Type:
  Journal Article
• Place as Subject:
  United States
• Location:
  North America
• Volume:
  23
• Issue:
  9
• Collection(s):
  Emerging Infectious Diseases
• Main Document Checksum:
  urn:sha256:8ac2bd2336abaeced22e4136cdc39d8ca7eba7b9545d86fef173dadb02d8f5ca
• Download URL:
  https://stacks.cdc.gov/view/cdc/47972/cdc_47972_DS1.pdf
• File Type:
  [PDF - 719.39 KB ]