Comparison of four enzymatic library preparation kits for sequencing Shiga toxin-producing Escherichia coli for surveillance and outbreak detection

J Microbiol Methods. 2021 Nov:190:106329. doi: 10.1016/j.mimet.2021.106329. Epub 2021 Sep 22.

Abstract

Four enzymatic DNA library preparation kits were compared for sequencing Shiga toxin-producing E. coli. All kits produced high quality sequence data which performed equally well in the downstream analyses for surveillance and outbreak detection. Important differences were noted in the workflow user-friendliness and per sample cost.

Keywords: Allele detection; Escherichia; GC bias; Library preparation; WGS.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Bacterial / isolation & purification
  • Disease Outbreaks
  • Epidemiological Monitoring
  • Escherichia coli Infections / diagnosis*
  • Escherichia coli Infections / microbiology
  • Gene Library
  • Genome, Bacterial
  • Humans
  • Reagent Kits, Diagnostic / economics*
  • Reagent Kits, Diagnostic / microbiology*
  • Sequence Analysis, DNA
  • Shiga-Toxigenic Escherichia coli / genetics*
  • Shiga-Toxigenic Escherichia coli / isolation & purification*
  • Whole Genome Sequencing
  • Workflow

Substances

  • DNA, Bacterial
  • Reagent Kits, Diagnostic