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Sequenced-Based Typing of Prokaryotes

  • Henrik ChristensenEmail author
  • John Elmerdahl Olsen
Chapter
Part of the Learning Materials in Biosciences book series (LMB)

Abstract

The reason to investigate prokaryotic populations is introduced with focus on the population-genetic mechanisms responsible for the formation and conservation of populations. Multilocus sequence typing revolutionized molecular typing by proving information that could be compared between different laboratories and that could be analyzed in well-curated databases on servers via the Internet. The success of MLST has continued based on the analysis of the whole genomic sequence whereby the genetic information analyzed has been extended with hundreds of genes for wgMLST. The other use of whole genomic sequences for typing has been single-nucleotide polymorphism (SNP) analysis where the reads from high-throughput sequencing are compared to a reference sequence allowing very detailed comparison at the single-nucleotide level in order to trace single strains. For certain, mainly human pathogenic bacteria like Escherichia coli and Salmonella enterica, organism-specific prediction in databases on dedicated servers is available where serotype, antimicrobial resistance profile, and wgMLST can be predicted based on the whole genomic sequence uploaded via the Internet.

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Copyright information

© Springer Nature Switzerland AG 2018

Authors and Affiliations

  1. 1.Department of Veterinary Animal SciencesUniversity of CopenhagenCopenhagenDenmark

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