PLoS ONE (Jan 2012)

CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections.

  • Laëtitia Fabre,
  • Jian Zhang,
  • Ghislaine Guigon,
  • Simon Le Hello,
  • Véronique Guibert,
  • Marie Accou-Demartin,
  • Saïana de Romans,
  • Catherine Lim,
  • Chrystelle Roux,
  • Virginie Passet,
  • Laure Diancourt,
  • Martine Guibourdenche,
  • Sylvie Issenhuth-Jeanjean,
  • Mark Achtman,
  • Sylvain Brisse,
  • Christophe Sola,
  • François-Xavier Weill

DOI
https://doi.org/10.1371/journal.pone.0036995
Journal volume & issue
Vol. 7, no. 5
p. e36995

Abstract

Read online

Laboratory surveillance systems for salmonellosis should ideally be based on the rapid serotyping and subtyping of isolates. However, current typing methods are limited in both speed and precision. Using 783 strains and isolates belonging to 130 serotypes, we show here that a new family of DNA repeats named CRISPR (clustered regularly interspaced short palindromic repeats) is highly polymorphic in Salmonella. We found that CRISPR polymorphism was strongly correlated with both serotype and multilocus sequence type. Furthermore, spacer microevolution discriminated between subtypes within prevalent serotypes, making it possible to carry out typing and subtyping in a single step. We developed a high-throughput subtyping assay for the most prevalent serotype, Typhimurium. An open web-accessible database was set up, providing a serotype/spacer dictionary and an international tool for strain tracking based on this innovative, powerful typing and subtyping tool.