title: CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections.
abstract: 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.
authors.affiliation: Institut Pasteur, Unité des Bactéries Pathogènes Entériques, Paris, France.
authors.forename: Laëtitia
authors.initials: L
authors.lastname: Fabre
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.forename: Ghislaine
authors.initials: G
authors.lastname: Guigon
authors.forename: Simon
authors.initials: S
authors.lastname: Le Hello
authors.forename: Véronique
authors.initials: V
authors.lastname: Guibert
authors.forename: Marie
authors.initials: M
authors.lastname: Accou-Demartin
authors.forename: Saïana
authors.initials: S
authors.lastname: de Romans
authors.forename: Catherine
authors.initials: C
authors.lastname: Lim
authors.forename: Chrystelle
authors.initials: C
authors.lastname: Roux
authors.forename: Virginie
authors.initials: V
authors.lastname: Passet
authors.forename: Laure
authors.initials: L
authors.lastname: Diancourt
authors.forename: Martine
authors.initials: M
authors.lastname: Guibourdenche
authors.forename: Sylvie
authors.initials: S
authors.lastname: Issenhuth-Jeanjean
authors.forename: Mark
authors.initials: M
authors.lastname: Achtman
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brisse
authors.forename: Christophe
authors.initials: C
authors.lastname: Sola
authors.forename: François-Xavier
authors.initials: FX
authors.lastname: Weill
mesh_terms: D030541:Databases, Genetic; D006801:Humans; D020407:Internet; D055029:Inverted Repeat Sequences / Q000235:genetics*; D011110:Polymorphism, Genetic / Q000235:genetics*; D011159:Population Surveillance / Q000379:methods*; D012480:Salmonella Infections / Q000175:diagnosis* / Q000235:genetics; D012486:Salmonella typhimurium / Q000235:genetics*; D012703:Serotyping / Q000379:methods*