title: Canonical insertion-deletion markers for rapid DNA typing of Francisella tularensis.
abstract: To develop effective and accurate typing of strains of Francisella tularensis, a potent human pathogen and a putative bioterrorist agent, we combined analysis of insertion-deletion (indel) markers with multiple-locus variable-number tandem repeat analysis (MLVA). From 5 representative F. tularensis genome sequences, 38 indel markers with canonical properties, i.e., capable of sorting strains into major genetic groups, were selected. To avoid markers with a propensity for homoplasy, we used only those indels with 2 allelic variants and devoid of substantial sequence repeats. MLVA included sequences with much diversity in copy number of tandem repeats. The combined procedure allowed subspecies division, delineation of clades A.I and A.II of subspecies tularensis, differentiation of Japanese strains from other strains of subspecies holarctica, and high-resolution strain typing. The procedure uses limited amounts of killed bacterial preparations and, because only 1 single analytic method is needed, is time- and cost-effective.
authors.affiliation: Swedish Defence Research Agency, Umeå, Sweden.
authors.forename: Pär
authors.initials: P
authors.lastname: Larsson
authors.forename: Kerstin
authors.initials: K
authors.lastname: Svensson
authors.forename: Linda
authors.initials: L
authors.lastname: Karlsson
authors.forename: Dimitri
authors.initials: D
authors.lastname: Guala
authors.forename: Malin
authors.initials: M
authors.lastname: Granberg
authors.forename: Mats
authors.initials: M
authors.lastname: Forsman
authors.forename: Anders
authors.initials: A
authors.lastname: Johanssont
mesh_terms: D016172:DNA Fingerprinting / Q000379:methods*; D017931:DNA Primers / Q000235:genetics; D005604:Francisella tularensis / Q000235:genetics* / Q000302:isolation & purification; D049810:Genetic Speciation; D016680:Genome, Bacterial / Q000235:genetics; D006801:Humans; D054643:INDEL Mutation; D018598:Minisatellite Repeats; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods
chemical_list: D017931:DNA Primers