title: Identification and typing of Francisella tularensis with a highly automated genotyping assay.
abstract: A PCR assay was developed to genotypically characterize Francisella tularensis and F. novicida. An integrated and partially redundant set of markers was selected to provide positive identification of these species, identify subspecies of F. tularensis and genotype 14 variable number tandem repeat (VNTR) markers. Assay performance was evaluated with 117 Francisella samples. Sample DNA was amplified, and the masses of the PCR products were determined with electrospray ionization/time of flight mass spectrometry (ESI-MS). The base compositions of the PCR amplicons were derived from these high-accuracy mass measurements and contrasted with databased information associated with each of the 25 assay markers. Species and subspecies determinations for all samples were fully concordant with results from established typing methods, and VNTR markers provided additional discrimination among samples. Sequence variants were observed with a number of assay markers, but these did not interfere with sample characterization, and served to increase the genetic diversity detected by the assay.
authors.affiliation: Ibis Biosciences, an Abbott company, Carlsbad, CA, USA. david.duncan@abbott.com
authors.forename: D D
authors.initials: DD
authors.lastname: Duncan
authors.forename: A J
authors.initials: AJ
authors.lastname: Vogler
authors.forename: M J
authors.initials: MJ
authors.lastname: Wolcott
authors.forename: F
authors.initials: F
authors.lastname: Li
authors.forename: D S
authors.initials: DS
authors.lastname: Sarovich
authors.forename: D N
authors.initials: DN
authors.lastname: Birdsell
authors.forename: L M
authors.initials: LM
authors.lastname: Watson
authors.forename: T A
authors.initials: TA
authors.lastname: Hall
authors.forename: R
authors.initials: R
authors.lastname: Sampath
authors.forename: R
authors.initials: R
authors.lastname: Housley
authors.forename: L B
authors.initials: LB
authors.lastname: Blyn
authors.forename: S A
authors.initials: SA
authors.lastname: Hofstadler
authors.forename: D J
authors.initials: DJ
authors.lastname: Ecker
authors.forename: P
authors.initials: P
authors.lastname: Keim
authors.forename: D M
authors.initials: DM
authors.lastname: Wagner
authors.forename: M W
authors.initials: MW
authors.lastname: Eshoo
mesh_terms: D000818:Animals; D015373:Bacterial Typing Techniques / Q000379:methods*; D001482:Base Composition; D004269:DNA, Bacterial / Q000235:genetics; D005604:Francisella tularensis / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D005819:Genetic Markers; D005838:Genotype; D018598:Minisatellite Repeats; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D021241:Spectrometry, Mass, Electrospray Ionization; D013987:Ticks / Q000382:microbiology; D014406:Tularemia / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D005819:Genetic Markers