title: Comparative genomics of 2009 seasonal plague (Yersinia pestis) in New Mexico.
abstract: Plague disease caused by the gram-negative bacterium Yersinia pestis routinely affects animals and occasionally humans, in the western United States. The strains native to the North American continent are thought to be derived from a single introduction in the late 19(th) century. The degree to which these isolates have diverged genetically since their introduction is not clear, and new genomic markers to assay the diversity of North American plague are highly desired. To assay genetic diversity of plague isolates within confined geographic areas, draft genome sequences were generated by 454 pyrosequencing from nine environmental and clinical plague isolates. In silico assemblies of Variable Number Tandem Repeat (VNTR) loci were compared to laboratory-generated profiles for seven markers. High-confidence SNPs and small Insertion/Deletions (Indels) were compared to previously sequenced Y. pestis isolates. The resulting panel of mutations allowed clustering of the strains and tracing of the most likely evolutionary trajectory of the plague strains. The sequences also allowed the identification of new putative SNPs that differentiate the 2009 isolates from previously sequenced plague strains and from each other. In addition, new insertion points for the abundant insertion sequences (IS) of Y. pestis are present that allow additional discrimination of strains; several of these new insertions potentially inactivate genes implicated in virulence. These sequences enable whole-genome phylogenetic analysis and allow the unbiased comparison of closely related isolates of a genetically monomorphic pathogen.
authors.affiliation: United States Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, United States of America. henry.gibbons.civ@mail.mil
authors.forename: Henry S
authors.initials: HS
authors.lastname: Gibbons
authors.forename: Michael D
authors.initials: MD
authors.lastname: Krepps
authors.forename: Gary
authors.initials: G
authors.lastname: Ouellette
authors.forename: Mark
authors.initials: M
authors.lastname: Karavis
authors.forename: Lisa
authors.initials: L
authors.lastname: Onischuk
authors.forename: Pascale
authors.initials: P
authors.lastname: Leonard
authors.forename: Stacey
authors.initials: S
authors.lastname: Broomall
authors.forename: Todd
authors.initials: T
authors.lastname: Sickler
authors.forename: Janet L
authors.initials: JL
authors.lastname: Betters
authors.forename: Paul
authors.initials: P
authors.lastname: McGregor
authors.forename: Greg
authors.initials: G
authors.lastname: Donarum
authors.forename: Alvin
authors.initials: A
authors.lastname: Liem
authors.forename: Ed
authors.initials: E
authors.lastname: Fochler
authors.forename: Lauren
authors.initials: L
authors.lastname: McNew
authors.forename: C Nicole
authors.initials: CN
authors.lastname: Rosenzweig
authors.forename: Evan
authors.initials: E
authors.lastname: Skowronski
mesh_terms: D005819:Genetic Markers; D014644:Genetic Variation; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D009516:New Mexico; D010930:Plague / Q000235:genetics* / Q000382:microbiology; D014774:Virulence / Q000235:genetics; D015010:Yersinia pestis / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D005819:Genetic Markers