title: Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection.
abstract: Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, is considered a tier 1 biothreat agent. Detection and surveillance of F. tularensis may be confounded by the presence of uncharacterized, closely related organisms. Through DNA-based diagnostics and environmental surveys, novel clinical and environmental Francisella isolates have been obtained in recent years. Here we present 7 new Francisella genomes and a comparison of their characteristics to each other and to 24 publicly available genomes as well as a comparative analysis of 16S rRNA and sdhA genes from over 90 Francisella strains. Delineation of new species in bacteria is challenging, especially when isolates having very close genomic characteristics exhibit different physiological features-for example, when some are virulent pathogens in humans and animals while others are nonpathogenic or are opportunistic pathogens. Species resolution within Francisella varies with analyses of single genes, multiple gene or protein sets, or whole-genome comparisons of nucleic acid and amino acid sequences. Analyses focusing on single genes (16S rRNA, sdhA), multiple gene sets (virulence genes, lipopolysaccharide [LPS] biosynthesis genes, pathogenicity island), and whole-genome comparisons (nucleotide and protein) gave congruent results, but with different levels of discrimination confidence. We designate four new species within the genus; Francisella opportunistica sp. nov. (MA06-7296), Francisella salina sp. nov. (TX07-7308), Francisella uliginis sp. nov. (TX07-7310), and Francisella frigiditurris sp. nov. (CA97-1460). This study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria.
  
  
  
  DNA-based detection and sequencing methods have identified thousands of new bacteria in the human body and the environment. In most cases, there are no cultured isolates that correspond to these sequences. While DNA-based approaches are highly sensitive, accurately assigning species is difficult without known near relatives for comparison. This ambiguity poses challenges for clinical cases, disease epidemics, and environmental surveillance, for which response times must be short. Many new Francisella isolates have been identified globally. However, their species designations and potential for causing human disease remain ambiguous. Through detailed genome comparisons, we identified features that differentiate F. tularensis from clinical and environmental Francisella isolates and provide a knowledge base for future comparison of Francisella organisms identified in clinical samples or environmental surveys.
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: Jean F
authors.initials: JF
authors.lastname: Challacombe
authors.affiliation: Division of Vector-Borne Infectious Diseases, Centers for Disease Control and Prevention, Fort Collins, Colorado, USA.
authors.forename: Jeannine M
authors.initials: JM
authors.lastname: Petersen
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA.
authors.forename: La Verne
authors.initials: V
authors.lastname: Gallegos-Graves
authors.affiliation: Chemical and Biological Division, Science and Technology Directorate, Department of Homeland Security, Washington, DC, USA.
authors.forename: David
authors.initials: D
authors.lastname: Hodge
authors.affiliation: Office of Laboratory Science and Safety, U.S. Food and Drug Administration, Silver Spring, Maryland, USA.
authors.forename: Segaran
authors.initials: S
authors.lastname: Pillai
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA Kuske@lanl.gov.
authors.forename: Cheryl R
authors.initials: CR
authors.lastname: Kuske
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D005420:Flavoproteins / Q000235:genetics*; D005603:Francisella / Q000145:classification* / Q000235:genetics* / Q000472:pathogenicity; D014644:Genetic Variation; D016680:Genome, Bacterial; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA; D014774:Virulence
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D005420:Flavoproteins; D012336:RNA, Ribosomal, 16S; C084271:SdhA protein, Bacteria
keywords: Allofrancisella; Francisella frigiditurris (CA97-1460); Francisella holarctica; Francisella novicida; Francisella opportunistica (MA06-7296); Francisella philomiragia; Francisella salina (TX07-7308); Francisella species; Francisella tularensis; Francisella uliginis (TX07-7310); amino acid identity; new Francisella species; nucleic acid sequence identity; whole-genome comparisons