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. Wemore »
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Centers for Disease Control and Prevention, Fort Collins, CO (United States)
- Dept. of Homeland Security, Washington, D.C. (United States)
- U.S. Food and Drug Administration, Silver Springs, MD (United States)
- Univ. of Bayreuth (Germany)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- DHS; USDOE
- OSTI Identifier:
- 1338768
- Report Number(s):
- LA-UR-16-20885
Journal ID: ISSN 0099-2240
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Applied and Environmental Microbiology
- Additional Journal Information:
- Journal Volume: 83; Journal Issue: 3; Journal ID: ISSN 0099-2240
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biological Science
Citation Formats
Challacombe, Jean Faust, Petersen, Jeannine M., Gallegos-Graves, La Verne A., Hodge, David, Pillai, Segaran, Kuske, Cheryl Rae, and Drake, Harold L. Whole-genome relationships among Francisella bacteria of diverse origins define new species and provide specific regions for detection. United States: N. p., 2016.
Web. doi:10.1128/AEM.02589-16.
Challacombe, Jean Faust, Petersen, Jeannine M., Gallegos-Graves, La Verne A., Hodge, David, Pillai, Segaran, Kuske, Cheryl Rae, & Drake, Harold L. Whole-genome relationships among Francisella bacteria of diverse origins define new species and provide specific regions for detection. United States. https://doi.org/10.1128/AEM.02589-16
Challacombe, Jean Faust, Petersen, Jeannine M., Gallegos-Graves, La Verne A., Hodge, David, Pillai, Segaran, Kuske, Cheryl Rae, and Drake, Harold L. Wed .
"Whole-genome relationships among Francisella bacteria of diverse origins define new species and provide specific regions for detection". United States. https://doi.org/10.1128/AEM.02589-16. https://www.osti.gov/servlets/purl/1338768.
@article{osti_1338768,
title = {Whole-genome relationships among Francisella bacteria of diverse origins define new species and provide specific regions for detection},
author = {Challacombe, Jean Faust and Petersen, Jeannine M. and Gallegos-Graves, La Verne A. and Hodge, David and Pillai, Segaran and Kuske, Cheryl Rae and Drake, Harold L.},
abstractNote = {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). Lastly, this study provides a robust comparative framework to discern species and virulence features of newly detected Francisella bacteria.},
doi = {10.1128/AEM.02589-16},
journal = {Applied and Environmental Microbiology},
number = 3,
volume = 83,
place = {United States},
year = {Wed Nov 23 00:00:00 EST 2016},
month = {Wed Nov 23 00:00:00 EST 2016}
}
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- International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 2
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- Frontiers in Cellular and Infection Microbiology, Vol. 8
Innate Immune Recognition: An Issue More Complex Than Expected
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- Frontiers in Cellular and Infection Microbiology, Vol. 9
A Polyphasic Approach for Phenotypic and Genetic Characterization of the Fastidious Aquatic Pathogen Francisella noatunensis subsp. orientalis
journal, December 2017
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- Frontiers in Microbiology, Vol. 8
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journal, September 2017
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- PLOS ONE, Vol. 12, Issue 9