ArticleBMC microbiology2009
Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay.
Article in BMC microbiology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
26 citing papers in PubMed, 52 citations in OpenAlex.
- Evidente-a visual analytics tool for data enrichment in SNP-based phylogenetic trees.Bioinformatics advances · 2022Article
- Development, Phenotypic Characterization and Genomic Analysis of aFrontiers in microbiology · 2021Article
- The Francisella tularensis Polysaccharides: What Is the Real Capsule?Microbiology and molecular biology reviews : MMBR · 2020Review
- Whole-Genome Relationships among Francisella Bacteria of Diverse Origins Define New Species and Provide Specific Regions for Detection.Applied and environmental microbiology · 2017Article
- Russian isolates enlarge the known geographic diversity of Francisella tularensis subsp. mediasiatica.PloS one · 2017Article
- Rapid Identification and Characterization of Francisella by Molecular Biology and Other Techniques.The open microbiology journal · 2016Article
- Population analysis of Streptococcus suis isolates from slaughtered swine by use of minimum core genome sequence typing.Journal of clinical microbiology · 2014Article
- Francisella tularensis subsp. tularensis group A.I, United States.Emerging infectious diseases · 2014Article
- Virulence difference between the prototypic Schu S4 strain (A1a) and Francisella tularensis A1a, A1b, A2 and type B strains in a murine model of infection.BMC infectious diseases · 2014Article
- Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data.BMC bioinformatics · 2014Article
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- German Francisella tularensis isolates from European brown hares (Lepus europaeus) reveal genetic and phenotypic diversity.BMC microbiology · 2013Article
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- Adaptive mutations and replacements of virulence traits in the Escherichia coli O104:H4 outbreak population.PloS one · 2013Article
- Genomic comparison between a virulent type A1 strain of Francisella tularensis and its attenuated O-antigen mutant.Journal of bacteriology · 2012Article
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- Use of temperature for standardizing the progression of Francisella tularensis in mice.PloS one · 2012Article
- Differential chitinase activity and production within Francisella species, subspecies, and subpopulations.Journal of bacteriology · 2011Article
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Authors and funding
11 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundA low genetic diversity in Francisella tularensis has been documented. Current DNA based genotyping methods for typing F. tularensis offer a limited and varying degree of subspecies, clade and strain level discrimination power. Whole genome sequencing is the most accurate and reliable method to identify, type and determine phylogenetic relationships among strains of a species. However, lower cost typing schemes are necessary in order to enable typing of hundreds or even thousands of isolates.
resultsWe have generated a high-resolution phylogenetic tree from 40 Francisella isolates, including 13 F. tularensis subspecies holarctica (type B) strains, 26 F. tularensis subsp. tularensis (type A) strains and a single F. novicida strain. The tree was generated from global multi-strain single nucleotide polymorphism (SNP) data collected using a set of six Affymetrix GeneChip resequencing arrays with the non-repetitive portion of LVS (type B) as the reference sequence complemented with unique sequences of SCHU S4 (type A). Global SNP based phylogenetic clustering was able to resolve all non-related strains. The phylogenetic tree was used to guide the selection of informative SNPs specific to major nodes in the tree for development of a genotyping assay for identification of F. tularensis subspecies and clades. We designed and validated an assay that uses these SNPs to accurately genotype 39 additional F. tularensis strains as type A (A1, A2, A1a or A1b) or type B (B1 or B2).
conclusionWhole-genome SNP based clustering was shown to accurately identify SNPs for differentiation of F. tularensis subspecies and clades, emphasizing the potential power and utility of this methodology for selecting SNPs for typing of F. tularensis to the strain level. Additionally, whole genome sequence based SNP information gained from a representative population of strains may be used to perform evolutionary or phylogenetic comparisons of strains, or selection of unique strains for whole-genome sequencing projects.
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