ArticlePloS one2014
TaqMan real-time PCR assays for single-nucleotide polymorphisms which identify Francisella tularensis and its subspecies and subpopulations.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 38 citations in OpenAlex.
- Detection of Francisellaceae and the differentiation of main European F. tularensis ssp. holarctica strains (Clades) by new designed qPCR assays.BMC microbiology · 2025Article
- Development of a Real-Time PCR Assay for the Detection ofMicroorganisms · 2024Article
- Reorganized Genomic Taxonomy ofMicroorganisms · 2021Article
- Differences in Blood-derivedMicroorganisms · 2020Article
- Optimized MALDI TOF Mass Spectrometry Identification ofMicroorganisms · 2020Article
- Differentiation of Francisella tularensis Subspecies and Subtypes.Journal of clinical microbiology · 2020Article
- Phylogenetic Lineages ofFrontiers in cellular and infection microbiology · 2018Review
- Environmental Surveillance of ZoonoticFrontiers in cellular and infection microbiology · 2018Article
- Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model.PLoS neglected tropical diseases · 2017Article
- A new real-time PCR protocol for detection of avian haemosporidians.Parasites & vectors · 2015Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Francisella tularensis, the etiologic agent of tularemia and a Class A Select Agent, is divided into three subspecies and multiple subpopulations that differ in virulence and geographic distribution. Given these differences, there is a need to rapidly and accurately determine if a strain is F. tularensis and, if it is, assign it to subspecies and subpopulation. We designed TaqMan real-time PCR genotyping assays using eleven single nucleotide polymorphisms (SNPs) that were potentially specific to closely related groups within the genus Francisella, including numerous subpopulations within F. tularensis species. We performed extensive validation studies to test the specificity of these SNPs to particular populations by screening the assays across a set of 565 genetically and geographically diverse F. tularensis isolates and an additional 21 genetic near-neighbor (outgroup) isolates. All eleven assays correctly determined the genetic groups of all 565 F. tularensis isolates. One assay differentiates F. tularensis, F. novicida, and F. hispaniensis from the more genetically distant F. philomiragia and Francisella-like endosymbionts. Another assay differentiates F. tularensis isolates from near neighbors. The remaining nine assays classify F. tularensis-confirmed isolates into F. tularensis subspecies and subpopulations. The genotyping accuracy of these nine assays diminished when tested on outgroup isolates (i.e. non F. tularensis), therefore a hierarchical approach of assay usage is recommended wherein the F. tularensis-specific assay is used before the nine downstream assays. Among F. tularensis isolates, all eleven assays were highly sensitive, consistently amplifying very low concentrations of DNA. Altogether, these eleven TaqMan real-time PCR assays represent a highly accurate, rapid, and sensitive means of identifying the species, subspecies, and subpopulation of any F. tularensis isolate if used in a step-wise hierarchical scheme. These assays would be very useful in clinical, epidemiological, and/or forensic investigations involving F. tularensis.
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