Reorganized genomic taxonomy of francisellaceae enables design of robust environmental PCR assays for detection of francisella tularensis

Caroline Öhrman, Jason W. Sahl, Andreas Sjödin, Ingrid Uneklint, Rebecca Ballard, Linda Karlsson, Ryelan F. McDonough, David Sundell, Kathleen Soria, Stina Bäckman, Kitty Chase, Björn Brindefalk, Shanmuga Sozhamannan, Adriana Vallesi, Emil Hägglund, Jose Gustavo Ramirez-Paredes, Johanna Thelaus, Duncan Colquhoun, Kerstin Myrtennäs, Dawn BirdsellAnders Johansson, David M. Wagner, Mats Forsman

Research output: Contribution to journalArticlepeer-review

Abstract

In recent years, an increasing diversity of species has been recognized within the family Francisellaceae. Unfortunately, novel isolates are sometimes misnamed in initial publications or multiple sources propose different nomenclature for genetically highly similar isolates. Thus, unstructured and occasionally incorrect information can lead to confusion in the scientific community. Historically, detection of Francisella tularensis in environmental samples has been challenging due to the considerable and unknown genetic diversity within the family, which can result in false positive results. We have assembled a comprehensive collection of genome sequences representing most known Francisellaceae species/strains and restructured them according to a taxonomy that is based on phylogenetic structure. From this structured dataset, we identified a small number of genomic regions unique to F. tularensis that are putatively suitable for specific detection of this pathogen in environmental samples. We designed and validated specific PCR assays based on these genetic regions that can be used for the detection of F. tularensis in environmental samples, such as water and air filters.

Original languageEnglish (US)
Article number146
Pages (from-to)1-21
Number of pages21
JournalMicroorganisms
Volume9
Issue number1
DOIs
StatePublished - Jan 2021

Keywords

  • Assay
  • Francisella taxonomy
  • Phylogeny
  • Tularemia

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)
  • Virology

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