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 Birdsell; Anders Johansson; David M. Wagner; Mats Forsman

doi:10.3390/microorganisms9010146

Microorganisms (Jan 2021)

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 Birdsell,
Anders Johansson,
David M. Wagner,
Mats Forsman

Affiliations

Caroline Öhrman: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Jason W. Sahl: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
Andreas Sjödin: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Ingrid Uneklint: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Rebecca Ballard: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
Linda Karlsson: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Ryelan F. McDonough: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
David Sundell: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Kathleen Soria: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
Stina Bäckman: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Kitty Chase: US Army Medical Research Institute, Fort Detrick, MD 21702, USA
Björn Brindefalk: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Shanmuga Sozhamannan: Logistics Management Institute supporting Defense Biological Product Assurance Office (DBPAO) Joint Project Lead, CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD 21702, USA
Adriana Vallesi: School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy
Emil Hägglund: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Jose Gustavo Ramirez-Paredes: Ridgeway Biologicals Limited a Ceva Santé Animale Company, Units 1-3 Old Station Business Park, Compton, Berkshire, England RG20 6NE, UK
Johanna Thelaus: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Duncan Colquhoun: Fish Health Research Group, Norwegian Veterinary Institute, Oslo, Pb 750 Sentrum, 23 N-0106 Oslo, Norway
Kerstin Myrtennäs: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden
Dawn Birdsell: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
Anders Johansson: Department of Clinical Microbiology, Clinical Bacteriology, and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 85 Umeå, Sweden
David M. Wagner: Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
Mats Forsman: CBRN Defence and Security, Swedish Defence Research Agency, FOI, SE 901 82 Umeå, Sweden

DOI: https://doi.org/10.3390/microorganisms9010146
Journal volume & issue: Vol. 9, no. 1
p. 146

Abstract

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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.

Published in Microorganisms

ISSN: 2076-2607 (Online)
Publisher: MDPI AG
Country of publisher: Switzerland
LCC subjects: Science: Biology (General)
Website: https://www.mdpi.com/journal/microorganisms

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