Whole Genome Sequencing (WGS) and Single Nucleotide Polymorphisms (SNPs)

Multi-faceted approach to the molecular typing of Francisella tularensis strains.

WGS Test: Molecular typing of Francisella tularensis strains using Whole Genome Sequencing data.

SNP Test: Molecular typing of Francisella tularensis strains to determine genetic variations between members of a species, using canonical single nucleotide polymorphisms.

• Tularemia

Pure bacterial culture.

Pure bacterial culture – plate or swab.

Store bacterial cultures refrigerated until shipped for testing.

Shipping of specimens shall be done by a TDG certified individual in accordance with TDG regulations. For additional information regarding classification of specimens for the purposes of shipping, consult either Part 2 Appendix 3 of the TDG Regulations or section 3.6.2 of the IATA Dangerous Goods Regulations as applicable.

Confirmed Francisella tularensis infection.     

Completed Bioforensics Assay Development and Diagnostics requisition including sender name, address and telephone number. Patient name or identifier (referring lab #), date of birth, suspected exposure, test(s) requested, clinical history, travel history, type of specimen and date collected.

N/A

WGS Test: The phylogenetic relationships and subtype strains are determined using Whole Genome Sequencing data based on single base pair variants (SNVs) at specific genomic locations.

SNP Test: The SNP pattern will be determined through PCR and/or WGS data, looking for single base pair mutations at a specific locus which usually consists of two alleles. 

14 calendar days for a final result.

1. Birdsell DN, et al. 2014 TaqMan Real-Time PCR Assays for Single-Nucleotide Polymorphisms Which Identify Francisella tularensis and ts Subspecies and Subpopulations. PLoS ONE 9(9): e107964. https://doi.org/10.1371/journal.pone.0107964
2. Keim, P. 2009. Real-Time PCR Canonical SNP assay for Genotyping Francisella tularensis. Northern Arizona University. Guidelines and Standard operating Procedures for Forensic Analysis. V.20Mar09

Pathogen Safety Data Sheets: Infectious Substances – Francisella tularensis

Case Definitions for Communicable Diseases under National Surveillance - 2009 - Tularemia

Tularemia - Frequently Asked Questions