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

Multi-faceted approach to the molecular typing of Yersinia pestis strains.

WGS Test: Molecular typing of Yersinia pestis strains using Whole Genome Sequencing data.

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

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 Yersinia pestis 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 species specific SNP profile is determined through real-time PCR (accredited) and/or WGS data (non-accredited) and compared to control strains.

14 calendar days for a final result.

1. Vogler AJ et al., 2008. Assays for the rapid and specific identification of North American Yersinia pestis and the common laboratory strain CO92 Biotechniques. February ; 44(2): 201–207
2. Ciammaruconi A et al., 2009. A rapid allele variant discrimination method for Yersinia pestis strains based on high-resolution melting curve analysis. Diagnostic Microbiology and Infectious Disease 65; 7–13
3. Morelli G et al., 2010. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity.Nat Genet. December; 42(12): 1140–1143. doi:10.1038/ng.705.