Bacterial Strain Typing by Next Generation Sequencing

Method
Whole Genome Sequencing (WGS) is performed using Ion Torrent sequencing chemistry. Reference-free pairwise comparisons are performed using short, overlapping sequence matching (kmer) analysis. Relationships are determined by the percent of kmers that match between isolate pairs.

Interpretation
Predicted relatedness is based on the total number of differences between the isolates, applying the thresholds shown in the table. The dendrogram and relationship matrix (see enhanced report) illustrate isolate relatedness. Interpretation of strain relatedness should be performed by an investigator knowledgeable about whole genome strain typing procedures and based on all available epidemiological evidence. Inferred relationships based on any strain typing method should not be used for individual patient management.

WGS Strain Typing provides substantial improvements in resolution and reproducibility when compared to pulsed-field gel electrophoresis (PFGE) and can be performed on a broad range of microorganisms. Test was validated for Staphylococcus, Acinetobacter, Enterococcus, Escherichia, Pseudomonas, Stenotrophomonas, Serratia, and Klebsiella species.

This test was developed and its performance characteristics determined by ARUP Laboratories. It has not been cleared or approved by the US Food and Drug Administration. This test was performed in a CLIA certified laboratory and is intended for clinical purposes.