Strain Typing by Next Generation Sequencing



Figure 1. Genome diversity in Corynebacterium. jeikeium as determined by whole genome sequencing. Clinical isolates (outer colored rings) were sequenced by NGS and compared to the reference genome of C. jeikeium K411. The intensity of coloration is proportional to the degree of sequence identity relative to the reference, with white indicating sequences not present in the reference strain. Figure adapted from PMID: 25116839

About Strain Typing by Next Generation Sequencing

Whole genome sequencing (WGS) is a relatively new means for tracking disease outbreaks. Using “next-generation” (or “massively parallel”) DNA sequencing technology, it is now possible to sequence and compare the genomes of bacterial isolates, cataloging the polymorphisms that distinguish among strains (Figure 1). This provides information about the genetic relatedness of bacterial isolates (Figure 2) that is useful in outbreak investigations when it is coupled with patient biogeographic data and the dates of strain isolation. Although pulsed field gel electrophoresis (PFGE) has long been considered the gold-standard for bacterial strain typing in molecular epidemiological investigations, work by our laboratory and others indicate that WGS substantially outperforms PFGE in terms of discriminatory power and reproducibility (Salipante et al. 2015).


About Our Assay

Our lab utilizes high-fidelity next-generation sequencing to perform whole genome shotgun sequencing of bacterial isolates. Our genomic strain typing assay (NGSTYP) reports the absolute number of genomic differences identified between strains and provides a visual representation of strain relatedness (Figure 2). Interpretive guidelines for discriminating strains as indistinguishable, closely related, or unrelated are provided. Our methods are validated for a broad variety of culturable bacterial species.
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Figure 2. Relationships of bacterial isolates inferred by genomic strain typing. The inferred relationships of seven clinical isolates and an external reference genome are depicted. The branching order of the tree indicates groupings of the isolates, with the number of genomic differences separating strains indicated along the Y-axis. Suggested breakpoints for classifying isolates as indistinguishable or closely related are indicated by blue and red broken lines, respectively, with isolates considered unrelated falling above the red broken line.

To learn more about clinical applications and methodology:

Contact molmicdx@u.washington.edu for details or questions.


Clinical Reporting

Upon completion of testing, our report describes the results of strain typing by next generation sequencing. To view a sample report, click here or the thumbnail at left.

For additional information on how to submit a request and recieve a report, please contact us!