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).
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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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.
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