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 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 performs whole genome shotgun sequencing of bacterial isolates using Illumina sequencing chemistries. Our genomic strain typing assay (NGSTYP) reports the number of single nucleotide polymorphisms (SNPs) differentiating isolates from one another. Distinguishing SNPs are identified using a reference free method which allows pairwise comparison of genomic sequences shared between isolates (Uricaru et al. 2015). The number of distinguishing SNPs are counted in order to estimate the degree of relatedness among isolates. The number of polymorphisms which distinguish isolate pairs is proportional to their time of divergence from a common ancestor. Our assay is not intended to (1) identify all genomic differences distinguishing isolates, (2) detect genomic differences resulting from structural variation, gene acquisition or loss, gain or loss of extrachromosomal elements such as plasmids, or large sequence insertions or deletions. Our assay is 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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