• Accurate, multi-locus strain typing to assess relatedness of cases
  • Configurable: add markers for resistance and virulence to established MLST schemas
  • Easy-to-use, point-and-click workflow from raw data to strain analysis
  • Web-based, secure, sequence data management and interpretation solutions requiring no investment in local IT

Sanger-based methods of multi-locus sequence typing (MLST) replaced pulsed field gel electrophoresis (PFGE) as the gold standard approach for strain analysis and outbreak surveillance of bacteria. Standards have been adopted internationally for many organisms of interest defining both the panel of housekeeping genes to be analyzed for that species and the typing nomenclature to be applied to report unambiguously the specific strain which is identified. Importantly, such sequence-based approaches can be consistently and comparably reproduced by different institutions and at different times. This greatly improves the accuracy and timeliness of the surveillance activity, whether the scenario is a national outbreak of a food-borne pathogen or the suspicion of cross-contamination of an intermediate or final product across an international BioPharmaceutical supply chain.

With the advent of NGS technology, typing becomes much quicker and less expensive than Sanger-based sequencing of multiple genes of an isolated organism. NGS enables more rapid and higher resolution typing and tracking of bacterial or fungal strains.

SmartGene provides Web-based applications to support typing, both by Sanger and by NGS methods. Typically, SmartGene’s typing modules are implemented according to the established MLST schema for the organism in question.  Additional genes of interest may be added to the panel, for example to provide higher resolution for assessing case relatedness, to analyze resistance genes or to address markers of virulence and pathogenicity. If the user is running NGS methods, SmartGene recommends its genome target analysis (GTA) pipeline.

GTA assumes that shotgun whole genome sequencing is being used in the laboratory to create the sequence reads for an isolated organism.  The user loads these several million reads for the sample into the GTA pipeline, and the aligners within the pipeline then select all the reads which map to the defined panel of genes.  The panel has been established to answer the specific goals of the analysis. This selective mapping process of GTA efficiently addresses the questions at hand by analyzing only the informative regions of the genome without requiring the time and computational burden to execute, unnecessarily, a whole genome assembly. As other typing questions arise over time, the analytical panel of genes can be expanded accordingly, and the entire raw data set from the shotgun sequencing can be re-interpreted by the updated pipeline without incurring the time and expense of resequencing. Thus, the SmartGene modules enable the user to efficiently sequence once, yet interpret multiple times.

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