PathoGenetix’s Genome Sequence Scanning (GSS) technology provides a unique approach to rapidly typing thousands of bacterial strains in a single test.
The GSS technology, which employs a single reagent set, extracts genomic bar codes from microbial DNA as it flows through a microfluidic chip at 150 million base pairs per second. Complex biological specimens can be scanned to detect and identify strains of pathogenic organisms in approximately three hours, days faster and at lower cost that current techniques. GSS can be applied to advanced research in microbial genomics, food and pharmaceutical product safety, and clinical infectious disease diagnostics.
Approach
Under GSS, an automated sample preparation system extracts genomic DNA from a biological sample (e.g. complex biological specimens, clinical specimens, food samples).
DNA is cut into large fragments and labeled with a fluorescent tag that recognizes a frequently occurring 6-8 base-pair sequence, and then linearized in a microfluidic device. Linearized DNA fragments in the size range 100-300 kilobases flow at 150 megabases/sec past a detection system, where the fragment length and spatial pattern of tags along each DNA fragment is recorded. This tag pattern on each fragment is based on the underlying DNA sequence and is conceptually similar to a genomic barcode.
The genomic barcode of each fragment passing the detector is compared to patterns in a database to enable identification of the bacteria, including the specific strain, from which the DNA fragment is derived. Unlike approaches that require specific reagents for detecting each pathogen, GSS employs a single reagent set to create the barcodes that can then be used to simultaneously detect and identify thousands of strains from hundreds of microbial species. Genomic barcodes in the database can be generated from a known sequence or by measurement in the system. GSS analyzes samples directly; neither PCR nor other amplification techniques are used. Current sample-to-answer time is approximately three hours.
