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PathoGenetix, Applied Math Collaborate on Pathogen Strain Typing

NEW YORK (GenomeWeb News) – PathoGenetix and Applied Maths today announced a deal to integrate each other's technologies into a solution for rapid pathogen strain typing.

The two firms will integrate Woburn, Mass.-based PathoGenetix's Resolution System and Belgium-based Applied Maths' BioNumerics software, resulting in a solution that will also allow public health and safety food testing laboratories to share and compare outbreak strain data, they said.

Additionally, serotype and strain type information generated by Resolution will be able to be compared to datasets generated through other identification methods, including pulsed field gel electrophoresis, or PFGE, and whole-genome sequencing.

The Resolution System uses PathoGenetix's Genome Sequence Scanning technology, which was developed for the detection of biothreat pathogens in environmental samples. The genotyping technology isolates and analyzes microbial DNA directly from complex mixtures without the need for a pure culture and provides molecular serotype and strain type information for all target bacteria present in the sample at detectable levels, PathoGenetix and Applied Maths said.

In April, the US Food and Drug Administration inked a collaborative agreement with PathoGenetix to evaluate the Genome Sequence Scanning technology for use in foodborne illness outbreak investigation and response.

BioNumerics is a software suite for managing integrative biological data and comparative analyses. The product includes data mining, clustering, identification, and statistical applications. Earlier this month, Applied Maths and OpGen announced a partnership to build software for microbial genomics and molecular strain typing, using the BioNumerics product.

"The Resolution System with BioNumerics software will offer public health and food testing labs the ability to seamlessly integrate, curate and compare new outbreak strain information with their existing PFGE and whole-genome sequence data sets," PathoGenetix President Ann Merrifield said in a statement. "With time-to-results reduced to just five hours, and a seamless connection to existing strain databases and laboratory tools, we can shorten outbreak investigation and response, and improve public health."