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AMD Achievements

Achievements made through CDC’s AMD activities are revolutionizing disease detection and surveillance. The scientific advances made through AMD will reduce the time needed to identify the source of disease outbreaks, increase the ability of public health professionals to track outbreaks, and maximize resources for outbreak responses.

CDC Names Winner of the “No-Petri-Dish” Diagnostic Test Challenge

CDC works to foster innovation in epidemiology, bioinformatics, and next-generation genomic sequencing through its Advanced Molecular Detection (AMD) activities. In 2014, CDC announced the winner of its “No Petri Dish” Diagnostic Test Challenge – Reference Genomics, Inc. and their One Codex bioinformatics platform.

Contestants in the “No Petri Dish” Diagnostic Test Challenge submitted proposals to describe a novel or innovative method to straintype and characterize pathogenic organisms, such as Shiga toxin-producing Escherichia coli (STEC), directly from a complex clinical sample (such as stool). The developers of One Codex succeeded in demonstrating how their platform can rapidly identify STEC from complex clinical samples and provide meaningful information about its straintype and characteristics, even when the pathogens are present at levels too low to support assembly-based methods. Reference Genomics, Inc. and One Codex developers Nik Krumm, PhD and Nick Greenfield received the $200,000 Challenge prize to continue development of their platform.

UPDATE

Through the “No-Petri Dish” Diagnostic Test Challenge, One Codex further developed its platform to support advanced public health and microbiome use cases. Upgrades made through the “No-Petri Dish” Diagnostic Test Challenge sped development of the next version of One Codex’s cloud-based microbial classifier, which rapidly identifies microbes from a database of 40,000 whole genomes. The new platform maintains sensitivity of pathogen detection and decreases the number of false-positive results. This work also led One Codex to become a partner in the White House’s National Microbiome Initiative by launching a public portal for microbiome data that will allow researchers, clinicians, and other public health professionals more access to microbiome data.

CDC continues to foster innovation through partnerships that improve pathogen detection and allow sharing of genomic sequence data between federal, state, and private-sector partners.

AMD Accomplishments

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  • Page last reviewed: June 10, 2016
  • Page last updated: June 10, 2016
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