Pattern Genomics and CDC to Develop New Ways to Identify Shiga-toxin Producing E. coli

June 16, 2014

Pattern Genomics and the Centers for Disease Control and Prevention have launched a collaboration to investigate new molecular surveillance tools for identifying Shiga toxin-producing Escherichia coli (STEC) bacteria in clinical samples. Pattern Genomics will use its proprietary Daydreamer™ platform and CDC’s bacterial genomics data to identify sequence targets that are present in STEC but absent in related bacteria for potential use in the design of PCR primers and probes. This work may facilitate development of downstream applications such as droplet digital polymerase chain reaction (ddPCR), a promising method for quantifying genetic material and linking genes from individual strains in a complex matrix. 

“We are delighted to have the opportunity to work with the CDC’s world-leading scientists in developing important new analytical tools for surveillance of infectious diseases,” remarked Dr. Daniel Fasulo, the founder and president of Pattern Genomics.

About STEC

STEC bacteria are estimated by CDC to cause about 265,000 cases of diarrheal disease annually in the United States. Characterization of STEC bacteria for routine surveillance is currently performed by using conventional methods that rely on the availability of pure cultures. However, primary diagnostic laboratories are increasingly using culture-independent methods for diagnosing diarrheal illness. In order to preserve routine surveillance in the United States, it is critical to develop identification and subtyping approaches that could be applied directly to the primary stool samples. 

“New bioinformatics tools may make it possible to shave years off assay development, allowing CDC to better adapt to the rapidly changing world of diagnostic microbiology,” said John Besser, Deputy Chief of the Enteric Diseases Branch at CDC. 

About Pattern Genomics

Pattern Genomics, based in Madison, CT, is a biotechnology startup that uses its proprietary Daydreamer™ bioinformatics platform to design highly sensitive and specific molecular diagnostics.  Daydreamer™ is capable of simultaneously analyzing of hundreds of genomes and selecting optimal primers and probes for the specified detection technology, thus assuring sensitivity across a broad range of strains and specificity to the target genomes. The company, founded by Daniel Fasulo, Ph.D., was a recent participant in the Massachusetts Biotechnology Council MassCONNECT Mentoring Program ( and is funded by Connecticut Innovations ( and private investors. For more information, see:

About CDC

CDC works 24/7 saving lives and protecting people from health threats to have a more secure nation.  Whether these threats are chronic or acute, manmade or natural, human error or deliberate attack, global or domestic, CDC is the U.S. health protection agency. For more information about E. coli, please visit:


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