Consortium Conducting Largest-Ever Metagenomics Study

On February 1, the CDC officially declared that the E. coli outbreak linked to Chipotle restaurants late last year was over, but not before the disease had sickened 58 people across 12 states. That was after hundreds of Chipotle customers had fallen victim to two norovirus outbreaks in California and Massachusetts. Not surprisingly, the chain’s stock price took a dive of 40 percent in early January and Chipotle announced it expected to lose 15 percent of its profits this year.

While the outbreak was winding down, the Consortium for Sequencing the Food Supply Chain (CSFSC) announced that chromogenic- and molecular-testing firm BioRad had joined their team. Formed out of a meeting between industry, government, and academic experts on food safety, the CSFSC is anchored in a collaboration between IBM Research and Mars Inc. and is working toward large-scale sequencing of the DNA and RNA of major food ingredients in order to help reduce outbreaks like those at Chipotle.

“As the food supply chain becomes more global and complex,” says Jeff Welser, vice president and lab director of IBM Research-Almaden in San Jose, “new, innovative approaches that use genetic data to better understand and improve food safety are emerging, holding the promise of unparalleled insight and understanding of the total supply chain.”

The goal of the CSFSC, he says, is to conduct the largest-ever metagenomics study to categorize and understand the growth and behaviour of microorganisms in a factory environment and help identify, interpret, and promote healthy and protective microbial management systems.

“Often, as in the case with Chipotle,” Welser says, “we don’t know there’s an outbreak until someone gets sick. By monitoring the microbiome, we hope it will be possible to identify changes earlier in the food supply chain, giving us a chance to react sooner. In other words, it’s possible the data could enable us to prevent pathogen contamination and spread before anyone succumbs to illness.”

The CSFSC’s scientists are beginning with a close investigation of the genetic fingerprints of organisms like bacteria, fungi, and viruses, and exploring the way they grow across a variety of environments. Subsequently, they will use big data analysis to investigate bacterial interactions.

BioRad is a supplier of rapid food-testing methods, software, and reagents, with which the CSFSC hopes to speed the progress of its testing. Welser adds that the consortium is also in talks with other prospective partners at the moment, and invites interested parties to contact them as well.

Norman Schwartz, president and CEO at BioRad, says that his company has made its name providing innovative approaches to life-science research and clinical diagnostics, as well as an expertise in applied microbiology.

“These two capabilities are very complementary to those of our partners of the consortium,” says Schwartz. “Bio-Rad hopes that the consortium will validate new food-testing approaches that could enlarge Bio-Rad’s product offering in this area and leverage a targeted NGS technology that Bio-Rad recently acquired.”  Welser, meanwhile, says the CSFSC’s findings will be published in public journals and shared globally with the food-safety community. “We will also be building tools and analytics the industry can implement in their normal operations,” he says.