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Working Together on the Transition to Whole Genome Sequencing, Making Our Food Supply Safer

Posted By Rima Khabbaz, MD, Director, National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Wednesday, September 18, 2019
Updated: Wednesday, September 18, 2019

As the multi-year effort of rolling out whole genome sequencing (WGS) for PulseNet successfully completes its transition, I am pleased to report that thanks to the herculean efforts of our laboratory and epidemiology partners, the entire country is now able to sequence all foodborne disease pathogens. Public health departments across the country are starting to use the powerful tools of advanced molecular detection (AMD) to detect and investigate outbreaks and better understand antibiotic-resistant bacteria so we can stop their spread.

For more than 20 years, PulseNet has helped detect, investigate, and stop outbreaks and improve our food safety system nationwide, reducing the overall burden of enteric disease in the United States. In 2019, we have seen the culmination of an exceptional effort to transform foodborne disease surveillance in the era of next-generation sequencing. We hope our state epidemiology partners from Florida to Washington appreciate how their diligence in this effort will strengthen all infectious disease surveillance for years to come.

We will look to you as leaders to not only use this technology to track and prevent other diseases, but also to help us at CDC learn about the many ways this tool can be harnessed to drive future innovation and prevention research. You well know that this has been a long, arduous process and would not have been accomplished without the contributions of our federal, state, and local partners. I would like to express sincere gratitude on behalf of our agency for your dedication and commitment to this forward-thinking transition of our public health system.

As we did 23 years ago at the dawn of PulseNet, we will work collaboratively to optimize this technology and further improve our efficiencies. As with any major technological transition, technical or logistical challenges may emerge – we hear you at CDC and are committed to working with you to make this transition as smooth as possible. We think this technology will empower public health decision-making at the local, state, and federal levels, and we anticipate its increasing use internationally.

I am fortunate to be the director of a center at CDC that strives to push forward public health science, but without partnership with groups like CSTE, we’d be hard pressed to accomplish anything close to what we have done over the last few years for enteric disease prevention. I’d like to reflect on the many interactions with our state and local health department partners who have attended a number of CDC-sponsored trainings and meetings over the course of this transition. We have been most struck by the large number of bright, young public health scientists drawn to the field with laboratory, epidemiology, and environmental health training who were excited about the challenges and the potential innovations at hand. Just as it has from the beginning, PulseNet will continue to find more ways to drive the prevention of foodborne and other enteric illnesses, make our food supply safer, and keep all of us healthier.

Rima F. Khabbaz, MD, is director of the National Center for Emerging and Zoonotic Infectious Diseases (NCEZID) at the Centers for Disease Control and Prevention (CDC). NCEZID’s experts work around the clock to protect people from a multitude of health threats and advance the agency’s cross-cutting infectious disease priorities, including the integration of advanced molecular detection (AMD) technologies into public health. For more information about PulseNet and the transition to whole genome sequencing, please visit NCEZID’s PulseNet Lab transition to WGS page.

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