The Hot Zone Meets the Genome: Staying Ahead of the Next Outbreak through Advanced Molecular Detection

By Allen D. Segal, Director, Public Policy and Advocacy, American Society for Microbiology

When diseases and disasters strike, a federal response is critical to mitigating the crisis. When it comes to protecting public health, the Centers for Disease Control and Prevention (CDC) plays an indispensable role in the rapid detection and containment of diseases, outbreaks, biosecurity threats and environmental hazards. For the past 20 years, the CDC has relied heavily on the growing Laboratory Response Network (LRN) for Biological Threats when an infectious disease or high-consequence pathogen emerges. A critical component of CDC’s response to biological threats is the Advanced Molecular Detection (AMD) program. These partnerships between federal agencies and state governments exemplify how federal investments in “basic” or “fundamental” research are translated into practical “real world” applications in public health, and then deployed across the country when a crisis hits.

AMD is part of CDC’s National Center for Emerging and Zoonotic Infectious Diseases (NCEZID). When an infectious disease or food-borne illness outbreak occurs, AMD partners across the LRN, including at state public health labs or at CDC headquarters, are able to genetically sequence the pathogens involved. The technological advances in sequencing, even during the last five years, have greatly enhanced our ability to track down the sources of outbreaks, enabling officials to take action before they become more widespread.

Before the AMD program was authorized and funded by Congress in 2014, it was becoming painfully clear that the technology “gap” between research and medicine, and public health, was widening. The U.S. public health system was not realizing the potential of advances in pathogen genomics.  With middle eastern respiratory syndrome (MERS) and Ebola raging in areas around the world, and avian flu striking the U.S., CDC needed more rapid and accurate means to prevent and address these serious outbreaks.

Since 2014, the AMD program has received annual funding level of $30 million. This has allowed the agency to rapidly incorporate next-generation sequencing (NGS), a novel and versatile technology developed with funding from NIH, into CDC operations and bring it to the front lines of public health.

AMD has broad and important implications for U.S. health and security, such as food safety, tracking emerging infections, improving vaccines, and combatting antimicrobial resistance. 

Consider the following:

·         State-of-the-art AMD methods help solve infectious disease outbreaks from foodborne pathogens faster by linking food sources to clusters of illness.

·         Studying the genetic makeup of micro-organisms helps identify and track rare and deadly pathogens such as Ebola and Zika viruses, and AMD has uncovered previously unknown threats such as the Bourbon virus.

·         Applying AMD methods to vaccine-preventable diseases, such as whooping cough and flu, helps CDC monitor genetic changes and understand why vaccine effectiveness may decrease.

·         AMD methods lead to more rapid and accurate tests to detect antimicrobial resistance.

Thanks to the effectiveness of the AMD program, today the U.S. public health system has closed the technology gap when it comes to addressing infectious disease outbreaks. But now, AMD’s decreasing ability to support innovation is threatening to open it up again. To maximize its potential, this $30 million program needs a significant increase in funding to support current operations and expand the scope of innovation to ensure cutting edge technology is working to protect Americans from disease.  


·         Next generation sequencing technologies continue to advance at an astounding pace, giving us new and expanded tools to detect disease faster, identify outbreaks sooner, and protect people from emerging and evolving disease threats.

·         More funding would allow previously unimaginable techniques to be deployed, such as the sequencing of pathogens directly from specimens without a need for culture, critical to addressing bacterial foodborne illness, or developing more effective vaccines by targeting evolving pathogens.

·         Additional funding would allow CDC to better assist the LRN, develop and improve diagnostics, and ensure molecular tests can be deployed rapidly when needed and where they will have the greatest impact.  

In its first five years, the AMD program has transformed many areas of public health, and its success has demonstrated the critical importance to the nation’s health security of staying abreast of technologies that are both cutting edge and relevant. But it is important to understand this role in the context of the larger picture. The AMD program exemplifies one of the many ways that CDC supports the work of critical partner agencies at the state and local level and with the LRN’s nonprofit partners like the American Society for Microbiology and the Association of Public Health Laboratories.

In short, CDC puts science into action for the benefit of public health, and funding for this agency must keep pace. To carry out its mission, CDC requires an unwavering commitment from Congress to provide significant funding increases so that we can keep public health on the cutting edge of science and medicine.