AMD Activities: 2019

Use of Pathogen Genomics in Public Health

Posted on Thursday, December 26, 2019

Figure 1 shows unsorted dots with multiple colors. Figure 2 shows dots sorted into groupings that are mostly one color but other colors are mized in. Figure 3 has clusters of dots that are more accurately sorted by color with only a few colors in the wrong place.

Each dot in these figures represent surveillance data for a foodborne pathogen, Salmonella enterica serovar Enteritidis. Panel A displays cases randomly, without regard to molecular subtyping. Panel B represents cases grouped by pulsed-field gel Electrophoresis (PFGE). The groupings include many cases unrelated to the outbreak, which complicates the investigation and reduces the likelihood of finding the food source. Panel C shows the finer resolution afforded by whole-genome sequencing was more effective in segregating outbreak cases.

A December 26 reportexternal icon by CDC scientists and colleagues in the New England Journal of Medicine (NEJM) highlights how a set of new technologies, collectively known as “next-generation sequencing,” have revolutionized scientists’ ability to decode DNA. These technologies are transforming the response to infectious disease outbreaks, providing new insights into disease emergence and transmission, expediting pathogen characterization, and promoting data sharing.

The AMD program has shown that CDC and other public health scientists can quickly and effectively adapt, incorporate and deploy novel, highly effective and transformative technologies into the public health system. Before AMD, the U.S. public health system (both CDC and state and local health departments) was lagging in the use of innovative new laboratory technologies. Now, it is a global leader. CDC and state and local public health agencies are now using these technologies on a daily basis to detect outbreaks quicker, investigate them more effectively, get a clearer understanding of disease transmission and, ultimately, develop better approaches to prevent infections and outbreaks of infectious disease from occurring in the first place.

You can read more about the transformative role pathogen genomics have on public health in the December 26th special report from the NEJMexternal icon.

NGS Quality Initiative website goes live

Posted on Wednesday, November 13th, 2019

colorful and decorative representation of ngs data

Next-generation Sequencing (NGS) is evolving quickly, and even though CDC, APHL, and others have published guidance documents, a need persists for additional laboratory resources.

The NGS Quality Initiative is developing an NGS-focused quality management system (QMS) to address the many challenges public health and clinical laboratories encounter when they develop and implement NGS-based tests, by providing ready-to-implement guidance documents, customizable standard operating procedures, and other tools. The project is funded by CDC’s Office of Advanced Molecular Detection, and is co-led by the Division of Laboratory Systems, the Office of the Deputy Director for Infectious Diseases, and the Association of Public Health Laboratoriesexternal icon.

Posted on Thursday, October 10th, 2019

thumbnail image of HIV data

In August 2016, a community of homeless people in Boston started showing up at a clinic with HIV. By June 2018, the outbreak involved more than 120 people, predominantly in the cities of Lawrence and Lowell in northeastern Massachusetts. The Massachusetts Department of Public Health (MDPH) asked for CDC’s help in investigating and responding to the outbreak.

Posted on Wednesday, August 21th, 2019

a woman kneels beside a hot tub with a swab in one hand and a sample container in the other

Ah, summertime at the beach; a time to relish the sun, the sand, and the ocean. Millions of people flock to the seashore each year to enjoy summertime fun. One resort town in New Hampshire draws many visitors from neighboring states each summer to its sandy beaches along the Atlantic shore. But in the summer of 2018, with the town’s annual seafood festival just weeks away, the town faced an unwelcomed visitor. Several people landed in the hospital with a severe form of pneumonia after visiting the town. A team of state, local, and federal investigators leapt into action to find the cause of the illnesses.

Scientists use bacterial genome sequences to stop a deadly multi-facility outbreak

Posted on Friday, May 24th, 2019

computer-generated image of a group of Gram-positive, Streptococcus pyogenes

Recent research in the Streptococcus Lab (StrepLab) at CDC is improving how scientists identify outbreaks of group A strep infections. While CDC’s scientists were developing the cluster detection tool in 2017, epidemiologists in Minnesota noticed an increase in these kinds of infections. StrepLab’s new technology helped researchers detect and investigate a deadly multi-facility outbreak that might have otherwise been missed.

PulseNet Laboratories Transition to Whole Genome Sequencing

Posted on Friday, May 24th, 2019

Scientist pointing at monitor

This year, the PulseNet national laboratory network is transitioning from pulsed-field gel electrophoresis (PFGE) to whole genome sequencing (WGS) to combat foodborne diseases more effectively. PulseNet public health scientists from laboratories across the United States will now have the tools to generate, analyze, and share their WGS results of foodborne bacteria with the other network participants.

AMD leads to better analysis and tracking of Cyclospora

Posted on Monday, May 13th, 2019

Micrograph showing circular oocysts of the parasite C. cayetanensis

Cyclospora cayetanensis is a particularly challenging pathogen to analyze, but thanks to AMD and a prototype typing tool that creates a “DNA fingerprint,” it may become easier for disease detectives to crack the code on Cyclospora outbreaks. CDC scientists are prepared to type samples in real time during the 2019 Cyclospora season to evaluate the new tool’s utility for outbreak detection. With this new tool, researchers hope to assist public health officials to detect more outbreaks and to learn how these pathogens are getting into the food system.

Building a consensus on genomic software needs in public health
Greg Armstrong and Duncan MacCannell outside of the Gates Foundation building in Seattle

Posted on Monday, April 8, 2019

The AMD program has partnered with the CDC Foundation and the Bill and Melinda Gates Foundation (BMGF) on a one-year project to define what software infrastructure is needed to support the complex information workflows required by AMD technologies.

In March, OAMD’s Greg Armstrong and Duncan MacCannell and NCIRD’s Elizabeth Neuhaus met with the project team, which also includes Africa CDC officials, Trevor Bedford’s laboratory at the University of Washington, and a group of experts in bioinformatics and open software development.  The group seeks consensus on a sustainable framework for this software—a framework that will facilitate the application of pathogen genomics to public health both in high-income countries such as the United States as well as in low- and middle-income countries.

AMD Director Greg Armstrong said, “It was remarkable how strongly the participants felt about the need for this meeting and for an effort to coordinate the development of software that will support pathogen genomics in public health.”

OAMD joins with CSTE and APHL to host AMD Academy

Posted on Monday, March 11, 2019

The Office of Advanced Molecular Detection (OAMD) welcomed epidemiologists and microbiologists from state and local health departments across the nation to the first AMD Academy, hosted with the Association of Public Health Laboratories (APHL) and the Council of State and Territorial Epidemiologists (CSTE). Held in Atlanta during the last week of January, OAMD presented a 2-day molecular epidemiology course for epidemiologists (January 30–31) and a 4-day, intermediate-level bioinformatics course for microbiologists (January 28–31).

New article and podcast on next generation sequencing (NGS)
image of flow chart in JAMA Article

Posted on Tuesday, March 5, 2019

On February 14, the Journal of the American Medical Association (JAMA) published an articleexternal icon describing ongoing advances being made by CDC’s Advanced Molecular Detection (AMD) program in the field of next generation sequencing (NGS). JAMA also published a related clinical review podcastexternal icon, where they interviewed two of the authors, Marta Gwinn, MD, MPH, and Gregory L. Armstrong, MD, from the Office of AMD about the potential NGS holds for improving clinical and public health microbiology.

Page last reviewed: January 29, 2020