Pathogen Genomics

COVID-19 Portal on Genomics and Precision Health

SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology, and Surveillance (SPHERES)

The Emerging Role of Pathogen Genomics in Public Health.
CDC Public Health Grand Rounds, January 21, 2020

Pathogen Genomics in Public Health.external icon
Armstrong GL, MacCannell DR, Taylor J, Carleton HA, Neuhaus EB, Bradbury RS, Posey JE, Gwinn M.
N Engl J Med. 2019 Dec 26;381(26):2569-2580.

Next-Generation Sequencing of Infectious Pathogens.external icon
Gwinn M, MacCannell D, Armstrong GK.
JAMA, February 14, 2019

The Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance for Foodborne Pathogens in the United States, MMWR, April 2018.

Innovating Solutions: How CDC combines genome sequencing & advanced computing to solve complex infectious disease mysteries

Integrating advanced molecular technologies into public health.external icon
Gwinn M, MacCannell DR, Khabbaz RF.
J Clin Microbiol. 2016 Dec 28.

Changes in Clinical Diagnostics and Tracking Infectious Diseases, CDC Public Health Grand Rounds, 1-hour video, October 18, 2016

The Centers for Disease Control and Prevention (CDC) is well known for its work in monitoring, investigating, and controlling infectious diseases in the United States and worldwide. Genetic information from viruses, bacteria, and other infectious organisms has long played a crucial role in these efforts.

Advances in molecular technologies and bioinformatics have made it possible to examine pathogen genomes in much greater detail. Now, falling cost and turnaround time are bringing high-throughput genetic sequencing within reach for use by clinical and public health investigators.

Public health applications of pathogen genomics include:

CDC’s Advanced Molecular Detection (AMD) Initiativepdf icon[PDF 392.40 KB] aims to build critical molecular sequencing and bioinformatics capacities at national and state levels to support public health efforts to control infectious diseases. For additional information, see the A New Landscape for Combatting Infectious Diseases.pdf icon[PDF 693.38 KB]

CDC website: Advanced Molecular Detection (AMD) and Response to Infectious Disease Outbreaks

AMD in Action: Stories about the potential of AMD to help solve infectious disease outbreaks

AMD Basics: Get more information about what this advanced technology can do

Advanced Molecular Detection (AMD) Program Projects

Check out the Weekly Advanced Molecular Detection Clips. Topics include methods, evolution & pathogenicity, detection & diagnosis, outbreaks, epidemiology & transmission, antimicrobials, vaccines & host-pathogen interactions. The weekly clips also include news, reviews, commentaries, tools and databases.

Applying New Technologies to Advance Disease Detection: 2016 Accomplishmentspdf icon[9.95 MB]

CDC 2015 AMD Accomplishments

CDC 2014 AMD Accomplishments

Search the CDC Public Health Genomics Knowledge Base on public health and genomic information for infectious diseases and pathogen-host interactions

OGPPH blog posts on pathogen genomics:

Page last reviewed: December 30, 2019