Pathogen Genomics

Pathogen Genomics

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.
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:

• Diagnosing infection (Legionella; Mycoplasma pneumoniae)
• Investigating outbreaks (Listeria; Ebola virus)
• Describing transmission patterns (Tuberculosis;Hepatitis C)
• Monitoring antimicrobial resistance (Gonorrhea; Candida auris)
• Developing interventions, including vaccines (Influenza; Polio eradication)

CDC’s Advanced Molecular Detection (AMD) Initiative[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 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 Accomplishments[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

OPHG blog posts on pathogen genomics:

• Infectious Diseases: Precision Medicine for Public Health, (September 24, 2015)
• What is a “rare disease”? Polio eradication and primary immunodeficiency (November 26, 2014)
• Outsmarting Antimicrobial-Resistant Pathogens (October 30, 2014)
• Genomes at CDC: Man, mouse, and microbe—it’s a genomic world! (May 23, 2013)
• Now watch this: Genomic epidemiology (September 6, 2012)
• No genome is an island (January 12, 2012)
• Genome vs. genome: E. coli sprouts in Germany (June 30, 2011)