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Pathogen Genomics

Pathogen Genomics for Public Health


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) Initiative [PDF 723.20 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

AMD 2014 projects that use genomic technologies to advance public health

CDC information: 2014 Advanced Molecular Detection Projects transforming networks, programs, and systems

CDC information: Using Advanced Molecular Detection for specific diseases or pathogens

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.

CDC 2014 AMD Accomplishments


OPHG blog posts on pathogen genomics:

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)


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  • Additional information for Public Health Genomics is available on our contact page. The U.S. Government's Official Web PortalDepartment of Health and Human Services
Centers for Disease Control and Prevention   1600 Clifton Road Atlanta, GA 30329-4027, USA
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