Pathogen Genomics
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.
New Engl J Med, December26, 2019.
Next-Generation Sequencing of Infectious Pathogens. external icon
Gwinn M, MacCannell D, Armstrong GK.
JAMA, February 14, 2019.
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 costs and turnaround times are bringing high-throughput genetic sequencing within reach for use by clinical and public health investigators. CDC’s Office of Advanced Molecular Detection (OAMD) works with infectious disease programs to leverage these tools against a variety of pathogens at national, state, and local levels.
Public health applications of pathogen genomics include:
- Diagnosing infection (HIVexternal icon, parasitesexternal icon)
- Investigating outbreaks (Salmonellaexternal icon, SARS-CoV-2)
- Describing transmission patterns (Tuberculosisexternal icon, Influenzaexternal icon)
- Monitoring antimicrobial resistance Gonorrheaexternal icon, Candidaexternal icon)
- Developing and evaluating interventions, including vaccines (SARS-CoV-2external icon, Polioexternal icon)
Analysis of SARS-CoV-2 genome sequences is central to the global public health response to COVID-19. CDC, state and local health departments, and other public health organizations nationwide contribute to genomic surveillance of SARS-CoV-2. CDC’s Office of Advanced Molecular Detection (OAMD) conducts several activities to support these efforts, including:
SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES)
OAMD established SPHERES as an open consortium of scientists from clinical and public health laboratories, academic institutions, and the private sector to coordinate SARS-CoV-2 sequencing in the US. As part of this initiative, CDC has made 29 awards to academic and research organizations to fill knowledge gaps and promote innovation.
COVID-19 Genomic Epidemiology Toolkit
OAMD recruited a group of scientists from CDC and state and local health departments to develop the COVID-19 Genomic Epidemiology Toolkit. Specifically tailored to epidemiologists, the Toolkit is a practical introduction to using SARS-CoV-2 genomics to investigate and control COVID-19.
OGPPH Resources
Check out the Weekly Advanced Molecular Detection Clips. Clips are selected weekly from a variety of sources, including PubMed, journal tables of contents, and online media. Special emphasis is given to the use of next-generation genetic sequencing in infectious disease public health surveillance, investigation, and development of new diagnostics and interventions.
Search the Pathogen Advanced Molecular Detection Database for information on genomic sequencing and diagnostic methods, evolution, antimicrobial resistance, outbreak investigation, and host-pathogen interactions.
Use the COVID-19 GPH portal to search for publications on emerging discoveries and applications of genomic, molecular, and other precision health tools in the investigation and control of COVID-19.
Recent OGPPH blog posts on infectious diseases and microbial genomics:
- The Contributions of Host Genomics Research to the COVID-19 Response: It’s Not Just About Genes! Emily Drzymalla, Marta Gwinn and Muin J. Khoury (August 3, 2021)
- Tracking the Scientific Literature on SARS-CoV-2 Variants Using the COVID-19 Genomics and Precision Health Knowledge Base, Merline Feero, Marta Gwinn, and Muin J. Khoury (July 27, 2021)
- Host Genomics and COVID-19: One Year Later, Muin J. Khoury, Marta Gwinn and George A. Mensah (April 2, 2021)
- mRNA COVID-19 Vaccines: An Incredible Feat of Genomic Technology, Joanne Cono, W. David Dotson, Ridgely Fisk Green, and Muin J. Khoury (March 5, 2021)
- One Health – A Comprehensive Approach To Preventing Disease, Saving Lives, CB Behravesh, CDC Global Voices Blog Post (November 2, 2020)
- Precision Public Health and the COVID-19 Response, Sonja A. Rasmussen, Muin J. Khoury and Carlos del Rio (August 17, 2020)
- The Public Health Impact of COVID-19: Why Host Genomics? Muin J. Khoury, Marta Gwinn and Priya Duggal (April 21, 2020)
- Manipulating the Human Microbiome for Precision Public Health: Prospects and Challenges, Melia Haile, Alison Laufer Halpin, Christopher Elkins, Muin J. Khoury, and Clifford McDonald (March 31, 2020)
- Progress in Pathogen Genomics as a Prototype for Precision Public Health (January 2, 2020)