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The Genomics Landscape

Changing the Face of Diagnostics in Clinical Microbiology

NHGRI Director Eric Green, M.D., Ph.D.
Eric Green
By Eric D. Green, M.D., Ph.D.
Director, National Human Genome Research Institute
November 4, 2014

This month, I would like to bring to your attention a short new video that we recently completed, which 'tells the story' of NHGRI- our history, our organization, and our programs. This 'silent documentary' gives an overview of NHGRI through text, images, graphics, and video clips. I encourage you to visit to view the video.

In this issue of The Genomics Landscape, I describe the evolution of genome sequencing and its impact on public health surveillance and infectious disease diagnostics. I also highlight the first BD2K awards, National Family History Day, the appointment of a new NHGRI Executive Officer, as well as share details on how to comment on our recent genome sequencing workshop. See details below, along with other information items that I hope will be of interest to you.

Specifically, November's The Genomics Landscape features stories about:

All the best,

Changing the Face of Diagnostics in Clinical Microbiology

Healthcare-associated infections affect approximately two million people in the United States each year, resulting in ~100,000 deaths. Antibiotic-resistant infections cost the U.S. $20-35 billion annually in healthcare expenses. Emerging infectious diseases need urgent containment and treatment. It is clear that in the U.S. and across the globe, we need better means to understand and control these infections.

From L to R: SARS-associated coronavirus, Klebsiella pneumoniae, and Ebola virus.
SARS, Klebsiella, Ebola viruses

Recent public-health crises have brought to light the increasing real-time use of genomics in the area of infectious disease diagnostics. However, the potential role of genomics in this context was evident over a decade ago. For example, in 2003, Dr. Marco Marra and colleagues sequenced the genome of the SARS-associated coronavirus (Marra, et al., Science, 2003), aiding the understanding of the infectious outbreak in real time.

The advent of cheaper, faster DNA sequencing methods has created exciting new opportunities in the areas of public health and hospital epidemiology. Recently, NHGRI's own Dr. Julie Segre and colleagues used cutting-edge genomics to track an antibiotic-resistant strain of Klebsiella pneumoniae that was responsible for a deadly outbreak in the NIH Clinical Center (Snitkin et al., Sci Transl Med 2012). This past summer, Dr. Pardis Sabeti and colleagues sequenced the genomes of Ebola virus isolates from the recent outbreak in an effort to understand their origin and transmission (Gire et al., Science 2014).

patient-to-patient outbreak

Genome sequencing is serving many purposes in this rapidly-expanding area of infectious disease diagnostics. In addition to the above examples of patient-to-patient outbreak detection, new and unexpected microbes causing infection are being identified; investigators are finding genes conferring antibiotic-resistance or new modes of developing resistance; the origins of food-borne illnesses are being traced; reference genomes of clinical pathogens are being generated; the genomic variation of pathogens within patients is being investigated; and genome sequencing is being used for biodefense purposes, such as identifying specific genomic features of bacterial strains and tracing their origins via comparative genomics.

These developments have collectively pointed to the important role of genomics in infectious disease research and diagnostics. As a result, the President's Council of Advisors on Science and Technology (PCAST), an advisory group to the President consisting of top scientists and engineers in the U.S., recently prepared a report on combating antibiotic resistance. In the report, several actions were recommended: improving our surveillance capabilities, increasing the longevity of current antibiotics, and accelerating the rate at which new antibiotics and other interventions are discovered and developed. Genomics can contribute much to these efforts, especially surveillance and detection of resistance genes and strains, and is mentioned throughout the report.

Report to the President on Combating Antibiotic Resistance

The PCAST report highlights the urgent need for additional research to develop approaches for combating antibiotic resistance. This issue surfaces in hospitals, homes, businesses, and schools across the world, and genomics has an important role to play in addressing these challenges. Large-scale genomic surveillance of pathogens, healthcare-related and otherwise, and the generation of reference microbial genome sequences will be crucial. The face of diagnostics and clinical microbiology is changing, and bright minds and improved technologies in genomics are helping to lead the way.

More From the Genomics Landscape

NIH News of Interest

NIH Funds Research Consortia to Study More than 200 Rare Diseases
NIH Grantee Honored With 2014 Nobel Prize in Chemistry

NIH Awards ~$31 Million to Enhance Diversity in the Biomedical Research Workforce
NIH Grants Examine How Genomic Information Can Affect Patients' Health
Genomics Database Gets a Patient Portal

Funding News

Informational Webinar: 4D Nucleome Initiatives
Webinars on NIH Application Submission and Review (R15, Fs, SBIR/STTR & R01)

Media Availability

TCGA Study Improves Understanding of Genetic Drivers of Thyroid Cancer
Researchers Uncover New Evidence Revealing Molecular Paths to Autism

Genomics Research

Advancing the Microbiome Research Community
Nature Reviews Genetics 'Clinical Applications of Next-Generation Sequencing
Whole Exome Sequencing Closer to Becoming "New Family History"

Study: Most Respond Well to Genetic Testing Results
Exomes in the Clinic
Thyroid Cancer Genome Analysis Finds Markers of Aggressive Tumors
Autism Linked to Dozens of Genetic Mutations in Major New Studies

Genome Advance of the Month

Exploring Harmful Interactions Between Artificial Sweeteners and Gut Microbiota

Genomics On Air

Conversations on Health CareŽ: Eric Green

Funding Opportunities

Notice of Intent to Publish: Centers for the Genomics of Common Disease (UM1)
Notice of Intent to Publish: Centers for Mendelian Genomics (UM1)

NIH Director's Early Independence Awards (DP5)
NIH Offers Niche Assessment Program to SBIR and STTR Phase I Awardees

New Genomics Videos

Genome: Unlocking Life's Code Exhibition Closing Symposium - Genomics and Global Health: What Does the Future Hold
Genomic Medicine Centers VII Meeting: Genomic Clinical Decision Support

NHGRI Showcase Video

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Last Updated: November 12, 2014
Posted: August 4, 2008