New American Academy of Microbiology Report Provides Recommendations for Implementing Next-Generation Sequencing to Clinical Microbiology Settings

Washington, D.C. — January 27, 2015 Next-generation sequencing (NGS) has the capacity to provide crucial clinical benefits in patient care, patient outcomes, and public health, however, clinical laboratories must find ways to overcome operational, technical, regulatory, and strategic challenges in order to effectively employ NGS-based diagnostic tests, says a new report from the American Academy of Microbiology.

The report is based on a two-day colloquium hosted by the American Society for Microbiology in April 2015. The event brought together experts from across and outside of the U.S. to answer a series of questions regarding the use of NGS technologies in the clinical and public health microbiology laboratories.

“ASM is playing a critical role in bringing together key players to strengthen the implementation of NGS into clinical microbiology settings,” said Stefano Bertuzzi, Ph.D., CEO, ASM.

NGS refers to high-throughput DNA sequencing strategies that can produce large amounts of genomic data. The transition from use of this technology in the research capacity to the diagnosis and identification of infectious disease agents has been perceived by many members of the scientific community as slow. However, NGS is capable of performing a wide diagnostic repertoire that can identify the invading microbial culprit no matter the organism – bacterial, viral, fungal, or parasitic. “This subverts the diagnostic guessing-game that wastes precious time for the patient and could be the difference between life and death," said Charles Chiu, M.D., University of California, San Francisco. “Delays in microbe identification increase the risk of ineffective treatment and spread of infection,” he added. NGS has the potential to replace the armory of tests, some of which are laborious and time-consuming, that are currently implemented in public health and clinical microbiology. It is predicted that in the not too distant future, NGS applications will supersede other molecular technologies.

Beyond the potential lifesaving impact of NGS methodologies, the report examines the main deterrents and shortcomings of the technology such as the data analysis and management pipelines, regulatory concerns and reimbursement issues, and the creation and maintenance of curated and secure databases. “Moving the NGS process from the research lab to widespread clinical application is the payoff of the remarkable odyssey of DNA sequencing breakthroughs over the last decade. But there are major obstacles which the report lays out and suggests how to combat,” said George Weinstock, Ph.D., Chair, Colloquium Steering Committee.”

The National Press Club will host a panel of NGS experts, including Dr. Stefano Bertuzzi, CEO, ASM, Dr. George Weinstock, chair of the report’s steering committee and Dr. Charles Chiu, to mark the report’s release on February 19th.


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The American Academy of Microbiology is the honorific leadership group of the American Society for Microbiology.  The mission of the Academy is to recognize scientific excellence, as well as foster knowledge and understanding in the microbiological sciences.  A full list of Academy colloquia reports can be found at  For more information about the American Society for Microbiology, visit