ASM Takes the Lead on Moving Next-Gen Sequencing into Clinical Microbiology

April 11, 2016

Microbial sciences are undergoing a phenomenal renaissance, triggered in large part by powerful new technologies. Nothing better exemplifies this fact than next-generation sequencing. Until recently, we have been very limited in what we can learn about microbes, with roughly 10 percent of the microbes in our human bodies culturable. 

The landscape dramatically changed with the advent of “next-gen” sequencing, which allows us a spectacularly fine grained and nuanced look at the human biome, especially at the trillions of microbes which live with us, both as helpers and threats. Microbes greatly outnumber our own human cells with a nucleus. Indeed, if there were a “one-cell, one-vote” election, the human vote would be swamped.

Next-generation sequencing (NGS for the aficionados) refers to high-throughput DNA sequencing strategies that can quickly label and sort massive quantities of genomic data. This technology has already changed the landscape of basic science and of basic microbial sciences in particular. We are now poised to see what radical changes next-gen will bring to clinical microbiology. This has not yet happened for several reasons. For one, while we have FDA-approved test systems today which allow laboratories to develop and validate sequencing of any part of the patient genome or assays to detect changes in cystic fibrosis transmembrane conductance regulator (CTFR), we do not yet have FDA approval for microbial diagnostic use.

Yet I believe that NGS will come to clinical microbiology sooner rather than later. As NGS technology is added to the clinical microbiology toolkit, there will be enormous opportunities before us from rapid, accurate diagnostics for known and unknown pathogens to precision medicine, to antimicrobial stewardship and much more. But there are also barriers to the effective deployment of NGS in clinical microbiology and public health laboratories. We need to lower the activation energy requirements here such as the cost of entry, the need for complex data analysis, the lack of standardized report formats, and the unknown but likely daunting regulatory issues.

I am proud that one of my first events as ASM CEO was to host a press conference at the National Press Club to announce the release of the American Academy of Microbiology report titled “Applications of Clinical Microbial Next-Generation Sequencing” in February 2016.  We heard from University of California, San Francisco, physician-scientist Charles Chiu who said that NGS could sidestep the diagnostic guessing-game which wastes precious time for patients. This can make a life-or-death difference because delays in microbe identification increase the risk of ineffective treatment and spread of infection. Indeed, Chiu was able to show what a difference NGS can make, presenting the case of the Osborne family where thanks to an experimentally-sanctioned use of NGS diagnostics, Chiu’s team was able to cut short a microbial testing odyssey, diagnosing their 14-year-old son with neuroleptospirosis, which months of current clinical testing had been unable to identify. This was a powerful story of how basic discovery and technological application can change human lives.

NGS has the potential to replace an armory of current microbiological test procedures, some of which are laborious, slow and often nondecisive. It is predicted that NGS applications many supersede most molecular technologies in current use, yet we are along way from that. But there is little doubt that this powerful new technology will reshape the clinical world and that is why the Academy of Microbiology issued 19 recommendations in its Colloquium report.

Thanks to the Academy of Microbiology under the leadership of Michele Swanson and others, ASM is well positioned to advance the microbial sciences. In our membership, we have an amazing brain trust. In our society, we have the resources to take this report to the next stage. Since the release of the Academy report on NGS, ASM secretary Joe Campos and others have been at work building a new Coalition for NGS. Using the Academy recommendations as a starting point, ASM has convened several federal science and regulatory agencies, together with academia and industry partners to come together in an NGS Coalition. The high-speed high-throughput, high-technology of NGS is an engine that will drive science and health care in the decade ahead. I am proud that for NGS clinical microbiology, ASM has jumped into the driver’s seat, helping to deliver NGS clinic diagnostics, safely and quickly, to the global community. This technology offers hope to millions of patients around the world for precise diagnosis, tailored therapies, and rapid responses to infectious diseases where hours, not days, make the difference. Last month, I heard the story of one family rescued by “next-gen.” There will be millions more in the years to come and ASM’s efforts now will make us part of that future.

Author: Stefano Bertuzzi

Stefano Bertuzzi
Stefano Bertuzzi is the CEO of the American Society for Microbiology.