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Invited Commentary |

The Time Is Now for Gene- and Genome-Based Bacterial Diagnostics:  “You Say You Want a Revolution”

Garth D. Ehrlich, PhD1,2; J. Christopher Post, MD, PhD1,2
[+] Author Affiliations
1Center for Genomic Sciences, Allegheny-Singer Research Institute, Pittsburgh, Pennsylvania
2Departments of Microbiology and Immunology and Otolaryngology–Head and Neck Surgery, Drexel University College of Medicine, Pittsburgh, Pennsylvania
JAMA Intern Med. 2013;173(15):1405-1406. doi:10.1001/jamainternmed.2013.7042.
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Clinical microbiology is poised to move into a dynamic age by embracing molecular diagnostic techniques, such as polymerase chain reaction–based amplification techniques and whole-genome sequencing (WGS). These technologies will revolutionize data acquisition for theranostics and the tracking of outbreaks.

Whole-genome sequencing originally proved its worth through investigations of infectious agents.1 In this issue of JAMA Internal Medicine, Reuter et al2 now advocate WGS for routine diagnostics and public health microbiology. These ideas are not as far-fetched as they may initially sound. Although the cost and time to conduct WGS would have once been prohibitive, a bacterial WGS can be performed for less than $100 in 1 day’s time. Moreover, the computational systems for performing the analytics on the WGS data allow for rapid turnaround times. Collectively, these metrics make WGS competitive with any technology, including traditional methods of culturing bacteria. Although there are no commercial WGS analytics that could integrate with standard laboratory information systems now, such tools will be developed that can access cloud-based computing resources containing global strain databases annotated with respect to clinical origins, spread, and associated symptoms.

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