Targeting disease

Gene-sequencing technologies may help providers identify and characterize bacterial pathogens during an outbreak, such as the E. coli outbreak in Germany that sickened thousands of people in 2011.

Using metagenomics, which is the direct sequencing of DNA extracted from microbiologically complex samples and has been used to identify the cause of outbreaks of viral infections, researchers reconstructed the genome sequence of that outbreak strain without using laboratory culture, according to a study published in the Journal of the American Medical Association.

They found that the use of metagenomics could signal a new approach to identifying bacterial pathogens, as well as allow for more rapid and accurate identification and characterization of those pathogens, which would lead to better management of the disease.

The authors noted that the technology's performance is not adequate to be used in clinical settings at this time. “Challenges include speeding up and simplifying workflows, reducing costs and improving diagnostic sensitivity, all of which are likely to depend in turn on improvements in sequencing technologies,” they concluded.

The outbreak in Germany sickened more than 3,000 people and led to 50 deaths.

In an editorial accompanying the study, Dr. David Relman, a professor of the medicine, microbiology and immunology departments at Stanford University School of Medicine, wrote that whole-genome sequencing of viruses and bacteria has aided investigations into outbreaks and strain tracking.

“Yet, the rapid identification and characterization of microbial agents in routine cases of infectious disease is a major and increasing unmet need, made even more pressing by the alarming increase in antimicrobial resistance, and the dwindling availability of effective antimicrobial agents,” Relman wrote.

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