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.
“In conclusion, these results illustrate the potential of metagenomics as an open-ended, culture-independent approach for the identification and characterization of bacterial pathogens during an outbreak of diarrheal disease,” they concluded. “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.”
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 with 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.
The costs of sequencing may serve as a barrier. However, the study's authors said the expense of the technology may be justified when an outbreak “eludes standard diagnostic procedures.”
“In addition, obtaining a draft genome sequence of an outbreak strain may facilitate the development of simpler and cheaper diagnostic tests of the required sensitivity and specificity, as was shown during the (E. coli) outbreak,” they said.