Metagenomics reconstructs the genome sequence through the direct sequencing DNA extracted from microbiologically complex samples. A recent study published in the Journal of the American Medical Association (JAMA) highlights the potential of this approach to identify and characterize bacterial pathogens directly from clinical specimens. For the study, 45 samples were selected from fecal specimens obtained from patients in Germany with diarrhea during the 2011 STEC outbreak, and those samples were submitted to a 3-phase sequencing analysis.
The international team of researchers was coordinated by Mark Pallen, Professor of Microbial Genomics at Warwick Medical School, who summarized what this means for the identification of future outbreaks, “There are numerous drawbacks to the use of nineteenth-century approaches such as microscopy and culture when it comes to classification. Our results illustrate the potential of metagenomics as an open-ended, culture-independent approach for the identification and characterization of bacterial pathogens during an outbreak.
“There are challenges, of course, including speeding up and simplifying workflows, reducing costs and improving diagnostic sensitivity. However, given the dizzying pace of progress in high-throughput sequencing, these are not likely to remain problems for very long.”