Metagenomic sequencing may soon be a tool to identify which bacterium is making a patient sick, says [email protected]. A recent study published in the Journal of the American Medical Association used such a culture-free approach to identify the Shiga toxin-producing Escherichia coli behind an outbreak in Germany in 2011. With this approach, they were able to identify the outbreak strain in 27 of the 40 patients with laboratory-confirmed STEC. The study was included in JAMA's special issue on genomic medicine.
The last author on that study, University of Warwick's Mark Pallen tells [email protected] that a metagenomic approach would lessen the need for culturing. "The promise of metagenomics is that you can one day replace those work flows with a one-size-fits-all work flow," he says. "The complexity with metagenomics comes with analyzing the data. We are not there yet, but our results represent a proof of principle."
He also adds that the samples from which he and his team didn't get any results had very low bacterial loads. "I'm not too upset about the fact that we didn't get in hard cases. In each of those samples, we know the outbreak sequences are there, but we didn't go deep enough with the sequencing to find them," he says.
The researchers also were able to identify other bacterial strains such as Clostridium difficile in the samples, though they could not conclude if they were also contributing to illness.