On 2013 Oct 23, Stephen Turner commented:

This paper is a groundbreaking exploration of the use of metagenomics to investigate and determine the causal organism of an infectious disease outbreak. The authors retrospectively collected fecal samples from symptomatic patients from the 2011 Escherichia coli O104:H4 outbreak in Germany and performed high-throughput shotgun sequencing, followed by a sophisticated analysis to determine the outbreak's causal organism. The analysis included comparing genetic markers from many symptomatic patients' metagenomes with those of healthy controls, followed by de novo assembly of the outbreak strain from the shotgun metagenomic data. This illustrates both the power, but the real limitations, of using metagenomic approaches for clinical diagnostics. Also see David Relman's synopsis of the study in the same JAMA issue.

On 2013 Oct 23, Stephen Turner commented:

This paper is a groundbreaking exploration of the use of metagenomics to investigate and determine the causal organism of an infectious disease outbreak. The authors retrospectively collected fecal samples from symptomatic patients from the 2011 Escherichia coli O104:H4 outbreak in Germany and performed high-throughput shotgun sequencing, followed by a sophisticated analysis to determine the outbreak's causal organism. The analysis included comparing genetic markers from many symptomatic patients' metagenomes with those of healthy controls, followed by de novo assembly of the outbreak strain from the shotgun metagenomic data. This illustrates both the power, but the real limitations, of using metagenomic approaches for clinical diagnostics. Also see David Relman's synopsis of the study in the same JAMA issue.