(HealthDay News) – A three-phase metagenomic analysis, involving the direct sequencing of DNA extracted from microbiologically complex samples, can identify the bacterial pathogens involved in disease outbreaks, according to a study published April 10 in the Journal of the American Medical Association.

Nicholas J. Loman, MBBS, PhD, from the University of Birmingham in the United Kingdom, and colleagues assessed the potential of metagenomics for identifying and characterizing bacterial strains from an outbreak, without the need for laboratory culture. Forty-five samples from fecal specimens of patients with diarrhea during the 2011 German outbreak of Shiga-toxigenic Escherichia coli (STEC) O104:H4 were subjected to high-throughput sequencing followed by a three-phase analysis. A draft genome of the outbreak strain was obtained using a de novo assembly approach; the depth of coverage of the outbreak strain genome was determined; and sequences from each sample were compared with those of known bacteria.

The researchers found that the draft genome of the STEC outbreak strain was obtained in phase 1. The genome was recovered from 10 samples at >10-fold coverage and from 26 samples at >one-fold coverage. In 67% of 40 STEC-positive samples, sequences from the Shiga toxin genes were detected. Sequences from Clostridium difficile, Campylobacter jejuni, Campylobacter concisus, and Salmonella enterica were recovered in Phase 3.

“These results suggest the potential of metagenomics as a culture-independent approach for the identification of bacterial pathogens during an outbreak of diarrheal disease,” the authors write. “Challenges include improving diagnostic sensitivity, speeding up and simplifying workflows, and reducing costs.”

Several authors disclosed financial ties to the pharmaceutical and biotechnology industries.

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