Genomics Identify Organisms in Serious Infectious Disease Outbreaks

Metagenomics may help identify organisms in outbreaks of serious infectious disease without requiring laboratory culture.

Metagenomics is the direct sequencing of DNA extracted from microbiologically complex samples and allowed for the reconstruction of the genome sequence of an outbreak strain of Shiga-toxigenic Escherichia coli (STEC).

Microbiologists at the University of Birmingham (Edgbaston, UK) conducted a study to explore the potential of metagenomics to identify and characterize bacterial strains from an outbreak by determining genome sequence data. In this retrospective investigation, 45 samples were selected from fecal specimens obtained from patients with diarrhea during the 2011 outbreak of STEC O104:H4 in Germany. Samples were subjected to sequencing from August to September 2012, followed by a three-phase analysis conducted from November 2012 to February 2013.

In the first phase, a draft genome of the outbreak strain was constructed, using data obtained with the HiSeq 2500 instrument (Illumina, San Diego, CA, USA) in rapid-run mode. Outbreak-specific sequences were identified by subtracting sequences from the outbreak metagenome that were present in fecal samples from healthy individuals. In the second phase, the depth of coverage of the outbreak strain genome was determined in each sample. In the third phase, sequences from each sample were compared with sequences from known bacteria to identify pathogens other than the outbreak strain.

The scientist found that in the second phase the outbreak strain genome was recovered from 10 samples at greater than 10-fold coverage and from 26 samples at greater than 1-fold coverage. Sequences from the Shiga-toxin genes were detected in 27 of 40 (67%) STEC-positive samples. In the third phase sequences from Clostridium difficile, Campylobacter jejuni, Campylobacter concisus, and Salmonella enterica were recovered.

The authors concluded that their 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. 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 study was published on April 10, 2013, in the issue of the Journal of the American Medical Association (JAMA).

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