A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4

TY - JOUR

T1 - A culture-independent sequence-based metagenomics approach to the investigation of an outbreak of Shiga-toxigenic Escherichia coli O104:H4

AU - Loman, Nicholas J

AU - Constantinidou, Chrystala

AU - Christner, Martin

AU - Rohde, Holger

AU - Chan, Jacqueline Z-M

AU - Quick, Joshua

AU - Weir, Jacqueline C

AU - Quince, Christopher

AU - Smith, Geoffrey P

AU - Betley, Jason R

AU - Aepfelbacher, Martin

AU - Pallen, Mark J

PY - 2013/4/10

Y1 - 2013/4/10

N2 - IMPORTANCE: Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain.OBJECTIVE: To explore the potential of metagenomics, which is the direct sequencing of DNA extracted from microbiologically complex samples, as an open-ended clinical discovery platform capable of identifying and characterizing bacterial strains from an outbreak without laboratory culture.DESIGN, SETTING, AND PATIENTS: In a retrospective investigation, 45 samples were selected from fecal specimens obtained from patients with diarrhea during the 2011 outbreak of Shiga-toxigenic Escherichia coli (STEC) O104:H4 in Germany. Samples were subjected to high-throughput sequencing (August-September 2012), followed by a 3-phase analysis (November 2012-February 2013). In phase 1, a de novo assembly approach was developed to obtain a draft genome of the outbreak strain. In phase 2, the depth of coverage of the outbreak strain genome was determined in each sample. In phase 3, sequences from each sample were compared with sequences from known bacteria to identify pathogens other than the outbreak strain.MAIN OUTCOMES AND MEASURES: The recovery of genome sequence data for the purposes of identification and characterization of the outbreak strain and other pathogens from fecal samples.RESULTS: During phase 1, a draft genome of the STEC outbreak strain was obtained. During phase 2, 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 STEC-positive samples (67%). In phase 3, sequences from Clostridium difficile, Campylobacter jejuni, Campylobacter concisus, and Salmonella enterica were recovered.CONCLUSIONS AND RELEVANCE: These results suggest the potential of metagenomics as a culture-independent approach for the identification of bacterial pathogens during an outbreak of diarrheal disease. Challenges include improving diagnostic sensitivity, speeding up and simplifying workflows, and reducing costs.

AB - IMPORTANCE: Identification of the bacterium responsible for an outbreak can aid in disease management. However, traditional culture-based diagnosis can be difficult, particularly if no specific diagnostic test is available for an outbreak strain.OBJECTIVE: To explore the potential of metagenomics, which is the direct sequencing of DNA extracted from microbiologically complex samples, as an open-ended clinical discovery platform capable of identifying and characterizing bacterial strains from an outbreak without laboratory culture.DESIGN, SETTING, AND PATIENTS: In a retrospective investigation, 45 samples were selected from fecal specimens obtained from patients with diarrhea during the 2011 outbreak of Shiga-toxigenic Escherichia coli (STEC) O104:H4 in Germany. Samples were subjected to high-throughput sequencing (August-September 2012), followed by a 3-phase analysis (November 2012-February 2013). In phase 1, a de novo assembly approach was developed to obtain a draft genome of the outbreak strain. In phase 2, the depth of coverage of the outbreak strain genome was determined in each sample. In phase 3, sequences from each sample were compared with sequences from known bacteria to identify pathogens other than the outbreak strain.MAIN OUTCOMES AND MEASURES: The recovery of genome sequence data for the purposes of identification and characterization of the outbreak strain and other pathogens from fecal samples.RESULTS: During phase 1, a draft genome of the STEC outbreak strain was obtained. During phase 2, 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 STEC-positive samples (67%). In phase 3, sequences from Clostridium difficile, Campylobacter jejuni, Campylobacter concisus, and Salmonella enterica were recovered.CONCLUSIONS AND RELEVANCE: These results suggest the potential of metagenomics as a culture-independent approach for the identification of bacterial pathogens during an outbreak of diarrheal disease. Challenges include improving diagnostic sensitivity, speeding up and simplifying workflows, and reducing costs.

KW - Computational Biology

KW - DNA, Bacterial

KW - Diarrhea

KW - Disease Outbreaks

KW - Escherichia coli Infections

KW - Feces

KW - Humans

KW - Metagenomics

KW - Retrospective Studies

KW - Sensitivity and Specificity

KW - Sequence Analysis, DNA

KW - Shiga Toxin

KW - Shiga-Toxigenic Escherichia coli

KW - Time Factors

U2 - 10.1001/jama.2013.3231

DO - 10.1001/jama.2013.3231

M3 - SCORING: Journal article

C2 - 23571589

VL - 309

SP - 1502

EP - 1510

JO - JAMA-J AM MED ASSOC

JF - JAMA-J AM MED ASSOC

SN - 0098-7484

IS - 14

ER -