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Case Reports
. 2017 Dec 15;196(12):1610-1612.
doi: 10.1164/rccm.201703-0537LE.

Rapid Pathogen Identification in Bacterial Pneumonia Using Real-Time Metagenomics

Kathryn M Pendleton  1 , John R Erb-Downward  1 , Yuwei Bao  1 , William R Branton  1 , Nicole R Falkowski  1 , Duane W Newton  1 , Gary B Huffnagle  1   2 , Robert P Dickson  1   3
Affiliations
Case Reports

Rapid Pathogen Identification in Bacterial Pneumonia Using Real-Time Metagenomics

Kathryn M Pendleton et al. Am J Respir Crit Care Med. .
No abstract available

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Figures

Figure 1.
Figure 1.
Rapid identification of a respiratory pathogen using real-time metagenomics. (A) A 41-year-old woman developed hypoxic respiratory failure with bilateral infiltrates on chest X-ray. A miniature bronchoalveolar lavage was performed. (B) Nine hours later, a 3,217 base pair DNA sequence was detected in the lavage fluid using a MinION sequencer. The sequence was well aligned with previously sequenced strains of Pseudomonas aeruginosa (E ≤ 10−199). (C) Twenty-three hours after lavage, the hospital’s clinical microbiology laboratory reported the growth of >104 colony forming units of P. aeruginosa. (D) The genomic identity of the cultured strain was subsequently (48 hours later) confirmed via whole-genome sequencing performed with the MinION sequencer. The 3,217 base-pair sequence from the bronchoalveolar lavage fluid was well aligned with a segment of the sequenced genome of the cultured P. aeruginosa strain, which was in turn well aligned with a reference strain of P. aeruginosa (SCV20265) (E ≤ 10−199 for both). (E) Subsequent analysis of the lavage fluid using community sequencing of the bacterial 16S ribosomal RNA gene confirmed the presence of a low-diversity bacterial community dominated by P. aeruginosa. NCBI = National Center for Biotechnology Information.
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