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Volume 20, Number 6—June 2014

Letter

Rapid Metagenomic Diagnostics for Suspected Outbreak of Severe Pneumonia

Nicole Fischer1, Holger Rohde1, Daniela Indenbirken, Thomas Günther, Kerstin Reumann, Marc Lütgehetmann, Thomas Meyer, Stefan Kluge, Martin Aepfelbacher, Malik Alawi, and Adam GrundhoffComments to Author 
Author affiliations: University Medical Centre Hamburg–Eppendorf, Hamburg, Germany (N. Fischer, H. Rohde, M. Lütgehetmann, T. Meyer, S. Kluge, M. Aepfelbacher, M. Alawi); German Center for Infection Research, Hamburg (N. Fischer, A. Grundhoff); Heinrich Pette Institute Leibniz Institute for Experimental Virology, Hamburg (D. Indenbirken, T. Günther, K. Reumann, M. Alawi, A. Grundhoff)

Main Article

Figure

Next-generation sequencing of RNA (RNaseq) and DNA (DNaseq) isolated from bronchoalveolar lavage (BAL) samples from 3 patients with severe pneumonia, northern Germany. Shown are data from BLASTN (http://blast.ncbi.nlm.nih.gov/Blast.cgi) analysis of de novo assembled sequence contigs (www.virus-genomics.org/supplementals/EID1406.pdf). Relative abundance of contig reads mapping bacterial, fungal, or viral species is indicated by a heat map (scale bar). Gray indicates that no reads were detected. D

Figure. Next-generation sequencing of RNA (RNaseq) and DNA (DNaseq) isolated from bronchoalveolar lavage (BAL) samples from 3 patients with severe pneumonia, northern GermanyShown are data from BLASTN (http://blast.ncbi.nlm.nih.gov/Blast.cgi) analysis of de novo assembled sequence contigs (www.virus-genomics.org/supplementals/EID1406.pdf)Relative abundance of contig reads mapping to bacterial, fungal, or viral species is indicated by a heat map (scale bar)Gray indicates that no reads were detectedDiagnostic samples were obtained from 3 patients (lanes P1, P2, and P3)Lane B, control BAL sample (analyzed by using RNaseq only) from an influenza patient; lane1, MS: analysis on the Illumina MiSeq platform (www.illumina.com/systems.ilmn); lane 2, HS: analysis on the Illumina HiSeq platform (www.illumina.com/systems.ilmn); lane 3, HS dpl., RNA samples depleted of human rRNA before analysis on a HiSeq instrumentChlamydophila psittaci, which was unequivocally detected in all samples from patient 2 but not in samples from the other patients, is indicated by an arrowSymb., symbiont; Uncult., uncultured; Unclsfd., unclassified; SEN virus, strain of Torque teno virus.

Main Article

1These authors contributed equally to this article.

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