Session: 039. Diagnostics: Sequencing & Typing, Thursday, 12:15-1:30 p.m.
Background : Metagenomic sequencing of respiratory microbial communities may overcome the limitations of culture-based pneumonia diagnostics. Nonetheless, respiratory metagenomics require high-quality specimens, may miss deep-seated infections and cannot distinguish colonization from infection. Plasma microbial cell-free DNA (mcfDNA) sequencing may offer a non-invasive alternative for culture-independent diagnosis and help refine interpretations of respiratory metagenomics.
Methods : We obtained concurrent plasma and endo-tracheal aspirate (ETA) samples from 29 mechanically-ventilated patients (15 culture-positive, 11 culture-negative pneumonia, 3 uninfected control patients). We performed plasma mcfDNA sequencing (Karius®Test, Redwood City, CA) and ETA metagenomics (MiNION, Oxford Nanopore Technologies). We compared sequencing results with clinical microbiologic cultures for identified DNA pathogens.
Results : Uninfected control patients had negative signal for mcfDNA in plasma and oral bacteria in ETA specimens. In culture-positive pneumonia samples, Karius testing identified a median of 2 pathogens per sample (range 0-10), which were concordant with clinical isolates in 11/15 (73%) cases (Figure). In 5/11 (45%) of concordant cases, Karius and MiNION suggested polymicrobial infections with additional pathogens not identified by cultures. In culture-negative cases, Karius detected potential pathogens in 8/11 (73% cases), which matched the species identified in ETA specimens by MiNION. In cases of clinical aspiration, Karius detected more organisms (median 8, range 0-14) per sample mainly consisting of oral origin bacteria compared to cases without history of aspiration (median 1, range 0-6, p =0.04).
Conclusion : Metagenomic sequencing in plasma and ETA samples showed good concordance between the blood and lung compartments as well as with culture results in pneumonia patients. Metagenomics revealed potential pathogens missed by cultures in ~75% of culture-negative pneumonias and suggested polymicrobial infections especially in cases with aspiration. Further research is needed to evaluate the clinical utility of real-time metagenomics for pneumonia diagnosis in mechanically ventilated patients.
Georgios Kitsios– Assistant Professor of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA
Libing Yang– Research Associate, University of Pittsburgh, Pittsburgh, PA
Rachel Nettles– Research Associate, University of Pittsburgh, Pittsburgh, PA
Zia Haris– Resident in Internal Medicine, University of Pittsburgh Medical Center McKeesport, Pittsburgh, PA
Daniel Dunlap– Fellow in Pulmonary and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA
Sarah Rapport– Research Associate, University of Pittsburgh Medical Center, Pittsburgh, PA
Ghady Haidar– Assistant Professor of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA
Carine Ho– Clinical Research Associate, Karius, Inc, Redwood City, CA
Desiree Hollemon– Head of Clinical Affairs, Karius, Inc, Redwood City, CA
Asim Ahmed– Medical Director, Karius, Inc, Redwood City, CA
David Hong– Vice President, Medical Affairs and Clinical Development, Karius, Inc., Redwood City, CA
Alison Morris– Professor of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA
Bryan McVerry– Associate Professor of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA