Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study
Abstract Background Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinica...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-11-01
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| Series: | Respiratory Research |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12931-019-1218-4 |
| _version_ | 1819243492955652096 |
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| author | Libing Yang Ghady Haidar Haris Zia Rachel Nettles Shulin Qin Xiaohong Wang Faraaz Shah Sarah F. Rapport Themoula Charalampous Barbara Methé Adam Fitch Alison Morris Bryan J. McVerry Justin O’Grady Georgios D. Kitsios |
| author_facet | Libing Yang Ghady Haidar Haris Zia Rachel Nettles Shulin Qin Xiaohong Wang Faraaz Shah Sarah F. Rapport Themoula Charalampous Barbara Methé Adam Fitch Alison Morris Bryan J. McVerry Justin O’Grady Georgios D. Kitsios |
| author_sort | Libing Yang |
| collection | DOAJ |
| description | Abstract Background Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinical respiratory specimens. Methods We conducted a case-control study of mechanically-ventilated patients with pneumonia (nine culture-positive and five culture-negative) and without pneumonia (eight controls). We collected endotracheal aspirates and applied a microbial DNA enrichment method prior to metagenomic sequencing with the Oxford Nanopore MinION device. For reference, we compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing. Results Human DNA depletion enabled in depth sequencing of microbial communities. In culture-positive cases, Nanopore revealed communities with high abundance of the bacterial or fungal species isolated by cultures. In four cases with resistant clinical isolates, Nanopore detected antibiotic resistance genes corresponding to the phenotypic resistance in antibiograms. In culture-negative pneumonia, Nanopore revealed probable bacterial pathogens in 1/5 cases and Candida colonization in 3/5 cases. In controls, Nanopore showed high abundance of oral bacteria in 5/8 subjects, and identified colonizing respiratory pathogens in other subjects. Nanopore and 16S sequencing showed excellent concordance for the most abundant bacterial taxa. Conclusions We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive microbiologic cultures, and clinically actionable information obtained from sequencing in culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes. |
| first_indexed | 2024-12-23T14:56:34Z |
| format | Article |
| id | doaj.art-54bd73bc8c2841499f86ee59b1455dfb |
| institution | Directory Open Access Journal |
| issn | 1465-993X |
| language | English |
| last_indexed | 2024-12-23T14:56:34Z |
| publishDate | 2019-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Respiratory Research |
| spelling | doaj.art-54bd73bc8c2841499f86ee59b1455dfb2022-12-21T17:42:44ZengBMCRespiratory Research1465-993X2019-11-0120111210.1186/s12931-019-1218-4Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity studyLibing Yang0Ghady Haidar1Haris Zia2Rachel Nettles3Shulin Qin4Xiaohong Wang5Faraaz Shah6Sarah F. Rapport7Themoula Charalampous8Barbara Methé9Adam Fitch10Alison Morris11Bryan J. McVerry12Justin O’Grady13Georgios D. Kitsios14Center for Medicine and the Microbiome, University of PittsburghDivision of Infectious Diseases, University of Pittsburgh Medical Center and University of Pittsburgh School of MedicineInternal Medicine Residency Program, University of Pittsburgh Medical Center McKeesportCenter for Medicine and the Microbiome, University of PittsburghCenter for Medicine and the Microbiome, University of PittsburghCenter for Medicine and the Microbiome, University of PittsburghDivision of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical CenterDivision of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine and University of Pittsburgh Medical CenterBob Champion Research and Educational Building, University of East Anglia, Norwich Research ParkCenter for Medicine and the Microbiome, University of PittsburghCenter for Medicine and the Microbiome, University of PittsburghCenter for Medicine and the Microbiome, University of PittsburghCenter for Medicine and the Microbiome, University of PittsburghBob Champion Research and Educational Building, University of East Anglia, Norwich Research ParkCenter for Medicine and the Microbiome, University of PittsburghAbstract Background Metagenomic sequencing of respiratory microbial communities for pathogen identification in pneumonia may help overcome the limitations of culture-based methods. We examined the feasibility and clinical validity of rapid-turnaround metagenomics with Nanopore™ sequencing of clinical respiratory specimens. Methods We conducted a case-control study of mechanically-ventilated patients with pneumonia (nine culture-positive and five culture-negative) and without pneumonia (eight controls). We collected endotracheal aspirates and applied a microbial DNA enrichment method prior to metagenomic sequencing with the Oxford Nanopore MinION device. For reference, we compared Nanopore results against clinical microbiologic cultures and bacterial 16S rRNA gene sequencing. Results Human DNA depletion enabled in depth sequencing of microbial communities. In culture-positive cases, Nanopore revealed communities with high abundance of the bacterial or fungal species isolated by cultures. In four cases with resistant clinical isolates, Nanopore detected antibiotic resistance genes corresponding to the phenotypic resistance in antibiograms. In culture-negative pneumonia, Nanopore revealed probable bacterial pathogens in 1/5 cases and Candida colonization in 3/5 cases. In controls, Nanopore showed high abundance of oral bacteria in 5/8 subjects, and identified colonizing respiratory pathogens in other subjects. Nanopore and 16S sequencing showed excellent concordance for the most abundant bacterial taxa. Conclusions We demonstrated technical feasibility and proof-of-concept clinical validity of Nanopore metagenomics for severe pneumonia diagnosis, with striking concordance with positive microbiologic cultures, and clinically actionable information obtained from sequencing in culture-negative samples. Prospective studies with real-time metagenomics are warranted to examine the impact on antimicrobial decision-making and clinical outcomes.http://link.springer.com/article/10.1186/s12931-019-1218-4NanoporeMetagenomics sequencingPneumoniaPathogen detectionMechanical ventilation |
| spellingShingle | Libing Yang Ghady Haidar Haris Zia Rachel Nettles Shulin Qin Xiaohong Wang Faraaz Shah Sarah F. Rapport Themoula Charalampous Barbara Methé Adam Fitch Alison Morris Bryan J. McVerry Justin O’Grady Georgios D. Kitsios Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study Respiratory Research Nanopore Metagenomics sequencing Pneumonia Pathogen detection Mechanical ventilation |
| title | Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study |
| title_full | Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study |
| title_fullStr | Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study |
| title_full_unstemmed | Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study |
| title_short | Metagenomic identification of severe pneumonia pathogens in mechanically-ventilated patients: a feasibility and clinical validity study |
| title_sort | metagenomic identification of severe pneumonia pathogens in mechanically ventilated patients a feasibility and clinical validity study |
| topic | Nanopore Metagenomics sequencing Pneumonia Pathogen detection Mechanical ventilation |
| url | http://link.springer.com/article/10.1186/s12931-019-1218-4 |
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