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ABSTRACT: Effect of Metagenomic Next-Generation Sequencing on Clinical Outcomes of Patients with Severe Community-Acquired Pneumonia in the Intensive Care Unit

PROVIDER: PRJNA1000648 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28710300.fastq.gz	Fastqsanger.gz
	SRR28710400.fastq.gz	Fastqsanger.gz
	SRR28710500.fastq.gz	Fastqsanger.gz
	SRR28710301.fastq.gz	Fastqsanger.gz
	SRR28710401.fastq.gz	Fastqsanger.gz

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intensive care unit

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Multidimensional Assessment of the Host Response in Mechanically Ventilated Patients with Suspected Pneumonia

Project description:Rationale: Patients in the intensive care unit (ICU) are frequently exposed to unnecessary antibiotics. Markers of the host response to infection may aid pneumonia diagnosis and avoid antibiotic-induced complications. Objective: To assess the host response to suspected bacterial pneumonia through assessment of alveolar neutrophilia and transcriptomic profiling of alveolar macrophages. Methods: We determined the test characteristics of BAL neutrophilia for the diagnosis of bacterial pneumonia in 3 cohorts of mechanically ventilated patients. In one cohort, we also isolated alveolar macrophages from BAL fluid and used the transcriptome to identify signatures of bacterial pneumonia. Finally, we developed a humanized mouse model of Pseudomonas aeruginosa pneumonia to determine if pathogen-specific signatures can be identified in human alveolar macrophages. Measurements and Main Results: BAL neutrophilia was highly sensitive for bacterial pneumonia in both the retrospective (N = 851) and validation cohorts (N = 76 and N = 79) with a negative predictive value of over 90% when BAL neutrophil percentage was less than 50%. A transcriptional signature of bacterial pneumonia was present in both resident and recruited macrophages. Gene signatures from both cell types identified patients with bacterial pneumonia with test characteristics similar to BAL neutrophilia. Conclusions: A BAL neutrophil percentage of less than 50% is highly sensitive for bacterial pneumonia. Informative transcriptomic signatures can be generated from BAL fluid obtained during routine clinical care in the ICU. The identification of novel host response biomarkers is a promising approach to aid the diagnosis and treatment of pneumonia.

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