Translating Lung Microbiome Profiles into the Next-Generation Diagnostic Gold Standard for Pneumonia: a Clinical Investigator’s Perspective

Stepwise clinical translation of next-generation sequencing (NGS) diagnostics for pneumonia. (A) Scope of the clinical problem, as delays or the inability to establish an etiologic diagnosis of bacterial pneumonia based on culture results lead to empirical one-size-fits-all antibiotic regimens. (B) Current state of research in the field with comparisons of either point-of-care or standard sequencing device outputs with clinical, culture-based diagnoses of pneumonia. The lack of a diagnostic gold standard limits our ability to assess the diagnostic performance of NGS in this context. (C) Clinical validity assessment of NGS output (and specifically metagenomic sequencing) against construction of a gold standard (incorporating clinical variables, vital signs, chest radiography scores, culture results, and validated biomarkers of injury and inflammation) with the use of machine-learning algorithms to develop a sequencing-based definition of pneumonia (pneumonia index). (D) Clinical utility assessment of the developed pneumonia index in a randomized clinical trial design of NGS (metagenomics) versus standard-of-care cultures for assessment of NGS impact on antibiotic prescriptions and clinical outcomes.