Nanopore sequencing for microbiological diagnosis of bacterial pneumonia: A systematic review and meta-analysis.

PURPOSE: Accurate and timely diagnosis is essential to ensure effective management of bacterial pneumonia to improve patient outcomes. This study aims to evaluate the use of metagenomic nanopore sequencing in the microbiological diagnosis of pneumonia compared to standard diagnostic procedures. METHODS: A comprehensive literature search across multiple databases was performed. The risk of bias was assessed using the Quality Assessment of Diagnostic Accuracy 2 (QUADAS-2) tool. Pooled sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and area under the curve (AUC) were determined. RESULTS: Thirteen studies were included in the systematic review, with eight eligible for meta-analysis. In the microbiological diagnosis of bacterial pneumonia, the overall sensitivity of nanopore sequencing using both MinION and GridION platforms is 86.08% (95% CI 75.96–92.37) while specificity is 84.97% (95% CI 75.94–91.02). Results show a high PPV (85.13%; 95% CI 77.72–90.38) and high NPV (85.27%; 95% CI 76.79–91.01). Nanopore sequencing also has a high diagnostic value based on the computed AUC (0.922) and DOR (40.68; 95% CI 11.22–147.48). Sensitivity analyses suggest a trend toward higher diagnostic accuracy for bacterial pneumonia with the MinION device and lower accuracy with the GridION platform. We also found that accuracy is higher when the focus of diagnosis is ventilator-associated pneumonia (VAP) and when endotracheal aspirate alone is utilized as the sample type. CONCLUSIONS: Nanopore sequencing offers faster, real-time results compared to traditional culture. It also shows higher specificity than short-read metagenomic next-generation sequencing (mNGS), particularly in ventilator-associated pneumonia. Further research is warranted for subgroup analyses to optimize the use of nanopore sequencing in detecting bacterial pneumonia.