Prognostic value of Nanopore sequencing-based metagenomics next-generation sequencing in clinical infectious cases: A retrospective observational study

Objectives

This study aimed to evaluate the prognostic value of metagenomic next-generation sequencing(mNGS) using Nanopore sequencing technology (NST) versus traditional culture methods in infectious disease cases.

Methods

We conducted a retrospective, single-center observational study comparing clinical outcomes between patients and specimen types in NST group and those in culture-based control group. Cox Proportional Hazards regression and Kaplan-Meier survival analysis were conducted to evaluate the association between diagnostic strategy and 28-day mortality. To minimize bias, Propensity Score Matching (PSM) and robust multivariate Cox regression analysis were employed to control for confounding factors. Diagnostic accuracy was quantified by calculating sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV).

Results

The NST-based diagnosis was independently associated with a significantly reduced 28-day mortality rate, as indicated by the robust multivariate Cox regression analysis. (HR = 0.29, 95 %CI:0.09-0.91, p = 0.033). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of NST in detecting bacterium were 0.93,0.54, 0.5and 0.94, respectively. Additionally, the NST group was associated with higher Antibiotic De-escalation Rate (ADE) and reduced Duration of Therapy (DOT), with p values of 0.0238 and 0.008, respectively.

Conclusion

NST-based mNGS demonstrated superior performance in diagnosing bacterial infections compared to traditional culture methods. The NST group and positive pathogen detection were associated with a reduced 28-day mortality rate. Additionally, higher APACHE II scores upon admission were identified as independent predictors of worse prognosis, highlighting the importance of early severity assessment in patient outcomes.