Diagnostic value of metagenomic next-generation sequencing for bacterial and fungal detection and its role in antimicrobial therapy adjustment in critically ill patients with non-resolving pneumonia

Introduction Early targeted antibiotic therapy is critical for improving outcomes in ICU patients with pneumonia unresponsive to initial treatment. Metagenomic next-generation sequencing (mNGS) is a unique diagnostic tool; however, its effectiveness for high-risk populations remains unclear.Methods This retrospective study included 642 ICU patients with pneumonia unresponsive to initial treatment, categorized into single- or repeat-test groups based on mNGS testing frequency. We analyzed the results of mNGS and conventional microbiological tests (CMTs), compared microbial detection characteristics between patients with different immune statuses, assessed the impact of repeat testing on microbial detection and treatment adjustments and evaluated its association with patient prognosis using multivariable logistic regression and propensity score matching.Results Among 642 patients, patient-level agreement between mNGS and CMTs was low (κ = 0.180, p < 0.001). First bronchoalveolar lavage fluid (BALF)-mNGS results showed a higher microbial detection rate in immunocompromised than immunocompetent patients. Among patients undergoing repeat BALF-mNGS testing, partial concordance between first and second tests was most common pattern. Antibiotic treatments were modified in 67.6% of cases based on mNGS results, with a higher adjustment rate in the repeat-test group. Although ICU mortality was higher in the repeat-test group, multivariate logistic regression analysis revealed no significant association between repeat testing and mortality risk (adjusted odds ratio = 1.15, 95% CI: 0.64–2.06, p = 0.630). After propensity score matching, no significant difference was observed between two groups (absolute risk difference: 1.12%, 95% CI: −7.43% to 9.67%, p = 0.798).Conclusion mNGS is a valuable microbial detection tool for ICU patients with pneumonia unresponsive to initial treatment and can support early antimicrobial adjustment. Repeat testing can provide information on dynamic changes in the microbial spectrum during disease but was not associated with improved patient outcomes, suggesting that repeat testing frequency should be carefully considered to avoid unnecessary testing. mNGS results should be interpreted in conjunction with CMTs, host immune status and inflammatory biomarkers to optimise its clinical value in ICU pneumonia.