Clinical utility of Metagenomic Next-Generation Sequencing on bronchoalveolar lavage fluid in diagnosis of Lower Respiratory Tract Infections

Abstract

Abstract Introduction: In this study, we aimed to evaluate the clinical utility of Metagenomic Next-Generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) in diagnosis of Lower Respiratory Tract Infection (LRTIs). Methods: This retrospective study included 186 hospitalized patients with suspected LRTIs who visit The Fifth Affiliated Hospital of Sun Yat-Sen University from March 2023 to August 2023. Among them, each patient had undergone mNGS (DNA) testing; 155 patients had undergone both conventional culture and mNGS (DNA) testing. The detecting rate of mNGS was compared to the paired culture testing. The diagnostic efficacy was evaluated between mNGS and conventional culture. Results: The positive detection rates of pathogens between mNGS and conventional culture were significant different (81.29% vs 39.35%, P<0.05). The detection rate was still significantly different (70.32% VS 39.35%, P <0.05) with regard to bacteria and fungi detection. The sensitivity of mNGS in diagnosis of LRTIs was much higher than that of conventional culture (88.41% vs 43.48%; P <0.05), the specificity was opposite (76.47% vs 94.12%; P >0.05). Among 155 patients with paired conventional culture result, 77.54% and 35.51% of cases were detected as definite or probable pathogens by mNGS and culture respectively. Importantly, mNGS directly led to a change of treatment regimen in 58 (37.42%) cases, including antibiotic adjustment (29.68%) and ruling out active infection (7.74%). Moreover, treatment regimen remained unchanged in 97 (62.58%) cases as the current antibiotic therapy already covered the detected pathogens (36.13%) or empirical treatment was effective (11.68%). Conclusion: mNGS can identify a wide range of pathogens in LRTIs, with improved sensitivity and being more superior at diagnosing LRTIs etiologically. mNGS has the potential to enhance clinical outcomes by optimizing the treatment regimens.