The Application Value Of Bronchoalveolar Lavage Fluid Metagenomics Next-generation Sequencing In Pulmonary Infection

Background and objective:Pulmonary infection is one of the most common infectious diseases in clinical practice.Bronchoalveolar lavage fluid is a highly sensitive and less likely to be contaminated specimen obtained directly from the site of the disease,making it a reliable specimen to help diagnose pulmonary infections.Metagenomics next generation sequencing(mNGS)technology has been gaining clinical prominence in recent years,offering the advantages of rapid,accurate,comprehensive and unbiased sequencing.Therefore,the aim of this study was to retrospectively analyze the use of bronchoalveolar lavage fluid combined with mNGS technology in the diagnosis of clinical pulmonary infections and explore the value of mNGS combined with bronchoalveolar lavage fluid in the diagnosis of pulmonary infections Methods:This study retrospectively analyzed the data of 149 patients who were hospitalized with suspected pulmonary infection in a single center of Zhejiang Provincial People’s Hospital from January 2020 to September 2022,and underwent mNGS detection of alveolar lavage fluid during hospitalization.Using the final clinical diagnosis as the gold standard,the sensitivity,specificity and consistency test kappa values were calculated separately.Sensitivity,specificity and concordance test kappa values were calculated and ROC curves were plotted to compare the efficacy of mNGS,conventional assays and the combination of them,and to compare the differences in the detection and diagnosis of pulmonary infection pathogens and their efficacy in different subgroups.Data were statistically analyzed using SPSS 25.0 software,and comparisons of detections between the two assays were performed using a paired chi-square test.Results:1.Differences in pathogen detection results between mNGS and conventional testing methods: The mNGS has a higher positive pathogen detection rate than conventional tests(88.60% > 60.40%,P < 0.05)and detects a significantly higher variety and number of pathogens than conventional tests,especially for those that are rare and difficult to culture clinically.The positive rate of mNGS was higher for bacteria(67.11% vs 38.26%,P < 0.05)and lower for fungi(20.81% vs 30.20%,P < 0.05)than conventional tests.mNGS had a higher positive rate in the unilateral and bilateral pulmonary lesions groups(97.83%vs56.52% 、 84.47%vs62.14%),the combined underlying disease group(88.64%vs 60.61%)and the presence of immunosuppression group(100%vs52.63%)than conventional tests in the same group(P < 0.05).In addition,mNGS had a higher positive rate in the unilateral pulmonary lesions group than the bilateral pulmonary lesions group(97.83%vs84.47%,P < 0.05).2.mNGS versus conventional tests for pathogenic pathogens: The detection rate of pathogenic pathogens by mNGS was higher than that of conventional detection techniques(79.19% > 49.66%,P < 0.001),but the agreement between the two was poor(Kappa = 0.037,P > 0.05).3.Detection efficacy of mNGS,conventional assays and combined diagnostics of both: The mNGS has high diagnostic sensitivity,specificity and kappa values,and has the largest area under the Jorden Index and ROC curve.The sensitivity of mNGS,conventional assay and combined diagnosis were: 95.56%,64.44% and 98.52%respectively;the specificity was: 78.57%,78.57% and 71.43% respectively;the Jorden index fen was: 0.74,0.43 and 0.70;the area under the ROC curve was: 0.871,0.715 and0.850 in that order.Kappa values in order: 0.676,0.176 and 0.747.4.mNGS versus conventional assays for detection of mixed infections: mNGS was superior to conventional tests in detecting mixed infections(P < 0.05).The top three types of mixed infections detected were 21 cases of bacterial-bacterial mixed infections,10 cases of bacterial-fungal mixed infections and 6 cases of bacterial-viral mixed infections.5.Impact of pre-test antibiotic history on test results: The detection rate of mNGS in the group with or without history of antibiotic use was 96.49% and 90.48%respectively(P > 0.05),and the difference in detection rate between the two groups was not statistically significant.Conclusions:1.mNGS has a higher detection rate of pathogens and pathogenic agents than traditional pathogen detection methods and can detect a greater number of pathogens,especially for those that are rare or difficult to culture.2.mNGS has better detection efficacy than conventional tests and the combination of diagnostics can further increase its sensitivity,making it a useful complement to conventional pathogenic tests.3.mNGS has a higher detection rate of mixed infections,with the most common type of mixed infection being bacterial-bacterial,followed by bacterial-fungal and bacterial-viral.4.The results of the mNGS test are not affected by the history of antibiotic use before the test.