Application Comparison Between The Endotracheal Aspirates And Bronchoalveolar Lavage Fluid Metagenomic Next-generation Sequencing In The Pathogenic Diagnosis Of Severe Pneumonia

Objectives:To evaluate the efficacy of metagenomic next-generation sequencing(m NGS)in the microbiological diagnosis of severe pneumonia.The application values between endotracheal aspirate(ETA)vs.bronchoalveolar lavage fluid(BALF)in the microbiological diagnosis of severe pneumonia has been compared,and its influence differences on the prognosis of patients has also been elucidated.Methods:Clinical data of patients with severe pneumonia admitted to intensive care unit(ICU)of the First Affiliated Hospital of the University of Science and Technology of China from March 2018 to February 2022 were retrospectively collected.According to the established inclusion criteria,43 patients receiving ETA m NGS and 98 patients receiving BALF m NGS were eventually included in the study.The pathogen spectrum of m NGS was compared with that of conventional microbiological tests(CMT).Using CMT as reference,the sensitivity,specificity,positive predictive value(PPV)and negative predictive value(NPV)of m NGS were calculated.Subsequently,species accumulation curves,pathogen spectrum differences,reliability,and diagnostic efficacy of mixed infections were compared between ETA and BALF groups.Subgroup analysis was performed in 18 patients who received both ETA and BALF m NGS.Finally,the prognosis of patients in the ETA and BALF groups was compared.The primary endpoint was 28-day mortality,and the secondary endpoint was adjustment of anti-infective regimen,rate of pneumonia improvement,length of ICU stay,total mechanical ventilation time,and ICU mortality.Results:The percentage of m NGS samples that were positive for bacteria and fungi was significantly higher than that for CMT(P < 0.001).But there was no significant difference in virus detection between m NGS and CMT groups(P=0.429).Based on the results of CMT test,the sensitivity and specificity of ETA m NGS for bacterial detection were 95.2%(95%CI,89.5%-99.7%)and 45.1%(95%CI %,43.9%-62.5%).The diagnostic sensitivity and specificity of ETA m NGS for fungal detection were 62.3%(95% CI,58.5%-76.4%)and 74.3%(95% CI,59.9%-82.7%).The diagnostic sensitivity and specificity of BALF m NGS were 96.9%(95%CI,92.1%-103.5%)and 42.7%(95CI %,30.3%-51.8%).The diagnostic sensitivity and specificity of BALF m NGS for fungal detection were 69.5%(95% CI,61.8%--78.8%)and 78.1%(95% CI,63.5%-86.9%).10 cases(23.3%)were positive for ETA m NGS and only 2 cases(4.6%)were positive for CMT.Of the 26 patients who were positive by both methods,6(14%)were perfectly matched and 3(7%)were completely mismatched.The BALF group also had similar results,with 21 cases(21.4%)positive for m NGS alone and 3 cases(3.1%)positive for CMT alone.Of the 67 patients who were positive by both methods,19(19.4%)had a complete match and 5(5.1%)had a complete mismatch.The comparison of pathogen spectra between ETA m NGS and BALF m NGS showed that there were no significant differences in the detection of bacteria,fungi and viruses between the two groups(P > 0.05).However,a subgroup analysis of 18 patients who received both ETA and BALF m NGS showed a complete coincidence rate of only33.3%.Reliability analysis of each pathogen between the two groups showed that the BALF group had more confirmed pathogens and fewer probable pathogens than the ETA group(P=0.038).The proportion of patients initiating targeted therapy was significantly higher in the BALF group than in the ETA group(42.9% vs.20.9%;P = 0.030),the number of cases with no clinical benefit from ETA m NGS was significantly higher than that of BALF m NGS(16.3% vs.6.1%;P = 0.019).The recovery rate of pneumonia in BALF group was significantly higher than that in ETA group(86.73% vs.69.77%,P = 0.017).Mechanical ventilation duration(9 [4.25,18.25] d vs.11.00 [1.25,21.25] d,P = 0.033)and ICU stay(13 [10.00,26.75] vs.21 [12.25,36],P = 0.042)were also shorter than ETA group.However,there was no significant difference in ICU mortality(20.4% vs.25.6%,P = 0.495)or 28-day mortality(25.51% vs.34.88%,P = 0.41)between the two groups,which was further confirmed by Kaplan-Meier survival analysis.Conclusions:Compared with CMT,m NGS has obviously benefits in the etiological diagnosis of severe pneumonia patients.However,ETA is still not recommended as the preferred specimen for m NGS.