The Application Of Metagenomic Next-generation Sequencing In Diagnosis Of Pulmonary Infection

ObjectivesTo evaluate the diagnostic performance of metagenomic next-generation sequencing(mNGS)of bronchoalveolar lavage fluid(BALF),compared with conventional microbiological tests(CMTs),in patients suspected with pulmonary infection.Methods502 patients suspected pulmonary infection from The Second Affiliated Hospital of Nanchang University and Jiangxi Provincial People’s Hospital between April 2019 and September 2021 were retrospectively reviewed.All of them have underwent both mNGS of BALF and conventional microbiological tests(CMTs).Age,gender,comorbidities,results of laboratory tests,the image of lung,therapy of antibiotics and patient outcomes were recorded.Clinical comprehensive analysis about clinical manifestation,image of lung,serological tests,therapy of antibiotics,CMTs and mNGS was regarded as the reference standard.Firstly,every patient was assessed whether there was an infectious disease.Secondly,the causative pathogens were determined if patient were considered to have infectious diseases.The diagnostic value of mNGS was evaluated and compared with that of CMTs.The enrolled patients were classified into four groups based on the comorbidities: immunocompromised group,bronchiectasis group,other comorbidities group and simple pulmonary infection group.The spectrum of pathogens of different groups were analyzed and positive predictive values(PPVs)of different kinds of pathogens were calculated to explore if comorbidities and kinds of pathogens have guiding function in the interpretation of mNGS reports.Result:According to the comprehensive analysis of medical records and the results of mNGS,84.1%(422/502)patients were diagnosed as pulmonary infection,15.9%(80/502)patients were considered non-infectious diseases,including malignancies,organizing pneumonia,vasculitis,etc.104(20.7%)patients were classified into immunocompromised group.93(18.5%)patients were classified into bronchiectasis group.90 patients were classified into other comorbidities group.215(42.8%)patients were classified into simple pulmonary infection group.The sensitivity and diagnostic accuracy of mNGS were 72.5%(95%confidence interval [CI],68.2-76.8%)and 74.9%(95%CI,71.7-78.7%),respectively,outperformed those of CMTs(25.4% for Sensitivity,36.9% for diagnostic accuracy).In most pathogens,the detection rate of mNGS was higher than CMTs.Polymicrobial infections most often occurred in immunocompromised group(22.1%),followed by other comorbidities group(22.1% vs 13.3%,p= 0.13)and bronchiectasis group(22.1% vs 9.7%,p= 0.018).Only 2.3%(95%CI,0.3%-4.4%)patients developed polymicrobial infection in simple pulmonary infection group.In addition,the spectrums of pathogens also varied in different groups.In immunocompromised group,the most common pathogens were Pneumocystis yersini(31.0%)and Aspergillus(17.2%).In bronchiectasis group,the most common pathogens were Pseudomonas aeruginosa(24.1%)and Non-mycobacterium tuberculosis(24.1%).In other comorbidities group,the most common pathogens were Mycobacterium tuberculosis(20.3%),Aspergillus(14.5%)and Anaerobion(11.6%).In simple pulmonary infection group,the most common pathogens were Mycobacterium tuberculosis(37.3%)and Chlamydia psittaci(12.7%).The positive predictive values(PPVs)of mNGS were observed discrepant in pathogens: 94.9%(95%CI 89.1-100%)for Mycobacterium tuberculosis,86.2%(95%CI,72.9-99.6%)for Chlamydia psittaci,86.0%(95%CI,76.0-96.0%)for Aspergillus,67.6%(95%CI,51.1-84.2%)for Non-mycobacterium tuberculosis,67.3%(95%,54.1-80.5%)for Pneumocystis jeroveci;as for bacteria,the PPVs also show differences in different types of bacteria.Immunocompromised group had a higher PPV of Pneumocystis jeroveci than that of other three groups(80.5% vs12.8% p=0.006).Similarly,the PPV of Non-mycobacterium tuberculosis in bronchiectasis group was also higher than that of other three groups(90.5% vs30.8% p=0.001).ConclusionThe application of mNGS of BALF can highly enhance the detection rate of pathogens in patients with pulmonary infection.The spectrums of pathogens and the risk of polymicrobial infections varied in patients with different comorbidities.And the PPVs of mNGS were observed discrepant in different pathogens.The comorbidities and types of pathogens should be taken into consideration when interpreting the report of mNGS.