Value And Clinical Application Of Metagenomic Second-generation Sequencing In Diagnosis And Treatment Of Lower Respiratory Tract Infection

Background: Lower respiratory tract infections(LRTI)are common and highly harmful respiratory diseases in clinic.Timely etiological detection is crucial for the treatment and prognosis of LRTI.Although there are many traditional detection methods,they all have certain drawbacks.The emergence of Metagenomic next-generation sequencing(mNGS)breaks through the limitations of traditional detection methods such as low sensitivity and time consuming,with advantages such as high sensitivity,wide detection range and fast detection speed,and is now gradually applied to clinical detection of pathogenic microorganisms.Objective: Investigate the diagnostic performance and clinical application value of mNGS in patients with Lower respiratory tract infections(LRTI).Methods: 233 patients with suspected lower respiratory tract infection were reviewed from several large hospitals in Xi ’an from May 2018 to October 2022.Basic clinical data,including basic data,history,symptoms,laboratory examinations and imaging examinations,were collected after screening for inclusion and exclusion criteria.All patients undergo Conventional microbiological testing methods(CMTs)and mNGS,Traditional tests include culture,smear,serology,Polymerase chain reaction(PCR),etc.The samples for mNGS test mainly include Bronchoalveolar Lavage Fluid and blood,etc.Finally,the detection efficacy and diagnostic value of CMTs and mNGS were compared,as well as the ability to detect various pathogens was evaluated.Results: A total of 198 patients were included in this study.There were 140 male patients,accounting for 70.7% of the total number,and 58 female patients,accounting for29.3% of the total number,with an age of 61.86±16.998.mNGS samples were 168 bronchoalveolar lavage fluid,17 blood,8 sputum,2 pleural effusion,1 pus,1 fresh tissue and 1 secretion,respectively.There were 14 patients who underwent bronchoalveolar lavage fluid and blood test at the same time.A total of 106 pathogens were detected by mNGS and 60 by CMTs.Mc Nemar test was used to compare the results of mNGS detection and conventional detection,and the results showed that the difference between the two detection methods was statistically significant,P< 0.05,and kappa consistency analysis was performed,indicating that the detection results were highly inconsistent,kappa coefficient > 0.05.The positive rate of mNGS was 90.4%,and the traditional positive rate was 54%.The positive rate of mNGS was high and had obvious advantages.The sensitivity of mNGS detection was higher than that of traditional detection,but the specificity of traditional detection was higher than that of mNGS.The types and quantities of viruses,fungi and bacteria detected by mNGS were higher than those detected by traditional detection,with significant statistical differences.In terms of physical examination of other rare pathogens,the overall detection rate of mNGS in this study was higher than that by traditional detection,but there was no significant statistical difference.Bacterial mNGS were more likely to be detected in alveolar lavage solution than in blood,and viral mNGS were more likely to be detected in blood lavage solution than in blood lavage solution.Blood mNGS showed statistically significant differences in the detection of viruses compared with traditional tests,but did not show significant advantages in the detection of bacteria,fungi and other pathogens.In addition,we found that the bacterial infection in this study was more common in Pseudomonas aeruginosa,Klebsiella pneumoniae,Acinetobacter baumannii and other gram-negative bacteria.Human herpes virus was the main virus infection,and candida was the most common fungal infection.Conclusion: The positive rate of mNGS to pathogenic microorganisms of LRTI is higher than that of CMTs on the whole.However,compared with mNGS,the predicted positive value of traditional detection methods is higher,indicating a lower false positive rate.Therefore,mNGS cannot completely replace traditional detection methods,and the combination of mNGS with traditional detection methods is helpful to improve the level of clinical diagnosis and treatment.When the same patient was tested for mNGS in alveolar lavage fluid and blood at the same time,the bacterial detection rate of mNGS in alveolar lavage fluid was higher than that in blood,while the detection rate of mNGS virus in blood was higher.However,compared with the traditional test,the detection rate of bacteria,fungi and other pathogens in blood mNGS was not much advantage.Therefore,blood mNGS have the greatest significance only when patients suspect viral infection.For critically ill patients and patients with complex conditions suspected of lower respiratory tract infection,it is recommended to send alveolar lavage fluid for mNGS detection in time,which is helpful for timely diagnosis and treatment.