Discussion On The Application Value Of Metagenomics Next-generation Sequencing In Lower Respiratory Tract Infection

Research Background:Lower respiratory tract infection(LRTI)is the common infectious disease in the world,its etiology composition is complex and diverse,the morbidity and mortality is higher,especially for thos population who has a poor immunologic function,And with the continuous development of modern science and technology,the increasing of radiation and chemotherapy for all kinds of malignant tumor and the immunosuppressants and widespread using of antibiotics and glucocorticoids,The population showed a trend of increase.The infectious diseases of LRTI,including special pathogens,complex infections and multiple drug-resistant bacteria infections,have put forward higher requirements for clinicians.Early rapid and accurate diagnosis and targeted treatment to the disease is particularly important.However,the traditional etiological detection methods which are commonly used in clinical practice,such as isolation and culture,are time-consuming and have a low positive rate,especially for the detection of some special microbial infections and newly emerging pathogens,which are limited to a certain extent,and can not well meet the current diagnosis and treatment of LRTI.Compared with the traditional detection methods,metagenomics next-generation sequencing has the characteristics of short time consumption,high throughput,comprehensive and unbiased detection,which brings new possibilities for the etiological diagnosis of LRTI,but it still has many problems,its value still needs further discussion.Purpose:(1)Compare the differences between mNGS and traditional etiological detection methods in the microbiological diagnosis of LRTI.(2)Explore the application value of mNGS in the diagnosis and treatment of LRTI.Methods:Collecting the general information(name,gender,age),medical history,the main clinical symptoms,chest imaging examination,laboratory test results(white blood cell,count,C-reactive protein,Procalcitonin,GM test,G test),and other auxiliary examination(sputum smear and sputum cultivation,blood culture,alveolar lavage fluid,antibody detection,nucleic acid detection,etc.)of those patients suspected pulmonary infection that were hospitalized in the respiratory ward of the Second Affiliated Hospital of Nanchang University from May 2019 to February 2021.testing results of mNGS、anti-infection treatment、disease outcome and final clinical diagnosis.According to the inclusion criteria and exclusion criteria,114 patients with LRTI and 17 patients with non-pulmonary infection were finally included.SPSS25.0software was used for statistical analysis by Mc Nemar test,Kappa test,Fisher’s exact test and non-parametric test.Results:(1)There was no significant difference in the detection rate of pathogenic microorganisms of mNGS in infected patients and non-infected patients(91.23%VS94.12%,P=1.000>0.05),mNGS can not distinguish between infectious and non-infectious diseases of the lung.(2)The detection rate of mNGS to pathogenic microorganisms was significantly higher than that of traditional detection method(91.60%VS46.56%,P<0.01),but the consistency between the two detection methods was poor(Kappa<0.4).(3)The detection rates of mNGS for bacteria,fungi,viruses,atypical pathogens were significantly higher than those of traditional detection methods(51.91%VS19.08%,32.06%VS15.27%,40%VS0.76%,10.69%VS00.00%,P<0.05),the consistency of the detected fungi with the clinical diagnosis both of the two methods was high(50.00%VS60.00%,P=0.461>0.05),the combined detection could improve the clinical diagnosis and treatment of fungal infection.(4)There was no significant difference in the detection rates of mycobacterium tuberculosis by mNGS compared with the traditional methods(22.90%VS16.03%,P=0.160>0.05).However,the consistency with the clinical diagnosis both of them was high(83.33%VS100.00%,P=0.069>0.05),the combined detection could improve the clinical diagnosis of mycobacterium infection.(5)There was no significant difference in the coincidence rate of pathogenic microorganisms that by mNGS and the traditional detection methods(58.33%VS70.00%,P=0.128>0.05).(6)35.14%(26/74)patients adjusted the treatment plan according to mNGS,and36.11%(13/36)patients adjusted the treatment according to the traditional detection(P=0.920>0.05),the effective adjustment patients in the two groups was 53.85% and76.92%(P=0.295>0.05),there was no significant difference between mNGS and traditional detection methods in guiding treatment and improving the disease outcome of patients.(7)The intensity of antibiotic use was increased after treatment regimens were adjusted according to mNGS(P=0.020<0.05).Conclusions:(1)The detection rate of mNGS for LRTI pathogenic microorganisms was higher than that of traditional detection methods as a whole,and mNGS showed more unique advantages in the detection of viruses,atypical pathogens and rare pathogens.(2)mNGS combined with traditional detection can improve the level of clinical diagnosis and treatment of mycobacteria and fungi.(3)mNGS can not distinguish between infectious and non-infectious diseases of the lung,and have no obvious advantages in guiding the diagnosis and treatment of common pathogen infections.Incorrect screening of mNGS test results may lead to antibiotic abuse.