Clinical Data Analysis On The Application Of Metagenomic Next-generation Sequencing In Infectious Diseases

Objective: To analyze the difference between mNGS and traditional laboratory methods in pathogen detection,and to explore the application value of mNGS in the diagnosis and treatment of clinical infectious diseases.Method: The mNGS and traditional pathogen detection data of 99 patients with suspected infection in the first Hospital of Lanzhou University from December 2019 to December 2020 were analyzed retrospectively.the data were divided into four groups according to the types of mNGS samples,cerebrospinal fluid,bronchoalveolar lavage fluid,sputum and blood were used in this group.and the routine etiological detection methods of patients were collected,including cerebrospinal fluid examination,blood culture,sputum culture,G+GM test,blood routine,CRP,PCT,chest CT,and other clinical data.Combined with the process of clinical diagnosis and treatment of patients were analyzed.Results:1.A total of 99 patients,including 56 males and 43 females were collected,including 48(48%)cerebrospinal fluid(CSF),26(26%)blood,21(21%)bronchoalveolar lavage fluid(BALF),5(5%)sputum,81(81%)total positive samples and 19(19%)negative samples.2.Among the 48 cerebrospinal fluid samples,34 were positive(70.8%)and 3were positive in cerebrospinal fluid culture(6.25%).The positive rate of mNGS was higher than that of culture(70.8% vs 6.25%).The culture results of 3 cases were consistent with those of mNGS.22 positive samples were related to clinical diagnosis and treatment,7 supported suppurative meningitis and 15 supported viral encephalitis.The empirical treatment of 16 patients covered the results of mNGS,and the treatment was effective.5 patients adjusted the treatment according to the mNGS results,and the treatment was effective(100%).The mNGS results of 7 patients with viral encephalitis were all negative.3.Among the 21 bronchoalveolar lavage fluid samples,20(95.2%)were positive and 1(4.8%)negative,and 20 positive samples were involved in clinical diagnosis and treatment.The empirical treatment of 7 patients covered the results of mNGS,and the treatment was effective.13 patients adjusted the treatment plan according to the results of mNGS,and the treatment was effective(100%).4.Among the 5 sputum samples,the positive rate of mNGS was 100%.the 5positive samples were involved in clinical diagnosis and treatment.The empirical treatment of 1 patient covered the results of mNGS,and the treatment was effective.3patients were treated according to the results of mNGS,and the treatment was effective(100%).5.Among the 26 blood samples,22(84.6%)were mNGS positive and 3(11.5%)were positive in blood culture.The positive rate of mNGS was significantly higher than that of blood culture(84.6% vs 11.5%).The culture results of 3 cases were consistent with those of mNGS,21 positive samples were involved in the clinical diagnosis and treatment,The empirical treatment of 3 patients covered the results of mNGS,and the treatment was effective.17 patients adjusted the treatment according to the results of mNGS,and 14 patients were effective(82.4%).6.Using mNGS technique to observe the change of pathogen sequence to judge the disease progression and therapeutic effect.One patient with suppurative meningitis was tested by mNGS in cerebrospinal fluid before and after anti-infective treatment.The results showed that Haemophilus influenzae was positive.The reads of pathogens after treatment was significantly lower than that before treatment,accompanied by the improvement of infection index and clinical symptoms.7.Detection of free DNA in the blood of pathogens by mNGS technique for the diagnosis of pulmonary infection.The blood culture of 3 patients were all negativeand,the cell free DNA of pathogens in plasma of 3 patients was detected by mNGS technique,the results are Pneumocytosidia jevi,Mycobacterium tuberculosis and Aspergillus flavus,finally diagnosed as Pneumocystis carinii pneumonia,pulmonary tuberculosis and fungal pneumonia and all of them were treated well.8.Comparing the effect of antibiotic group and non-antibiotic group on the detection results of mNGS,the results showed that there was no significant difference between the two groups(P=0.201).Conclusion:1.mNGS has obvious advantages over traditional methods in pathogen physical detection,which is not only more sensitive and timely than culture methods,it can detect many types of pathogens at one time,especially for some pathogens that are difficult to detect by conventional methods.2.mNGS can be combined with traditional methods,patient history and related clinical examination to determine the diagnosis of infectious diseases and guide clinical treatment.3.The samples of patients in different treatment stages were detected by mNGS,and the disease progression and treatment effect were judged by observing the changes of pathogen sequence.4.The detection of plasma free DNA of pathogens by mNGS has a certain clinical application value for the clinical identification of pathogens in other infection sites.5.Traditional pathogen detection methods are greatly affected by antibiotics,while mNGS is less affected by antibiotics.