| ObjectiveTo analyze the value of Metagenomic Next-generation Sequencing(mNGS)in clinical diagnosis of infectious diseases.MethodWe collected clinical data of 126 patients who were hospitalized in neurology department,intensive care unit(ICU),pediatrics and infectious diseases department in Shandong University Qilu Hospital and underwent mNGS examination from April 2018 to February 2021.mNGS samples were collected from cerebrospinal fluid(CSF),blood or alveolar lavage fluid(BALF).A total of 25 cases which confirmed as non-infectious diseases and unknown cases were excluded.By retrospectively analyzing the general clinical data,conventional microbiologic tests results and mNGS test results of 101 patients with infectious diseases,the application value of mNGS in the clinical diagnosis of infectious diseases was analyzed.Results1.A total of 36 pathogens were detected in 101 cases of mNGS,including Pneumocystis jirovecii pneumonia,Epstein-Barr virus,Mycoplasma pneumoniae,Human herpesvirus 1 and 2,Mycobacterium tuberculosis,Acinetobacter baumannii,Aspergillus fumigatus,Cytomegalovirus,Streptococcus pneumoniae,Herpesvirus Suis 1 and so on.23 kinds of pathogens were not found in the conventional microbiologic test.The top-two pathogens detected by mNGS in this study were Pneumocystis jirovecii pneumonia type 9(15.5%),Epstein-Barr virus(12%).Burkholderia cepacia infection was detected in 1 child with severe pneumonia.Herpesvirus Suis 1 infections were detected in 3 adult patients with the work experience of animal farms and human parvovirus B19 infections were detected in 2 female patients.Taenia solium infection was detected in a patient with a long history of obstructive hydrocephalus.2.Among the 101 patients with infectious diseases,58 cases were positive for pathogens detected by mNGS,35 cases were positive for pathogens detected by conventional microbiologic test,68 cases were positive for pathogens detected by mNGS or conventional microbiologic test,and 25 cases were positive for both mNGS and conventional microbiologic test.The positive rate of mNGS detection was significantly higher than that of conventional microbiologic test(57.4%vs.34.6%,P<0.01).The positive rate of pathogen detection by the combination of the two methods was also significantly better than that by the conventional microbiologic test alone(67.3%vs.34.6%,P<0.01).3.Among 101 cases of different samples tested by mNGS,the highest positive rate of pathogens was detected in BALF,which was higher than that in CSF and blood(100%vs.48%,P<0.01;100%vs.66.7%,P<0.01).4.Grouping was carried out according to the clinical characteristics of the infected patients and the corresponding pathogen detection.Among the 101 infected patients,65 cases were identified pathogen group and 36 cases were not identified pathogen group.The sensitivity of mNGS was higher than that of conventional microbiologic test(84.61%vs.53.85%,P<0.01).It has no significant difference in specificity between the two groups(91.67%vs.100.00%,P>0.05).The positive predictive value(PPV)and negative predictive value(NPV)of mNGS were 94.83%(95%CI,84.70-98.65%)and 76.74%(95%CI,61.00-87.72%),respectively.The PPV and NPV of conventional microbiologic test were 100.00%(95%CI,87.68-100.00%),54.55%(95%CI,33.32-58.1 1%).5.Of the 101 infectious cases,89 were treated with antibiotics or antivirals prior to the mNGS test,and 12 were not.The positive rate of mNGS detection was better than that of conventional microbiologic test in the group receiving antibiotics or antivirals(58.43%vs.35.96%,P<0.05),and the positive rate of mNGS detection was similar in the group using or not using antibiotics or antivirals(58.43%vs.50%,P>0.05).6.Among the 101 samples of mNGS,antibiotic resistance genes were detected in 5 cases,and 8 kinds of antibiotic resistance genes were detected,including OXA,Ade,mel,Tet,ErmC,mecA,TEM,and InuA.In one case,the carbapenem-resistant Acinetobacter baumannii was cultured in the same period by traditional culture method,and the results of followed antimicrobial susceptibility test were consistent with mNGS.The two methods jointly assisted clinicians to adjust antibiotics.7.Among 101 cases of different ages,the positive rate of mNGA in patients from 41 to 60 years old is the the highest(80%).There was no significant difference in the positive rate of mNGS between patients from 41 to 60 years old and Patients younger than 18 years old.(80%vs.34.4%,P>0.05).The top pathogen detected by mNGS in children was Mycoplasma pneumonia(27.3%).ConclusionCompared with conventional microbiologic test,mNGS is more sensitive in the etiological diagnosis of infectious diseases,especially has more advantages in a rare infection pathogens,and is not affected by antimicrobial drugs or antiviral drugs.mNGS can provide diagnostic clues for patients with unknown etiology or suspected infection and evaluate antibiotic resistance genes,which can be used as a detection method for clinical etiology diagnosis of infectious diseases at present. |
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