| Background: Lower respiratory tract infection remains a disease with high morbidity and mortality nowadays,for the lack of diagnostic effectiveness of conventional etiological detection methods,which become increasingly prominent.The technique of metagenomics next-generation sequencing(mNGS)is progressing considerably,which are now become a promising candidate method of etiological diagnosis of lower respiratory tract infections and attracts more and more research efforts globally.Objective: To explore the application value of metagenomics next-generation sequencing(mNGS)in the etiological diagnosis of lower respiratory tract infection,and to investigate whether mNGS has any advantages over conventional methods in etiologies detection.Methods: We retrospectively analyzed the clinical data,together with medical history,signs,chest imaging and laboratory examinations,of 52 patients who were clinically diagnosed as lower respiratory infection in the First Affiliated Hospital of Bengbu Medical College with a duration of November 2018-January 2020.Bronchoalveolar lavage fluid(BALF)of 52 patients were collected.mNGS,conventional culture,smear or PCR detection were used to detect the microbe of all the samples.According to the pathogen detection and clinical analysis,all patients were divided into the confirmed pathogen group and the non-confirmed pathogen group.The detective sensitivity,specificity,positive predictive value(PPV)and negative predictive value(NPV)of mNGS and conventional culture in the microbial etiology diagnosis of lower respiratory tract infection were compared.McNemar test was implied for all the data with threshold of p<0.05 as statistical differences,and p<0.01 as the differences of significance.Results: 1.Totally,20 kinds of pathogens were detected in all 52 specimens with the DNA sequencing(DNAseq)of mNGS,including the Leptospira interrogans,Nocadia farcinica,Mycobacterium tuberculosis,Aspergillus fumigatus,Cryptococcus neoformans,Human herpesvirus 1,Human herpesvirus 4,Mycoplasma pneumoniae,Chlamydia psittaci and so on.Among which 12 pathogens were not found in the conventional culture.2.Among all 52 samples,43 were DNAseq positive,29 were conventional culture positive,45 were DNAseq or conventional culture positive,27 were DNAseq and conventional culture positive.The positive rate of DNAseq detection of pathogen was much higher than that of conventional culture(86.54% vs.53.85%,p<0.01).The positive rate of pathogens detected by the two methods in combination was also much higher than that detected by conventional culture alone(90.38% vs.53.85%,p<0.01).3.Of the 52 patients with lower respiratory tract infection,45 had a history of antimicrobials use and 7 had no history of antimicrobials use.Positive rate of mNGS DNAseq was better than that of the conventional culture in the antimicrobials use group and not use group(82.22% vs.53.33%,p<0.05).No difference in positive rate of DNAseq alone was demonstrated when compared with that of combined detection(82.22% vs.85.71%,p>0.05).4.Among the 52 patients,BALF samples of 32 patients had undertaken both PCR and DNAseq,among which 26 were DNAseq positive and 14 were PCR positive.DNAseq positive rate was significantly higher than PCR(81.25 vs.43.75,p<0.01).5.In 29 samples of lower respiratory tract infection,both DNAseq and RNAseq were performed,among which 25 cases were DNAseq positive and 7 cases were RNAseq positive.RNAseq positive pathogens include: Human parainfluenza virus1,Human coronavirus 229 E,influenza a virus(H1N1 H3N2),Human pneumonitis virus,etc,which are now lack of laboratorial detective methods.6.43 cases of the 52 patients were finally confirmed as definitive pathogen positive and 9 cases as indefinitive pathogen positive by microbials detection and clinical analysis.The sensitivity of DNAseq was higher than that of conventional culture(95.35% vs.67.44%,p<0.01).There was no statistical difference in specificity between DNAseq and conventional culture(77.78% vs.100.00%,p>0.05).The PPV and NPV of DNAseq were respectively 95.35%(95% CI,82.94-99.19%)and 77.78%(95% CI,40.19-96.05%)respectively.And the PPV and NPV of conventional culture was 100.00%(95% CI,85.44-100%)and 39.13%(95% CI,20.47-61.22%)respectively.Conclusion: When compared with conventional culture and PCR,DNAseq of mNGS is more sensitive in the etiological diagnosis of lower respiratory tract infection,which is especially true for rare pathogens.DNAseq of mNGS is less affected by previous antimicrobials use.RNAseq has obvious advantages in diagnosing infections by RNA viruses,which are hard to be routinely detected in clinical practice,which enriches the diagnostic methods for virus infections. |
