Preliminary Study On The Timing And Value Of Detection Of Pathogenic Microorganisms From Bronchoalveolar Lavage Fluids By Metagenomic Next-generation In The Diagnosis And Treatment Of Lower Respiratory Tract Infections

[Objective]Metagenomic next-generation sequencing(mNGS)can directly detect the pathogens of infectious diseases and has important reference value for the diagnosis of complex lower respiratory tract infections(LRTIs).This study explored the application value of early detection of pathogens from bronchoalveolar lavage fluids by metagenomic next-generation for lower respiratory tract infection diagnosis and treatment in patients unresponsive to initial empirical treatment.[Methods]From September 2018 to October 2019,37 LRTI patients unresponsive to initial empirical treatment were recruited from the department of respiratory and critical care medicine of the First Affiliated Hospital of Kunming Medical University,920th Hospital of Joint Logistics Support Sorce of PLA,the Third People’s Hospital of Yunnan Province and the First People’s Hospital of Kunming.The patients were carry out electronic bronchoscope.Bronchoalveolar lavage fluids(BALFs)from the lesion site of patients was sent for mNGS and routine examination(Culture and smear).Then analyzed and interpreted the results of mNGS and conventional pathogenic testing,and compared the differences between the two methods in the detection rate and time consumption of pathogenic bacteria.Based on the results of mNGS and the patient’s basic clinical data,identified the pathogenic bacteria and predicted the drug-resistant of the pathogenic bacteria,then adjusted the anti-infective treatment plan.Compared the average daily cost of antibiotics the initial empirical treatment and after adjusting the treatment regimen based on mNGS results.Combined with the patient’s treatment effect and clinical outcome,discussed the application timing and value of mNGS in LRTIs.[Results]In this study,BALFs were collected from 37 LRTI patients who failed to initial empirical treatment.MNGS test results were negative in 9 patients and positive in 28 patients,with a positive rate of 75.7%.A total of 25 pathogenic microorganisms were detected,including 2 viruses(Human Cytomegalovirus,Torque Teno virus),5 fungus(Candida albicans,Pneumocystis jiroveci,Aspergillus sp.Cryptococcus,Aspergillus fumigatus),2 atypical pathogens(Chlamydia pneumoniae,Legionella pneumophila),16 bacteria.The most detected pathogenic microorganisms were Streptococcus pneumoniae(6 cases)and Haemophilus influenzae(6 cases),followed by Klebsiella pneumoniae(5 cases),Escherichia coli(5 cases),Pseudomonas aeruginosa(3 cases).Only 8 patients obtained positive results by the culture method in 37 LRTI patients,and the positive rate was 21.6%.A total of 6 pathogenic microorganisms,1 fungus(Candida albicans)and 5 bacteria were detected.The positive rates of the two methods were compared and the difference was statistically significant(P<0.001).Of the 8 patients with positive traditional tests,all mNGS tests were positive,and of the 29 patients with negative traditional tests,20 patients(70%)had positive results with mNGS tests.Among the 28 mNGS positive samples,the microorganisms detected in 26 samples were considered to be pathogens,and the other 2 samples detected uncertain pathogens.Five samples were speculated to be drug-resistant bacterial infections by doctors basing on the results of mNGS combined with clinical features.The average time of spending on traditional detection method was 72 hours,while mNGS was only 24 hours.Among the 37 patients,26(70%)of them changed their antibiotic strategies basing on the result of mNGS combined with clinical data.The average cost of initial empirical treatment of 37 LRTIs patients was 612.33 RMB per day,and the average cost of antibiotic treatment after change the antibiotic strategies was 429.48 RMB per day.There was a statistical difference between the two therapeuticregimens(p=0.042).[Conclusions]1.The application of mNGS to lower respiratory tract infections where initial empirical anti-infective therapy is ineffective has a higher positive rate and detection efficiency than traditional detection methods,which helps to quickly identify pathogenic microorganisms,indicating that in lower respiratory tract infection cases,the initial empirical anti-infection treatment failure can also be used as an opportunity for mNGS application;2.The mNGS test results combined with clinical data can quickly correct and make up for the initial empirical anti-infective treatment plan,achieve precise and targeted anti-infection treatment,may help to speculate the resistance of the pathogen,can save the cost of anti-infective treatment,and ultimately improve clinical prognosis.