| Objective:Central nervous system(CNS)infection is a kind of disease that seriously endangers human life.More than half of the patients with central nervous system infection in clinical practice cannot know the etiology of infection,and the delay and insufficiency of treatment lead to increased mortality.Metagenomic Next-Generation Sequencing(m NGS)can detect pathogens in a short time,shorten the course of disease and reduce the medical burden.Comparison of metagenomic next-generation sequencing technology and traditional detection methods in clinical detection results and guidance for clinical diagnosis and treatment;This study provides more evidence for the clinical application of metagenomic next-generation sequencing technology.Methods:Data of 102 patients with suspected central nervous system infection in the Department of Neurology of the First People’s Hospital of Yunnan Province from January 2018 to August 2020 were collected: General information(gender,age),the related clinical signs and symptoms(headache,fever,vomiting,neck stiffness,nervous system defect/irritation symptom),laboratory data(blood routine,procalcitonin,C-reactive protein,γ-interferon release test,fungus(1-3)-β-D-glucan quantitative G test,CSF routine,CSF biochemical,CSF immunological,CSF culture,CSF TB-DNA test,CSF parasite antibody test,CSF Cryptococcus test,CSF anti-TORCH antibody test,CSF JE antibody test,),the NGS results,imaging data,changes in clinical diagnosis and disease outcomes.Taking the final clinical diagnosis as the gold standard,68 cases with incomplete data,final diagnosis of other diseases,and final diagnosis of unknown were excluded.IBM SPSS 25.0 software was used for statistical analysis.The measurement data were tested for normality,and the variables subject to normal distribution were expressed as mean ± standard deviation.Enumeration data were represented by "number of cases" and "rate".Pair test or Fisher’s exact probability method was used for comparison between groups,P ≤0.05 was considered statistically significant,while P ≤0.01 was considered extremely significant.Results:(1)Among the 68 patients enrolled,there were 38 males(55.88%)and 30 females(44.12%),with an age of 42.71 ? 15.86 years old,42.92 ? 15.48 years old for males and42.43 ? 16.60 years old for females.(2)Among the 68 patients with CNS infection enrolled,58 patients were simple infection and 10 patients were mixed infection,for a total of 78 infection samples,including 25 patients with viral infection,23 patients with tuberculous infection,20 patients with bacterial infection,5 patients with fungal infection,3 patients with parasitic infection and2 patients with rickettsial infection.(3)In 78 cases of infection samples,the positive rate of pathogens detected by m NGS was 52.6%,while the positive rate of pathogens detected by traditional detection method was 26.9%.The positive rate of pathogens detected by m NGS was higher than that by traditional detection method,and the difference between the two detection methods was statistically significant(P <0.01).Consistency analysis of the two detection methods showed that the two methods were consistent in diagnosis(Kappa value =0.20),and the results were statistically significant(P <0.05).(4)In viral CNS infectious diseases,the sensitivity,specificity,positive predictive value and negative predictive value of m NGS detection were 40.0%,93.0%,76.9% and 72.7%,which were consistent with clinical diagnosis(Kappa value =0.367),and the results were statistically significant(P <0.01).The sensitivity,specificity,positive predictive value and negative predictive value of the traditional detection method were 12.0%,100.0% and66.2%,which were consistent with the clinical diagnosis(Kappa value =0.147)and the results were statistically significant(P <0.05).In tuberculous CNS infectious diseases,the sensitivity,specificity,positive predictive value and negative predictive value of m NGS detection of pathogens were 65.2%,97.8%,93.8% and 84.6%,which were consistent with clinical diagnosis(Kappa value =0.681),and the results were statistically significant(P <0.01).The sensitivity,specificity,positive predictive value and negative predictive value were 39.1%,100.0% and 76.3%,respectively,which were consistent with the clinical diagnosis(Kappa value =0.460),and the results were statistically significant(P <0.01).In bacterial CNS infectious diseases,the sensitivity,specificity,positive predictive value and negative predictive value of m NGS were 35.0%,89.6%,58.3% and 76.8%,which were consistent with clinical diagnosis(Kappa value =0.278),and the results were statistically significant(P <0.05).The sensitivity,specificity,positive predictive value and negative predictive value were 35.0%,100.0% and 78.7%,respectively,which were consistent with the clinical diagnosis(Kappa value =0.432),and the results were statistically significant(P <0.01).In fungal CNS infectious diseases,the sensitivity,specificity,positive predictive value and negative predictive value of m NGS detection of pathogens were 100.0%,96.8%,71.4%and 100.0%,which were consistent with clinical diagnosis(Kappa value =0.818),the results were statistically significant(P <0.01).The sensitivity,specificity,positive predictive value and negative predictive value of the traditional detection method were40.0%,100.0% and 95.5%,which were consistent with the clinical diagnosis(Kappa value =0.553),and the results were statistically significant(P <0.01).(5)In the 25 patients with viral CNS infection,the positive rate of pathogens detected by m NGS was 40.0%,while the positive rate of pathogens detected by traditional detection method was 12.0%.The detection rate of pathogens detected by m NGS was higher than that by traditional detection method,and the difference was statistically significant(P=0.05).(6)Among the 23 patients with tuberculous CNS infection,the positive rate of pathogens detected by m NGS was 65.2%,while the positive rate of pathogens detected by traditional detection method was 39.1%.The detection rate of pathogens detected by m NGS was higher than that by traditional detection method,and the difference in detection was not statistically significant(P =0.14).(7)In 20 patients with bacterial CNS infection,the positive rate of pathogens detected by MNGS was 35.0%,while that by traditional detection method was 35.0%.The positive rate of pathogens detected by m NGS was the same as that by traditional detection method,and there was no difference between the two detection methods(P =1).(8)In 5 cases of fungal CNS infection,the positive rate of pathogens detected by m NGS method was 100.0%,and the positive rate of pathogens detected by traditional detection method was 40.0%.In the 3 cases of parasitic CNS infection,the positive rate of pathogens detected by m NGS method was 66.7%,while the positive rate of pathogens detected by traditional method was 0.0%.In 2 cases of Rickettsial CNS infection,the positive rate of pathogens detected by m NGS method was 100.0%,while the positive rate of pathogens detected by traditional method was 0.0%.In the above three CNS infected patients,the positive rate of pathogens detected by m NGS detection method was higher than that by traditional detection method.Due to the small sample size,it is still not possible to compare whether the positive rate difference between m NGS and traditional detection method in fungal infections is statistically significant.Conclusion:(1)In this study,among the 68 patients diagnosed with CNS infection,the positive rate of pathogens detected by m NGS was higher than that detected by traditional detection methods.(2)In this study,in the physical examination of pathogens of CNS infection,m NGS detection method has higher sensitivity and lower specificity than traditional detection method,and its positive predictive value is lower than traditional detection method,while its negative predictive value is higher.Namely,m NGS can detect pathogens more sensitively and better exclude other infections in the pathogen physical examination.However,in the background of high throughput and high sensitivity,m NGS may detect pathogens in the contaminated background,leading to its reduced specificity and lower positive prediction than traditional detection methods.(3)In this study,in the statistical analysis of viral central nervous system infectious diseases,the conclusion that the m NGS detection method has a higher detection rate of pathogens than the traditional detection method is of statistical significance.(4)In this study,in the statistical analysis of tuberculous and bacterial central nervous system infectious diseases,the conclusion that m NGS detection method has a higher detection rate of pathogens than traditional detection method cannot be considered statistically significant.(5)In this study,the fungi and parasites,rickettsia clinical rare,rare,the diagnosis of complex pathogen infection,m NGS detection positive rate is high,than the traditional methods for clinical diagnosis and treatment of adjustment has the realistic meaning,but still need to further increase the sample size to compare two methods of statistical differences are statistically significant. |
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