| Background: Due to the continuous emergence of a variety of new and re-emerging infectious diseases,the current situation of infectious diseases worldwide is serious,with diversified and complicated pathogens,posing a serious threat to public health.However,the conventional pathogenic detection methods currently used in clinical practice generally have obvious shortcomings such as poor timeliness,low sensitivity and incomplete coverage.Previous studies have reported that the emerging detection technology m NGS has significant characteristics of high efficiency and accuracy,and is expected to become an important means for the diagnosis of infectious diseases,which is a hot topic in recent years.Objective: To explore the application value of metagenomic sequencing（m NGS）in the identification of pathogenic microorganisms of infectious diseases（respiratory system infection,bloodstream infection and central nervous system infection）in emergency and ICU.Methods: A total of 112 patients with confirmed or suspected infectious diseases admitted to the emergency ward and ICU of Peking University Shenzhen Hospital from December 2019 to September 2021 were selected as consecutive subjects for a single-center retrospective cohort study.The subjects were divided into three groups according to the types of specimens collected: alveolar lavage fluid group（63/120）,cerebrospinal fluid group（15/120）and plasma group（42/120）.Meanwhile,m NGS test results of each group and routine culture（conventional alveolar lavage fluid culture,sputum culture,cerebrospinal fluid culture and blood culture）test results of corresponding patients were collected.The pathogen detection situation,pathogen detection type,detection time and detection cost of the specimens of the three groups were compared,and the application value of m NGS in the diagnosis and treatment of special infections was analyzed and evaluated.In addition,m NGS and conventional culture were compared and evaluated in patients diagnosed with sepsis or septic shock.Results: 1.In this study,the positive rate,sensitivity and specificity of m NGS pathogen detected in physical examination were compared with that in conventional culture:（1）In alveolar lavage fluid group,the positive rate of m NGS in alveolar lavage fluid group was 92.06%（58/63）,which was higher than that in alveolar lavage fluid culture group(31.75%（20/63）and sputum culture group（79.37%）,P < 0.05,the difference was statistically significant;m NGS sensitivity 82.76%（48/58）was higher than that of alveolar lavage fluid culture 34.48%（20/58）,P < 0.001,and the difference was statistically significant.m NGS specificity were compared with that of alveolar lavage fluid culture,m NGS sensitivity and specificity were compared with that of sputum culture,both P> 0.05,and the differences were not statistically significant.（2）In plasma group,the positive rate of m NGS was 64.29%（27/42）higher than that of BC 26.19%（11/42）,with P < 0.001,and the difference was statistically significant.m NGS sensitivity was 71.05%（27/38）higher than BC sensitivity 26.32%（10/38）,P < 0.001,and the difference was statistically significant.m NGS specificity and BC specificity,P=1.00,the difference was not statistically significant.（3）Cerebrospinal fluid group: m NGS pathogenic examination the positive m NGS compared with CSF cultures positive rate were 60.00%（9/15）was higher than CSF culture positive rate 13.33%（2/15）,P = 0.04,the difference is statistically significant;Compared with the sensitivity and specificity of CSF culture,both P> 0.05,and the differences were not statistically significant.2.In this study,the detection rate of m NGS virus in alveolar irrigation fluid group was 43.10%（25/58）,the detection rate of m NGS virus in plasma group was 74.07%（20/27）,and the detection rate of m NGS virus in cerebrospinal fluid was 44.45%（4/9）,while no virus was detected in conventional culture method.The detection rate of m NGS mixed infection 51.72%（30/58）was higher than that of alveolar lavage fluid culture mixed infection 15.00%（3/20）and sputum culture mixed infection（18.00%）（9/50）,both P < 0.05,the difference was statistically significant.3.In this study,the average detection period of m NGS（1.93±0.26）days was shorter than the average detection period of alveolar lavage fluid culture,sputum culture and blood culture,P values were all < 0.05,with statistically significant differences.Compared with the average m NGS detection period and CSF culture period,t=-0.35,P=0.73,the difference was not statistically significant.4.Compared with conventional culture method,the cost of m NGS test in this study is 2800 yuan/person,and the cost of conventional culture method is about 100~280yuan/item,so the cost of m NGS test is obviously higher than that of conventional detection method.5.In this study,m NGS was used to detect 16 cases of special pathogen infection（1/16 of SARS-Co V-2 cases,1/16 of rabies virus cases,1/16 of leptospirosis question mark cases,1/16 of Coxella benetticosis cases,3/16 of Mycobacterium,3/16 of Listeria monocytogenes cases,5/16 of Pneumocystis jiroi cases,and 1/16 of human gland cases）.The positive rate of m NGS detection was 100.00%（16/16）higher than that of conventional culture,which was 25.00%（4/16）.Fisher’s accurate probability test showed P < 0.001,and the difference was statistically significant.6.Among the 63 m NGS results in the alveolar perfusion fluid group,4/63 samples were found to have pathogen resistance genes,and all the 4 patients had the clinical characteristics of severe systemic infection,rapid progress or long course of antibiotics.The detection results combined with the laboratory drug sensitivity test can play a certain guiding role for clinicians to formulate and adjust anti-infection programs.7.A total of 38 patients were diagnosed with sepsis or septic shock in this study,among which the positive rate of m NGS was 89.47%（34/38）higher than that of conventional culture 71.05%（27/38）,χ2=4.07,P=0.04,and the difference was statistically significant.The positive rate of m NGS combined with conventional culture was 94.74%（36/38）higher than that of conventional culture 71.05%（27/38）,χ2=7.52,P=0.01,and the difference was statistically significant.Conclusion:1.Compared with conventional culture methods,m NGS technology has the advantages of higher positive rate,wider coverage,stronger sensitivity,higher detection rate of mixed infection and shorter detection period,especially in the detection of alveolar lavage fluid in patients with severe respiratory tract infection.However,the cost of m NGS detection is more expensive than conventional culture methods.2.Detection of emergency department and ICU indicatio of severe infection,compared to conduct regular training method,suitable types of samples carried out joint m NGS testing as soon as possible,timeliness,clinical diagnosis of consistency in pathogen detection,and set or adjust the treatment plan for clinicians to provide guidance and basis,thereby improving the prognosis of patients with clinical aspects and so on has certain advantage;Especially in the identification of viruses,mycobacterium tuberculosis,leptospirosis and other rare bacteria,caustic bacteria,as well as suspected infectious risk of special types of pathogen infection is more obvious advantages.3.m NGS technology has a certain potential in the detection of antibiotic resistance genes of pathogens.When the anti-infection treatment effect of patients with complex infections or multiple drug resistance is not good,m NGS can be used to detect and dynamically monitor the drug resistance genes of pathogens,so as to guide clinicians to adjust the appropriate treatment plan. |
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