The Value Of Next-generation Sequencing In Clinical Diagnosis And Treatment Of Severe Pneumonia

Objective:The purpose of this study was to explore the clinical value of next-generation sequencing(NGS)in the diagnosis and treatment of severe pneumonia.Methods:This is a retrospective study enrolling 148 severe pneumonia patients whose samples were collected between January 2017 and December 2019 in the department of Respiratory And Critical Care Medicine of Hunan Provincial People’s Hospital.A total of 33 patients was assigned to routine microbiological detection group(control group)using routine microbiologic tests to exam sputum,blood,or BALF fluid samples.In the NGS group,115 patients were collected,and samples of sputum,blood,and bronchoalveolar lavage fluid(BALF)were collected for routine microbiological detection.At the same time,patients in the NGS group also collected blood or BALF and sent them to the genetic company for NGS testing.Data,including basic information,clinical symptoms,routine microbiological test results,next-generation sequencing test results,Acute Physiology and Chronic Health Evaluation II(APACHE II score),CURB 65 score,length of stay in hospital,time of mechanical ventilation,antibiotic treatment plan,and outcome of the diseasewere,was collected.Results:1.The basic information: For patient demographics and baseline characteristics,there were no significant differences in sex,age,APACHE II scores,CURB 65 score.The mean mechanical ventilation time in the NGS group was(6.04±10.33)days shorter than that in the control group(10.94±11.20)days,and the difference was statistically significant(p=0.02).The average length of hospital stay in the NGS group was(14.52±9.06)days,which was shorter than that in the control group(19.38±11.82)days.The difference was statistically significant(p=0.03).2.Analysis of pathogen positive test: among 148 cases of severe pneumonia,126 cases were positive for pathogen,with a positive rate of85.13%.The most common type of infection among patients with severe pneumonia was mixed infection in 72 cases(57.14%),followed by simple bacterial infection in 31 cases(24.60%).Among the mixed infection types,bacterial and fungal mixed infection was the most common in 39 cases(30.95%),followed by bacterial and viral mixed infection in 13 cases(10.32%).3.Pathogen composition of the two groups: among the 126 patients with positive pathogen detection,a total of 396 pathogens were detected,including 239 bacterial strains(60.35%),78 fungal strains(19.70%),68 viral strains(17.17%),4 mycoplasma strains(1.01%),5 chlamydia strains(1.26%)and 2 leptospira strains(0.51%).Compared with routinemicrobiological detection methods,the positive rate of NGS in detection of bacteria(p=0.003),klebsiella pneumoniae(p=0.020)and haemophilus influenzae(p=0.029)was higher,with statistically significant differences.Especially in the detection of enterococcus faecalis(p=0.009),fungi(p=0.003)and pneumocystis(p=0.005),the positive rate of NGS was high,and the difference was statistically significant.4.There were 115 patients in the NGS group,all of whom underwent NGS detection and routine microbiological detection.NGS test results of 59 patients were the same as routine microbiological detection results,and the coincidence rate of the two test methods was calculated to be 51.3%.The positive rate of NGS detection was 90.4%,while the positive rate of routine microbiological detection was 47.8%.The positive rate of NGS detection was significantly higher than that of routine microbiological detection.The sensitivity of NGS detection was94.55%(104/110),and the specificity was 100%(5/5).The sensitivity of routine microbiological detection is 54.55%(60/110),and the specificity of routine microbiological detection is 100%(5/5).The sensitivity of ext-generation sequencing detection was higher than that of conventional microbial detection,and the difference was statistically significant(p<0.01).5.Adjustment of antibiotics: 104 patients(70.27%)adjusted their antibiotic regimen according to the results of next-generation sequencingdetection,and 22 patients(14.86%)adjusted their antibiotic regimen according to the results of routine microbiological detection,22 patients(14.86%)did not detect pathogens.6.There were 104 patients adjusted their antibiotic regimen according to the results of next-generation sequencing detection in the NGS group,of which 84 improved and 20 died.The fatality rate of patients in the NGS group was 19.23%.A total of 22 patients in the control group adjusted the antibiotic regimen based on the results of routine microbiological detection,of which 12 improved and 10 died.The case fatality rate of the control group was 45.45%.There was a statistically significant difference in the case fatality between the two groups(p=0.001),and the case fatality in the NGS group was significantly lower than that in the control group.Conclusion:1.Next-generation sequencing can increase the positive rate of pathogen detection.3.The sensitivity of next-generation sequencing are higher than that of routine microbiological detection.4.Adjusting the antibiotic regimen based on the next-generation sequencing detection results can shorten the length of hospital stay and mechanical ventilation,and reduce the case fatality rate.