Application Of Next-generation Sequencing And Routine Pathogen Detection In Community-acquired Pneumonia With Initial Treatment Failure

Objective:This study aimed to explore the application value of next-generation sequencing(NGS)in the diagnosis and treatment of community-acquired pneumonia patients with initial treatment failure.Methods:First,community-acquired pneumonia patients with initial treatment failure were enrolled,and according to whether they were performed bronchoalveolar lavage,they were divided into experimental group and control group.Then,for the experimental group,blood,bronchoalveolar lavage fluid(BALF)and other specimens of patients were collected for routine microbiological detection and sent BALF to Genetic Testing Laboratory for NGS.In the control group,we collected sputum,blood and other samples for routine microbiological detection.Besides,the patient demographics,clinical symptoms,routine microbiological test results,NGS test results,antibiotic schemes,days of hospitalization,prognosis and costs were collected for both groups.Finally,we analyzed the data of the two groups to evaluate whether NGS could improve the diagnostic rate,increase the burden of hospitalization and reduce the mortality of community-acquired pneumonia after initial treatment failure,so as to determine whether it has application values in clinical work.Results:1.Patients’ basic information:First,a total of 63 community-acquired pneumonia patients with initial treatment failure,who were admitted to the Department of Pulmonary and Critical Care Medicine of Ying Kou Central Hospital from March 2021 to October 2022,were enrolled.They were divided into experimental group(33 patients)and control group(30 patients).There was no statistical significance in gender,age,pneumonia severity index(PSI)and CURB65 score between the two groups.There was also no statistical significance in hospitalization costs,days of hospitalization and the severity of the disease between the two groups.2.Results of pathogen detection:Pathogenic microorganism was detected in all 33 patients in the experimental group by NGS,involving 27 kinds of pathogenic microorganisms,a total of 55 strains.There were 34 strains of bacteria(61.8%),7 strains of viruses(12.7%),6 strains of fungi(10.9%),2 strains of chlamydia(3.6%)and 6 strains of tuberculosis(10.9%).Meanwhile,NGS detected 13 strains with drug resistance genes,involving 14 kinds of drug resistance genes.In the experimental group,13 patients had positive results from conventional etiological tests,a total of 17 strains of 7 pathogenic microorganisms were detected by routine pathogen detection,including 11 strains of bacteria(64.7%)and 6strains of fungi(35.3%).In the experimental group,33 patients had positive NGS results(100%),while 13 patients had positive results from conventional etiological tests.A P value of 0.000 was considered statistically significant.Three samples were identified as contamination or colonization,so 30 cases(diagnostic rate 90.9%)were confirmed by NGS.Among 13 patients who positive by conventional methods,5 cases were completely consistent with NGS positive cases(diagnostic rate 15.2%),and 3 cases were partially consistent(9.1%).By comparing the two different detection methods,the diagnostic rate of NGS was better than that of traditional pathogen detections with P < 0.05.In the control group of 30 cases,9 kinds of microorganisms were detected,a total of 14 strains.There were 9 strains of bacteria(64.3%),3 strains of fungi(21.4%)and 2strains of atypical pathogens(14.3%).Among them,12 cases were positive(positive rate40.0%),9 cases were confirmed(positive rate 30.0%),and 3 cases were identified as contaminated or colonized.Compared with the control group,the diagnostic rate of the experimental group was better with statistical difference(P<0.05).3.Antibiotic adjustment status:The 30 confirmed cases in the experimental group included 29 cases whose antibiotic treatment was adjusted based on NGS results and 1 case whose antibiotic treatment was not changed because of the NGS results in line with the current treatment.Other 3 cases were treated empirically because of possible contamination or colonization.In the control group,the treatment plan was adjusted according to the results of drug sensitivity for 9 confirmed patients,while other 21 unconfirmed cases were given empirical treatment.4.Disease outcome:A total of 33 cases in experimental group,including 33 cured and improved cases.While 26 patients were cured and 4 died in Control group.The mortality rate of experimental group was lower than that of control group(P < 0.05).Conclusion:1.NGS detection is more sensitive than conventional detection methods.2.NGS test can improve diagnostic rate.3.NGS test could help reduce the mortality rate.4.NGS examination did not increase the hospitalization burden of the patients.