Application of alveolar lavage fluid metagenomic next-generation sequencing in patients with severe pneumonia of unknown pathogen / 中国基层医药

ABSTRACT

Objective:To evaluate the application value of metagenomic next-generation sequencing(mNGS) for patients with severe pneumonia of unknown pathogen.Methods:The clinical data of 8 patients with unknown pneumonia pathogens who were assisted by the alveolar lavage fluid mNGS technology treated in Affiliated Hospital of Yangzhou University from June 2019 to February 2020 were retrospectively analyzed, including alveolar lavage fluid smear, culture, and the sequencing result.The clinical characteristics and mNGS detection results were comprehensively analyzed.According to the results of mNGS and the judgment of the clinician, the patients were divided into confirmed pathogens group and undetermined pathogens group, and the Simpson's diversity index of two groups was compared.Results:Among 8 cases, there were 5 males and 3 females, and the median age was 62.5 years (ranged from 41 to 71 years). All of them had chronic diseases except 1 case, including diabetes, chronic obstructive pulmonary disease and kidney transplantation.mNGS was positive in 8 patients, and conventional test was positive in 3 patients.The comparison of the Simpson's diversity index between the identified pathogenic group and the undetermined pathogenic group showed statistically significant difference [(0.398 ± 0.222) vs.(0.763 ± 0.061), t=2.709, P=0.035]. The positive results of mNGS were different from that of conventional test in 2 patients.The nucleic acid number in 3 cases of Pneumocystis carinii with mNGS positive results ranged from 120 to 15 580, with genomic coverage rates from 24.6% to 99.8%. Conclusion:mNGS can help physicians acquire information of the pathogenic bacteria quickly and comprehensively, especially for patients with unknown pneumonia pathogenic bacteria.