Rapid identification of pathogens associated with ventilator-associated pneumonia by Nanopore sequencing

Respiratory Research

Changyu Tao¹  Chao Liu²  Piyush Ranjan³  John R. Erb-Downward³  Robert P. Dickson³  Jiajia Zheng⁴  Ence Yang⁵  Nan Wu⁶  Lin Yang⁶  Bei He⁶  Beibei Liu⁶  Wei Yan⁶  Chenxia Guo⁶  Ping Yang⁶  Wenting Wang⁶  Lina Sun⁶  Meng Wang⁶  Ning Shen⁶  Jianing Wen⁶  Qiaoshan Tian⁶  Shining Bo⁷ 

[1] Department of Human Anatomy and Histology and Embryology, Peking University;Department of Infectious Diseases, Peking University Third Hospital;Department of Internal Medicine, University of Michigan Medical School;Department of Laboratory Medicine, Peking University Third Hospital;Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center;Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital;Intensive Care Unit, Peking University Third Hospital;

关键词: Ventilator-associated pneumonia;    Endotracheal aspirate;    Pathogen identification;    Nanopore sequencing;    Clinical identification method;   

DOI  :  10.1186/s12931-021-01909-3

来源: DOAJ

【 摘 要 】

Abstract Background Aetiology detection is crucial in the diagnosis and treatment of ventilator-associated pneumonia (VAP). However, the detection method needs improvement. In this study, we used Nanopore sequencing to build a quick detection protocol and compared the efficiency of different methods for detecting 7 VAP pathogens. Methods The endotracheal aspirate (ETA) of 83 patients with suspected VAP from Peking University Third Hospital (PUTH) was collected, saponins were used to deplete host genomes, and PCR- or non-PCR-amplified library construction methods were used and compared. Sequence was performed with MinION equipment and local data analysis methods were used for sequencing and data analysis. Results Saponin depletion effectively removed 11 of 12 human genomes, while most pathogenic bacterial genome results showed no significant difference except for S. pneumoniae. Moreover, the average sequence time decreased from 19.6 h to 3.62 h. The non-PCR amplification method and PCR amplification method for library build has a similar average sensitivity (85.8% vs. 86.35%), but the non-PCR amplification method has a better average specificity (100% VS 91.15%), and required less time. The whole method takes 5–6 h from ETA extraction to pathogen classification. After analysing the 7 pathogens enrolled in our study, the average sensitivity of metagenomic sequencing was approximately 2.4 times higher than that of clinical culture (89.15% vs. 37.77%), and the average specificity was 98.8%. Conclusions Using saponins to remove the human genome and a non-PCR amplification method to build libraries can be used for the identification of pathogens in the ETA of VAP patients within 6 h by MinION, which provides a new approach for the rapid identification of pathogens in clinical departments.

【 授权许可】

Unknown