Nanopore Sequencing Technology: A Reliable Method for Pathogen Diagnosis in Elderly Patients with Community-Acquired Pneumonia

Abstract

Xiyue Zhang,1,* Jian Ye,2,* Limin Wang,1 Liuhai Zhang,1 Liusheng Wang,1 Hualiang Jin1 1Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China; 2Department of Respiratory Medicine, Zhejiang Hospital, Hangzhou, People’s Republic of China*These authors contributed equally to this workCorrespondence: Hualiang Jin, Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Huansha Road 261, Hangzhou, 310006, People’s Republic of China, Tel [phone], Fax [phone], Email [email protected]: Next-generation sequencing of the metagenome (mNGS) is gaining traction as a valuable tool for diagnosing infectious diseases. Compared to mNGS, pathogen detection based on Oxford Nanopore Technology further shortens the detection time. This study seeks to assess the efficacy of Nanopore sequencing in identifying pathogens associated with community-acquired pneumonia (CAP) among elderly individuals in China.Patients and Methods: From January 2023 to June 2023, elderly patients with CAP were prospectively recruited from Hangzhou First People’s Hospital. A comprehensive set of clinical data was gathered, and bronchoalveolar lavage (BAL) fluid samples were collected. Concurrently, pathogen identification was performed using conventional microbiological diagnostic methods, Illumina sequencing, and Nanopore sequencing, and the diagnostic efficacy of pathogen detection was compared.Results: The study included a total of 29 patients. The diagnostic positivity rates of traditional microbiological detection, Illumina sequencing, and Nanopore sequencing were 24.1%, 51.7%, and 48.3%, respectively. Their diagnostic specificities were 91.7%, 50%, and 75%, respectively. Compared to traditional microbiological detection, both Nanopore and Illumina sequencing showed significantly increased sensitivity. However, Nanopore sequencing exhibited relatively better consistency with the final clinical comprehensive diagnosis, with a Kappa value of 0.574. This outperformed traditional microbiological detection and Illumina sequencing, which had a Kappa value of 0.296 and 0.402, respectively. In addition, Nanopore sequencing required the shortest turnaround time.Conclusion: Nanopore sequencing technology demonstrates as a reliable and rapid method for detecting pathogens in elderly patients with CAP.Keywords: Nanopore sequencing technology, metagenomic next-generation sequencing, Elderly Community-Acquired Pneumonia, pathogen diagnosis

Keywords

• nanopore sequencing technology
• metagenomic next-generation sequencing
• elderly community-acquired pneumonia
• pathogen diagnosis