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Zhao M, Zhang Y, Chen L, Yan X, Xu T, Fu M, Han Y, Zhang Y, Zhang B, Cao J, Lin J, Shen D, Li S, Zhu C, Zhao W. Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario. Front Cell Infect Microbiol 2024; 14:1330788. [PMID: 38352054 PMCID: PMC10861792 DOI: 10.3389/fcimb.2024.1330788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/09/2024] [Indexed: 02/16/2024] Open
Abstract
Introduction Infectious diseases are major causes of morbidity and mortality worldwide, necessitating the rapid identification and accurate diagnosis of pathogens. While unbiased metagenomic next-generation sequencing (mNGS) has been extensively utilized in clinical pathogen identification and scientific microbiome detection, there is limited research about the application of nanopore platform-based mNGS in the diagnostic performance of various infectious fluid samples. Methods In this study, we collected 297 suspected infectious fluids from 10 clinical centers and detected them with conventional microbiology culture and nanopore platform-based mNGS. The objective was to assess detective and diagnostic performance of nanopore-sequencing technology (NST) in real-world scenarios. Results Combined with gold-standard culture and clinical adjudication, nanopore sequencing demonstrated nearly 100% positive predictive agreements in microbial-colonized sites, such as the respiratory and urinary tracts. For samples collected from initially sterile body sites, the detected microorganisms were highly suspected pathogens, and the negative predictive agreements were relatively higher than those in the microbial-colonized sites, particularly with 100% in abscess and 95.7% in cerebrospinal fluid. Furthermore, consistent performance was also observed in the identification of antimicrobial resistance genes and drug susceptibility testing of pathogenic strains of Escherichia coli, Staphylococcus aureus, and Acinetobacter baumannii. Discussion Rapid NST is a promising clinical tool to supplement gold-standard culture, and it has the potential improve patient prognosis and facilitate clinical treatment of infectious diseases.
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Affiliation(s)
- Manna Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yongyang Zhang
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu, China
| | - Li Chen
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xuebing Yan
- Department of Infectious Disease, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Tianmin Xu
- Department of Infectious Diseases, The Third People’s Hospital of Changzhou, Changzhou, Jiangsu, China
| | - Maoying Fu
- Infectious Diseases Department, Kunshan First People’s Hospital, Kunshan, Jiangsu, China
| | - Yangguang Han
- Department of Infectious Diseases, The Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ying Zhang
- Department of Infection Medicine, The Fifth People’s Hospital of Wuxi, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Bin Zhang
- Department of Infectious Diseases, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Juan Cao
- Emergency Department, Shanghai Shibei Hospital, Shanghai, China
| | - Jing Lin
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Dan Shen
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Shuo Li
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
- Medical Department, Nanjing Dian Diagnostics Group Co., Ltd., Nanjing, Jiangsu, China
| | - Chuanlong Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weifeng Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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