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Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections

文献类型：期刊论文

作者Deng, Qingmei3,4,5; Cao, Yongqing2; Wan, Xiaofeng3,4; Wang, Bin1; Sun, Aimin3,4; Wang, Huanzhong3,4; Wang, Yunfei1; Wang, Hongzhi3,4,5; Gu, Hongcang3,4,5
刊名FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
出版日期2022-09-20
卷号12
关键词cancer pathogen detection infections metagenomic sequencing nanopore amplicon sequencing
ISSN号2235-2988
DOI10.3389/fcimb.2022.943859
通讯作者Wang, Hongzhi(wanghz@hfcas.ac.cn) ; Gu, Hongcang(gu_hongcang@cmpt.ac.cn)
英文摘要Cancer patients are at high risk of infections and infection-related mortality; thereby, prompt diagnosis and precise anti-infectives treatment are critical. This study aimed to evaluate the performance of nanopore amplicon sequencing in identifying microbial agents among immunocompromised cancer patients with suspected infections. This prospective study enlisted 56 immunocompromised cancer patients with suspected infections. Their body fluid samples such as sputum and blood were collected, and potential microbial agents were detected in parallel by nanopore amplicon sequencing and the conventional culture method. Among the 56 body fluid samples, 47 (83.9%) samples were identified to have at least one pathogen by nanopore amplicon sequencing, but only 25 (44.6%) samples exhibited a positive finding by culture. Among 31 culture-negative samples, nanopore amplicon sequencing successfully detected pathogens in 22 samples (71.0%). Nanopore amplicon sequencing showed a higher sensitivity in pathogen detection than that of the conventional culture method (83.9% vs. 44.6%, P<0.001), and this advantage both existed in blood samples (38.5% vs. 0%, P=0.039) and non-blood samples (97.7% vs. 58.1%, P<0.001). Compared with the culture method, nanopore amplicon sequencing illustrated more samples with bacterial infections (P<0.001), infections from fastidious pathogens (P=0.006), and co-infections (P<0.001). The mean turnaround time for nanopore amplicon sequencing was about 17.5 hours, which was shorter than that of the conventional culture assay. This study suggested nanopore amplicon sequencing as a rapid and precise method for detecting pathogens among immunocompromised cancer patients with suspected infections. The novel and high-sensitive method will improve the outcomes of immunocompromised cancer patients by facilitating the prompt diagnosis of infections and precise anti-infectives treatment.
WOS关键词MICROBIAL SPECTRUM ; CHEMOTHERAPY ; TUBERCULOSIS ; DIAGNOSIS ; RESISTANT ; MINION ; RISK
资助项目Research and Development Funding for Medical and Health Institutions[2021YL007] ; Medical Health Science and Technology Project of Zhejiang Provincial Health Commission[2017188812]
WOS研究方向Immunology ; Microbiology
语种英语
WOS记录号WOS:000872779700001
出版者FRONTIERS MEDIA SA
资助机构Research and Development Funding for Medical and Health Institutions ; Medical Health Science and Technology Project of Zhejiang Provincial Health Commission
源URL[http://ir.hfcas.ac.cn:8080/handle/334002/129887]  
专题中国科学院合肥物质科学研究院
通讯作者Wang, Hongzhi; Gu, Hongcang
作者单位1.Zhejiang ShengTing Biotechnol Co, Hangzhou, Peoples R China
2.Univ Chinese Acad Sci, Chinese Acad Sci, Inst Basic Med & Canc, Canc Hosp, Hangzhou, Peoples R China
3.Chinese Acad Sci, Hefei Canc Hosp, Hefei, Peoples R China
4.Chinese Acad Sci, Inst Hlth & Med Technol, Hefei Inst Phys Sci, Anhui Prov Key Lab Med Phys & Technol, Hefei, Peoples R China
5.Univ Sci & Technol China, Sci Isl Branch, Grad Sch, Hefei, Peoples R China
推荐引用方式
GB/T 7714		 Deng, Qingmei,Cao, Yongqing,Wan, Xiaofeng,et al. Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections[J]. FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY,2022,12.
APA Deng, Qingmei.,Cao, Yongqing.,Wan, Xiaofeng.,Wang, Bin.,Sun, Aimin.,...&Gu, Hongcang.(2022).Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections.FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY,12.
MLA Deng, Qingmei,et al."Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections".FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY 12(2022).

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来源：合肥物质科学研究院

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