EBioMedicine (Dec 2021)
Multicenter assessment of shotgun metagenomics for pathogen detection
- Donglai Liu,
- Haiwei Zhou,
- Teng Xu,
- Qiwen Yang,
- Xi Mo,
- Dawei Shi,
- Jingwen Ai,
- Jingjia Zhang,
- Yue Tao,
- Donghua Wen,
- Yigang Tong,
- Lili Ren,
- Wen Zhang,
- Shumei Xie,
- Weijun Chen,
- Wanli Xing,
- Jinyin Zhao,
- Yilan Wu,
- Xianfa Meng,
- Chuan Ouyang,
- Zhi Jiang,
- Zhikun Liang,
- Haiqin Tan,
- Yuan Fang,
- Nan Qin,
- Yuanlin Guan,
- Wei Gai,
- Sihong Xu,
- Wenjuan Wu,
- Wenhong Zhang,
- Chuntao Zhang,
- Youchun Wang
Affiliations
- Donglai Liu
- National Institutes for Food and Drug Control, Beijing 100050, China
- Haiwei Zhou
- National Institutes for Food and Drug Control, Beijing 100050, China
- Teng Xu
- Key Laboratory of Animal Gene Editing and Animal Cloning in Yunnan Province and College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
- Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Xi Mo
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Dawei Shi
- National Institutes for Food and Drug Control, Beijing 100050, China
- Jingwen Ai
- Department of Infectious Diseases, Huashan Hospital affiliated to Fudan University, Shanghai 200040, China
- Jingjia Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, China
- Yue Tao
- The Laboratory of Pediatric Infectious Diseases, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
- Donghua Wen
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, PR China
- Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), College of Life Science and Technology, Beijing University of Chemical Technology. Beijing 100029
- Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, PR China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China
- Wen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing 102206, China
- Shumei Xie
- Vision Medicals Center for Infectious Diseases, Guangzhou, Guangdong 510000, China
- Weijun Chen
- BGI PathoGenesis Pharmaceutical Technology, BGI-Shenzhen, Shenzhen 518083, China
- Wanli Xing
- School of Medicine Tsinghua University, Beijing, China; CapitalBio Technology Co., Ltd., Yizhuang Biomedical Park Beijing, China
- Jinyin Zhao
- Dalian GenTalker Clinical Laboratory, Dalian 116635, China
- Yilan Wu
- Guangzhou Sagene Biotech Co., Ltd., Guangzhou, China
- Xianfa Meng
- Guangzhou Kingmed Diagnostics, Guangzhou, Guangdong 510330, China
- Chuan Ouyang
- Hangzhou MatriDx Biotechnology Co., Ltd, Hangzhou, China
- Zhi Jiang
- Genskey Medical Technology, Co., Ltd., Beijing 102206, China
- Zhikun Liang
- Guangzhou Darui Biotechnology, Co., Ltd., Guangzhou 510663, China
- Haiqin Tan
- Hangzhou IngeniGen XunMinKang Biotechnology Co., Ltd., Hangzhou 311121, China
- Yuan Fang
- Dinfectome Inc, Shanghai 201321, China
- Nan Qin
- Realbio Genomics Institute, Shanghai 201114, China
- Yuanlin Guan
- Hugobiotech Co., Ltd., Beijing 100000, China
- Wei Gai
- WillingMed Technology Beijing Co., Ltd., Beijing, China
- Sihong Xu
- National Institutes for Food and Drug Control, Beijing 100050, China; Corresponding authors.
- Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200123, PR China; Corresponding authors.
- Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital affiliated to Fudan University, Shanghai 200040, China; Corresponding authors.
- Chuntao Zhang
- National Institutes for Food and Drug Control, Beijing 100050, China; Corresponding authors.
- Youchun Wang
- National Institutes for Food and Drug Control, Beijing 100050, China; Corresponding authors.
- Journal volume & issue
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Vol. 74
p. 103649
Abstract
Background: Shotgun metagenomics has been used clinically for diagnosing infectious diseases. However, most technical assessments have been limited to individual sets of reference standards, experimental workflows, and laboratories. Methods: A reference panel and performance metrics were designed and used to examine the performance of shotgun metagenomics at 17 laboratories in a coordinated collaborative study. We comprehensively assessed the reliability, key performance determinants, reproducibility, and quantitative potential. Findings: Assay performance varied significantly across sites and microbial classes, with a read depth of 20 millions as a generally cost-efficient assay setting. Results of mapped reads by shotgun metagenomics could indicate relative and intra-site (but not absolute or inter-site) microbial abundance. Interpretation: Assay performance was significantly impacted by the microbial type, the host context, and read depth, which emphasizes the importance of these factors when designing reference reagents and benchmarking studies. Across sites, workflows and platforms, false positive reporting and considerable site/library effects were common challenges to the assay's accuracy and quantifiability. Our study also suggested that laboratory-developed shotgun metagenomics tests for pathogen detection should aim to detect microbes at 500 CFU/mL (or copies/mL) in a clinically relevant host context (10^5 human cells/mL) within a 24h turn-around time, and with an efficient read depth of 20M. Funding: This work was supported by National Science and Technology Major Project of China (2018ZX10102001).