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.
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).
