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Since January 2020 Elsevier Has Created a COVID-19 Resource Centre with Free Information in English and Mandarin on the Novel Coronavirus COVID- 19 Since January 2020 Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID- 19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre - including this research content - immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. Review STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies Tehmina Bharucha, Clarissa Oeser, Francois Balloux, Julianne R Brown, Ellen C Carbo, Andre Charlett, Charles Y Chiu, Eric C J Claas, Marcus C de Goffau, Jutte J C de Vries, Marc Eloit, Susan Hopkins, Jim F Huggett, Duncan MacCannell, Sofia Morfopoulou, Avindra Nath, Denise M O’Sullivan, Lauren B Reoma, Liam P Shaw, Igor Sidorov, Patricia J Simner, Le Van Tan, Emma C Thomson, Lucy van Dorp, Michael R Wilson, Judith Breuer, Nigel Field The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from Lancet Infect Dis 2020; all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. 20: e251–60 Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, Published Online virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics August 5, 2020 https://doi.org/10.1016/ involves complex and multistep processes and there are important technical and methodological challenges that S1473-3099(20)30199-7 require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert This online publication has group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing been corrected. The corrected platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory version first appeared at testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires thelancet.com/infection on October 23, 2020 pragmatism and caution in interpretation, and that this field is rapidly evolving. Department of Biochemistry (T Bharucha MRCP) and Nuffield Background Review; however, some similar considerations about Department of Medicine The term metagenome was coined in 1998 to describe the reporting of results apply. (L P Shaw PhD), University of collection of genomes from microbes present in environ­ Metagenomic sequencing has advantages for pathogen Oxford, Oxford, UK; Lao-Oxford-Mahosot Hospital- mental soil samples by using approaches previously used identification over conventional methods, such as culture Wellcome Trust Research Unit, 1 to study single genomes. The sequencing of genetic or targeted PCR, because many or most microbial species Microbiology Laboratory, material from clinical samples has become common present within a sample can be detected simultaneously Mahosot Hospital, Vientiane, practice in research on clinical microorganisms. In this with high taxonomic resolution. Detailed characterisation Laos (T Bharucha); Centre for Molecular Epidemiology and context, metagenomics refers to the application of of microbial communities and population dynamics also Translational Research sequencing methods that can identify coexistent genomic enables the study of ecological interactions. Furthermore, (C Oeser PhD, N Field PhD) material from any organism present in patient samples this method does not require culture techniques, and and UCL Genetics Institute (ie, microorganism and host nucleic acid), usually with (F Balloux PhD, L van Dorp PhD) and Division of Infection and the aim of pathogen identification for clinical diagnosis Immunity (S Morfopoulou PhD, 2–4 or research. Examples of practical applications include Key messages Prof J Breuer MD), University College London, London, UK; pathogen detection and discovery, species characterisation • The term metagenomics refers to the use of sequencing or subtyping, antimicrobial resistance detection, virulence Microbiology, Virology and methods to simultaneously identify genomic material Infection Prevention and profiling, and studies of the microbiome and micro­ from all organisms present in a sample, with the Control (J R Brown PhD), 5–12 ecological drivers of health and disease. Metagenomics advantage of greater taxonomic resolution than culture Great Ormond Street Hospital for Children, London, UK is also being introduced as a diagnostic tool for causal or other methods. studies of clinical syndromes (such as encephalitis),13,14 for (J Breuer); Department of • Applications include pathogen detection and discovery, Medical Microbiology, Leiden 15,16 exploring the microbiome, and for tracking disease species characterisation, antimicrobial resistance University Medical Center, 17,18 outbreaks. A current example of the transformational detection, virulence profiling, and study of the Leiden, Netherlands (E C Carbo MSc, E C H Claas PhD, effect of direct sequencing of clinical samples has been microbiome and microecological factors affecting health. the application for rapid investigation and dissemination J J C de Vries PhD, I Sidorov PhD); • Metagenomics involves complex and multistep processes Statistics, Modelling and of information on severe acute respiratory syndrome and there are important technical and methodological Economics Department, Public 11,12 coronavirus 2 (SARS­CoV­2), which causes COVID­19. challenges that require careful consideration to support Health England, London, UK (A Charlett PhD); Department of Metagenomics data are generated using high­ valid inference. throughput sequencing methods, also referred to as Laboratory Medicine, • We co-ordinated a multidisciplinary, international expert University of California deep, next­generation, massively parallel, or shotgun group to establish reporting guidelines that address San Francisco, San Francisco, sequencing. In this Review, for simplicity, we refer to all specimen processing, nucleic acid extraction, sequencing CA, USA (Prof C Chiu PhD); these approaches as sequencing. We also include capture Wellcome Sanger Institute, platforms, bioinformatics considerations, quality assurance, Hinxton, UK probe enrichment­based sequencing methods that use limits of detection, power and sample size, confirmatory (M C de Goffau PhD); 4 nucleotide probes to increase sensitivity and targeted testing, causality criteria, cost, and ethical issues. Department of Veterinary amplicon sequencing—eg, sequencing the 16S ribosomal • The guidance recognises that metagenomics research Medicine, University of 19 Cambridge, Cambridge, UK ribonucleic acid (rRNA) gene to identify bacteria. requires pragmatism and caution in interpretation, and that (M C de Goffau); Pathogen Capture probe enrichment­based sequencing and tar­ this field is rapidly evolving. Reporting standards should Discovery Laboratory, Institut geted amplicon sequencing might not be considered true support clarity, consistency, and robustness of research. Pasteur, Paris, France examples of metagenomics and are not the focus of our (Prof M Eloit PhD); www.thelancet.com/infection Vol 20 October 2020 e251 Review Healthcare-Associated therefore can be used for microbial species that are experts in the field who were directly involved with the Infection and Antimicrobial difficult or time consuming to grow. This is particularly studies. Resistance, Public Health relevant for diagnostic applications, where routine England, London, UK 20,21 (S Hopkins PhD); Infectious culture is in decline. Describing methods and study design Diseases Unit, Royal Free However, appropriate study design for metagenomics Describe specimen collection, handling and storage Hospital, London, UK research is not well defined and metagenomic tech­ processes, and nucleic acid extraction methods (S Hopkins); National nologies pose important technical challenges. These Steps involved in sample collection, handling, and Measurement Laboratory, LGC, Teddington, UK challenges include methodological artefacts introduced processing are frequently poorly reported in publications (J F Hugget PhD, by wet laboratory methods and the effect that different and yet they will have considerable effect on the results D M O’Sullivan PhD); School of computational approaches have on the analysis of and reproducibility of a study and could introduce Biosciences & Medicine, Faculty 27–30 multivariate and complex data. Furthermore, the ethical variability artefacts. In particular, many studies use of Health & Medical Sciences, University of Surrey, Guildford, implications of sequencing are substantial and data material banked and collected originally for other pur­ UK (J F Hugget); Office of privacy considerations are increasingly recognised. poses. In this Review, we describe important potential Advanced Molecular Detection, The multiple steps and different expertise required to sources of error and their contribution to bias. Centers for Disease Control and generate and analyse
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