STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies
The Lancet Infectious Diseases, vol. 20, pp. e251–e260
Abstract
The term metagenomics refers to the use of sequencing methods to simultaneously identify genomic material from all organisms present in a sample, with the advantage of greater taxonomic resolution than culture or other methods. Applications include pathogen detection and discovery, species characterisation, antimicrobial resistance detection, virulence profiling, and study of the microbiome and microecological factors affecting health. However, metagenomics involves complex and multistep processes and there are important technical and methodological challenges that require careful consideration to support valid inference. We co-ordinated a multidisciplinary, international expert group to establish reporting guidelines that address specimen processing, nucleic acid extraction, sequencing platforms, bioinformatics considerations, quality assurance, limits of detection, power and sample size, confirmatory testing, causality criteria, cost, and ethical issues. The guidance recognises that metagenomics research requires pragmatism and caution in interpretation, and that this field is rapidly evolving.
Authors 27
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Tehmina Bharucha corresponding
Mahosot Hospital · University of Oxford · Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit
Affiliation as printed
Department of Biochemistry, University of Oxford, Oxford, UK; Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos. Electronic address: t.bharucha@doctors.org.uk
Department of Biochemistry, University of Oxford, Oxford, UK
Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
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Affiliation as printed
Centre for Molecular Epidemiology and Translational Research, University College London, London, UK
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Affiliation as printed
UCL Genetics Institute, University College London, London, UK
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Affiliation as printed
Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children, London, UK
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Leiden University Medical Center
Affiliation as printed
Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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Affiliation as printed
Statistics, Modelling and Economics Department, Public Health England, London, UK
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University of California, San Francisco
Affiliation as printed
Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
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Leiden University Medical Center
Affiliation as printed
Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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University of Cambridge · Wellcome Sanger Institute
Affiliation as printed
Wellcome Sanger Institute, Hinxton, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
Wellcome Sanger Institute, Hinxton, UK
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Leiden University Medical Center
Affiliation as printed
Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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Affiliation as printed
Pathogen Discovery Laboratory, Institut Pasteur, Paris, France
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The Royal Free Hospital · Public Health England
Affiliation as printed
Healthcare-Associated Infection and Antimicrobial Resistance, Public Health England, London, UK; Infectious Diseases Unit, Royal Free Hospital, London, UK
Healthcare-Associated Infection and Antimicrobial Resistance, Public Health England, London, UK
Infectious Diseases Unit, Royal Free Hospital, London, UK
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Affiliation as printed
National Measurement Laboratory, LGC, Teddington, UK; School of Biosciences & Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
National Measurement Laboratory, LGC, Teddington, UK
School of Biosciences & Medicine, Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK
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Centers for Disease Control and Prevention
Affiliation as printed
Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Affiliation as printed
Division of Infection and Immunity, University College London, London, UK
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Affiliation as printed
Section of Infections of the Nervous System, National Institutes of Health, Bethesda, MD, USA
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Affiliation as printed
National Measurement Laboratory, LGC, Teddington, UK
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Affiliation as printed
Section of Infections of the Nervous System, National Institutes of Health, Bethesda, MD, USA
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Affiliation as printed
Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Leiden University Medical Center
Affiliation as printed
Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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Johns Hopkins University · Johns Hopkins Medicine
Affiliation as printed
Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Oxford University Clinical Research Unit
Affiliation as printed
Emerging Infections Group, Oxford University Clinical Research Unit, Ho Chi Minh city, Vietnam
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MRC University of Glasgow Centre for Virus Research
Affiliation as printed
MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
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Affiliation as printed
UCL Genetics Institute, University College London, London, UK
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University of California, San Francisco
Affiliation as printed
Weill Institute for Neurosciences and Department of Neurology, University of California, San Francisco, CA, USA
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Great Ormond Street Hospital · University College London
Affiliation as printed
Division of Infection and Immunity, University College London, London, UK; Great Ormond Street Hospital for Children, London, UK
Division of Infection and Immunity, University College London, London, UK
Great Ormond Street Hospital for Children, London, UK
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Affiliation as printed
Centre for Molecular Epidemiology and Translational Research, University College London, London, UK
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