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2 results on '"de Vries, Jutte JC"'

1. STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies

Author

Bharucha, Tehmina, Oeser, Clarissa, Balloux, Francois, Brown, Julianne R, Carbo, Ellen C, Charlett, Andre, Chiu, Charles Y, Claas, Eric CJ, de Goffau, Marcus C, de Vries, Jutte JC, Eloit, Marc, Hopkins, Susan, Huggett, Jim F, MacCannell, Duncan, Morfopoulou, Sofia, Nath, Avindra, O'Sullivan, Denise M, Reoma, Lauren B, Shaw, Liam P, Sidorov, Igor, Simner, Patricia J, Van Tan, Le, Thomson, Emma C, van Dorp, Lucy, Wilson, Michael R, Breuer, Judith, and Field, Nigel

Subjects
Biomedical and Clinical Sciences, Epidemiology, Clinical Sciences, Health Sciences, Medical Microbiology, Genetics, Human Genome, Good Health and Well Being, Computational Biology, Humans, Metagenomics, Molecular Epidemiology, Research Design, Public Health and Health Services, Microbiology, Clinical sciences, Medical microbiology
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.

Published
2020

2. Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid and antibody tests up to 22 August 2020

Author

Van Walle, Ivo, Leitmeyer, Katrin, Broberg, Eeva K, Van Esbroeck, Marjan, Beuselinck, Kurt, Vermeersch, Pieter, Karagiannis, Christos, Mentis, Andreas, Lampropoulou, Stavroula, Erlund, Iris, Melin, Merit, Ekström, Nina, Vihervaara, Terhi, Gaymard, Alexandre, Frobert, Emilie, Escuret, Vanessa, Kurolt, Ivan-Christian, Fournier, Guillaume, Abdelrahman, Tamir, Nguyen, Trung, Klak, Adrian, Bos, Anne E, Russcher, Anne, van ’t Veen, Annemarie, Stemerding, Annette M, van Corteveen-Splinter, Annette, van Hees, Babette C, Wintermans, Bas B, Herpers, Bjorn L, Reusken, Chantal BEM, van der Donk, Christel FM, Oliveira dos Santos, Claudy, GeurtsvanKessel, Corine H, Timmerman, Cornelis P, Ong, David SY, Kaersenhout, Deborah J, van Lochem, Ellen, Geeraedts, Felix, Rijkers, Ger T, Berkhout, Hannke, Koeleman, Hans GM, van Loo, Inge HM, Rahamat-Langendoen, Janette, Murk, Jean-Luc, Tjhie, Jeroen HT, Kissing, Johan, Reimerink, Johan, Kerremans, Jos J, de Vries, Jutte JC, Heemstra, Karen A, Thai, Khoa TD, Jim, Kin Ki, Mulder, Leontine, van den Beld, Maaike JC, Batstra, Manou R, Konstantinovski, Maria M, Wegdam-Blans, Marjolijn CA, Hoogewerf, Martine, de Graaf, Melanie J, de Jong, Menno D., Heron, Michiel, van Rijn, Michiel, Heusinkveld, Moniek, Van Burgel, Nathalie, Savelkoul, Paul HM, den Reijer, Paul Martijn, Wever, Peter C, Croughs, Peter, Zonneveld, Rens, van Gyseghem, Sim, Thijsen, Steven FT, Stoof, Susanne P, Jurriaans, Suzanne, Debast, Sylvia B, Mank, Theo, Hira, Vishal, Michalski, Aleksander, Siewierska-Puchlerska, Anna, Gajda, Ewa, Paciorek, Jarosław, Pakieła, Marta, Kołakowska-Kulesza, Agnieszka, Pancer, Katarzyna, Nowakowska, Magdalena, Costa, Inês, Zé-Zé, Líbia, Guiomar, Raquel, Hammas, Berit, Öckinger, Johan Brynedal, Prosenc, Katarina, and Berginc, Nataša

Subjects
Infecções Respiratórias, medicine.medical_specialty, Epidemiology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), diagnostic, specificity, Sensitivity and Specificity, Gastroenterology, Asymptomatic, Nucleic Acids, Virology, Internal medicine, medicine, Humans, media_common.cataloged_instance, European union, Pandemics, media_common, Infecções Sistémicas e Zoonoses, accuracy, biology, SARS-CoV-2, business.industry, Research, Public Health, Environmental and Occupational Health, COVID-19, sensitivity, Confidence interval, meta-analysis, Study heterogeneity, Meta-analysis, biology.protein, Nucleic acid, Antibody Tests, Antibody, medicine.symptom, business
Abstract

Background Reliable testing for SARS-CoV-2 is key for the management of the COVID-19 pandemic. Aim We estimate diagnostic accuracy for nucleic acid and antibody tests 5 months into the COVID-19 pandemic, and compare with manufacturer-reported accuracy. Methods We reviewed the clinical performance of SARS-CoV-2 nucleic acid and antibody tests based on 93,757 test results from 151 published studies and 20,205 new test results from 12 countries in the European Union and European Economic Area (EU/EEA). Results Pooling the results and considering only results with 95% confidence interval width ≤ 5%, we found four nucleic acid tests, including one point-of-care test and three antibody tests, with a clinical sensitivity ≥ 95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Nine nucleic acid tests and 25 antibody tests, 12 of them point-of-care tests, had a clinical specificity of ≥ 98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid point-of-care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for eight of 14 sensitivity and 68 of 84 specificity results with confidence interval width ≤ 5%, and lower for nucleic acid tests than antibody tests. Manufacturer-reported clinical performance was significantly higher than independently assessed in 11 of 32 and four of 34 cases, respectively, for sensitivity and specificity, indicating a need for improvement in this area. Conclusion Continuous monitoring of clinical performance within more clearly defined target populations is needed.

Published
2021

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