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The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks

Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and intervention during the United Kingdom’s second pandemic...

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Autores principales: Francis, Rodric V, Billam, Harriet, Clarke, Mitch, Yates, Carl, Tsoleridis, Theocharis, Berry, Louise, Mahida, Nikunj, Irving, William L, Moore, Christopher, Holmes, Nadine, Ball, Jonathan K, Loose, Matthew, McClure, C Patrick
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8522425/
https://www.ncbi.nlm.nih.gov/pubmed/34555152
http://dx.doi.org/10.1093/infdis/jiab483
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author Francis, Rodric V
Billam, Harriet
Clarke, Mitch
Yates, Carl
Tsoleridis, Theocharis
Berry, Louise
Mahida, Nikunj
Irving, William L
Moore, Christopher
Holmes, Nadine
Ball, Jonathan K
Loose, Matthew
McClure, C Patrick
author_facet Francis, Rodric V
Billam, Harriet
Clarke, Mitch
Yates, Carl
Tsoleridis, Theocharis
Berry, Louise
Mahida, Nikunj
Irving, William L
Moore, Christopher
Holmes, Nadine
Ball, Jonathan K
Loose, Matthew
McClure, C Patrick
author_sort Francis, Rodric V
collection PubMed
description Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and intervention during the United Kingdom’s second pandemic wave in late 2020. Phylogenetic analysis of WGS and epidemiological data pinpointed an initial transmission event to an admission ward, with immediate prior community infection linkage documented. High incidence of asymptomatic staff infection with genetically identical viral sequences was also observed, which may have contributed to the propagation of the outbreak. WGS allowed timely nosocomial transmission intervention measures, including admissions ward point-of-care testing and introduction of portable HEPA14 filters. Conversely, WGS excluded nosocomial transmission in 2 instances with temporospatial linkage, conserving time and resources. In summary, WGS significantly enhanced understanding of SARS-CoV-2 clusters in a hospital setting, both identifying high-risk areas and conversely validating existing control measures in other units, maintaining clinical service overall.
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spelling pubmed-85224252021-10-20 The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks Francis, Rodric V Billam, Harriet Clarke, Mitch Yates, Carl Tsoleridis, Theocharis Berry, Louise Mahida, Nikunj Irving, William L Moore, Christopher Holmes, Nadine Ball, Jonathan K Loose, Matthew McClure, C Patrick J Infect Dis Major Articles and Brief Reports Nosocomial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have severely affected bed capacity and patient flow. We utilized whole-genome sequencing (WGS) to identify outbreaks and focus infection control resources and intervention during the United Kingdom’s second pandemic wave in late 2020. Phylogenetic analysis of WGS and epidemiological data pinpointed an initial transmission event to an admission ward, with immediate prior community infection linkage documented. High incidence of asymptomatic staff infection with genetically identical viral sequences was also observed, which may have contributed to the propagation of the outbreak. WGS allowed timely nosocomial transmission intervention measures, including admissions ward point-of-care testing and introduction of portable HEPA14 filters. Conversely, WGS excluded nosocomial transmission in 2 instances with temporospatial linkage, conserving time and resources. In summary, WGS significantly enhanced understanding of SARS-CoV-2 clusters in a hospital setting, both identifying high-risk areas and conversely validating existing control measures in other units, maintaining clinical service overall. Oxford University Press 2021-09-23 /pmc/articles/PMC8522425/ /pubmed/34555152 http://dx.doi.org/10.1093/infdis/jiab483 Text en © The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Major Articles and Brief Reports
Francis, Rodric V
Billam, Harriet
Clarke, Mitch
Yates, Carl
Tsoleridis, Theocharis
Berry, Louise
Mahida, Nikunj
Irving, William L
Moore, Christopher
Holmes, Nadine
Ball, Jonathan K
Loose, Matthew
McClure, C Patrick
The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks
title The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks
title_full The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks
title_fullStr The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks
title_full_unstemmed The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks
title_short The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks
title_sort impact of real-time whole-genome sequencing in controlling healthcare-associated sars-cov-2 outbreaks
topic Major Articles and Brief Reports
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8522425/
https://www.ncbi.nlm.nih.gov/pubmed/34555152
http://dx.doi.org/10.1093/infdis/jiab483
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