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Francis RV, Billam H, Clarke M, Yates C, Tsoleridis T, Berry L, Mahida N, Irving WL, Moore C, Holmes N, Ball JK, Loose M, McClure CP. The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. J Infect Dis 2022; 225:10-18. [PMID: 34555152 PMCID: PMC8522425 DOI: 10.1093/infdis/jiab483] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022] Open
Abstract
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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Affiliation(s)
- Rodric V Francis
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Harriet Billam
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Mitch Clarke
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Carl Yates
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Theocharis Tsoleridis
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom.,Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Louise Berry
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Nikunj Mahida
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - William L Irving
- Department of Clinical Microbiology, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom.,School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom.,Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Christopher Moore
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nadine Holmes
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jonathan K Ball
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom.,Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
| | - Matthew Loose
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - C Patrick McClure
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom.,National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom.,Wolfson Centre for Emerging Virus Research, University of Nottingham, Nottingham, United Kingdom
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