The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.
The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.
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DOI：
10.1093/infdis/jiab483
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发表时间：
2022-01-05
期刊：
影响因子：
--
通讯作者：
COVID-19 Genomics UK (COG-UK) consortium
中科院分区：
文献类型：
--
作者：
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;COVID-19 Genomics UK (COG-UK) consortium
医院感染严重急性呼吸综合征冠状病毒2（SARS-CoV-2）严重影响了床位容量和患者流量。我们利用全基因组测序（WGS）在2020年底英国第二波大流行期间识别疫情并集中感染控制资源和干预措施。对WGS和流行病学数据的系统发育分析确定了最初的传播事件发生在一个入院病房，并记录了之前的社区感染联系。还观察到无症状工作人员感染具有相同基因病毒序列的高发病率，这可能促成了疫情的传播。WGS允许及时采取医院传播干预措施，包括入院病房即时检测和引入便携式HEPA 14过滤器。相反，WGS排除了2例具有时空联系的医院传播，节省了时间和资源。总之，WGS显著增强了对医院环境中SARS-CoV-2集群的理解，既确定了高风险区域，又反过来验证了其他单位的现有控制措施，总体上维持了临床服务。SARS-CoV-2全基因组测序结合经典流行病学，确定了院内传播事件，为英国第二波疫情期间的针对性感染预防措施提供了信息。相反，在2例具有时空联系的情况下，通过测序排除了院内传播，从而节省了时间和资源。
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. SARS-CoV-2 whole-genome sequencing, combined with classical epidemiology, identified nosocomial transmission events, informing targeted infection prevention measures during the UK’s second epidemic wave. Conversely, nosocomial transmission was excluded by sequencing in 2 instances with temporospatial linkage, conserving time and resources.
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DOI：
10.1126/science.abg3055
发表时间：
2021-04-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Davies NG;Abbott S;Barnard RC;Jarvis CI;Kucharski AJ;Munday JD;Pearson CAB;Russell TW;Tully DC;Washburne AD;Wenseleers T;Gimma A;Waites W;Wong KLM;van Zandvoort K;Silverman JD;CMMID COVID-19 Working Group;COVID-19 Genomics UK (COG-UK) Consortium;Diaz-Ordaz K;Keogh R;Eggo RM;Funk S;Jit M;Atkins KE;Edmunds WJ
通讯作者：
Edmunds WJ
影响因子：
3
作者：
Marquis B;Opota O;Jaton K;Greub G
通讯作者：
Greub G
影响因子：
--
作者：
O'Toole, Aine;Hill, Verity;Kraemer, Moritz U G
通讯作者：
Kraemer, Moritz U G
影响因子：
6.9
作者：
Carter, B.;Collins, J. T.;McCarthy, K.
通讯作者：
McCarthy, K.
影响因子：
11.8
作者：
Cheng, Vincent Chi-Chung;Fung, Kitty Sau-Chun;Yuen, Kwok-Yung
通讯作者：
Yuen, Kwok-Yung