经验教训：使用 WGS 实时调查疑似院内 SARS-CoV-2 暴发。
Lessons learned: use of WGS in real-time investigation of suspected intrahospital SARS-CoV-2 outbreaks.
机构信息
Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway.
出版信息
J Hosp Infect. 2023 Jan;131:81-88. doi: 10.1016/j.jhin.2022.10.003. Epub 2022 Oct 29.
BACKGROUND
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been a continuing source of hospital-acquired infection and outbreaks. At Akershus University Hospital in Norway, traditional contact tracing has been combined with whole-genome sequencing (WGS) surveillance in real-time to investigate potential hospital outbreaks.
AIM
To describe the advantages and challenges encountered when using WGS as a real-time tool in hospital outbreak investigation and surveillance during the SARS-CoV-2 pandemic.
METHODS
Routine contact tracing in the hospital was performed for all healthcare workers (HCWs) who tested positive for SARS-CoV-2. Viral RNA from all positive patient and HCW samples was sequenced in real-time using nanopore sequencing and the ARTIC Network protocol. Suspected outbreaks involving five or more individuals with viral sequences were described.
FINDINGS
Nine outbreaks were suspected based on contact tracing, and one outbreak was suspected based on WGS results. Five outbreaks were confirmed; of these, two outbreaks were supported but could not be confirmed by WGS with high confidence, one outbreak was found to consist of two different lineages, and two outbreaks were refuted.
CONCLUSIONS
WGS is a valuable tool in hospital outbreak investigations when combined with traditional contact tracing. Inclusion of WGS data improved outbreak demarcation, identified unknown transmission chains, and highlighted weaknesses in existing infection control measures.
背景
严重急性呼吸综合征冠状病毒 2 型（SARS-CoV-2）一直是医院获得性感染和暴发的源头。在挪威阿克什胡斯大学医院，传统的接触者追踪与实时全基因组测序（WGS）监测相结合，以调查潜在的医院暴发。
目的
描述在 SARS-CoV-2 大流行期间，将 WGS 用作医院暴发调查和监测的实时工具时遇到的优势和挑战。
方法
对所有检测出 SARS-CoV-2 呈阳性的医护人员（HCW）进行常规医院接触者追踪。使用纳米孔测序和 ARTIC 网络协议实时对所有阳性患者和 HCW 样本的病毒 RNA 进行测序。描述涉及五名或更多具有病毒序列个体的疑似暴发。
发现
根据接触者追踪，怀疑有 9 起暴发，根据 WGS 结果，怀疑有 1 起暴发。确认了 5 起暴发；其中，2 起暴发得到支持，但 WGS 无法高度置信地确认，1 起暴发由两种不同的谱系组成，2 起暴发被反驳。
结论
当与传统接触者追踪相结合时，WGS 是医院暴发调查的一种有价值的工具。WGS 数据的纳入改善了暴发的划分，确定了未知的传播链，并强调了现有感染控制措施的弱点。
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