Ninewells Hospital and Medical School, Dundee, UK.
School of Medicine, University of St Andrews, St Andrews, UK.
J Hosp Infect. 2021 Mar;109:1-9. doi: 10.1016/j.jhin.2020.11.001. Epub 2020 Nov 9.
Outbreaks pose a significant risk to patient safety as well as being costly and time consuming to investigate. The implementation of targeted infection prevention and control measures relies on infection prevention and control teams having access to rapid results that detect resistance accurately, and typing results that give clinically useful information on the relatedness of isolates. At present, determining whether transmission has occurred can be a major challenge. Conventional typing results do not always have sufficient granularity or robustness to define strains unequivocally, and sufficient epidemiological data are not always available to establish links between patients and the environment. Whole-genome sequencing (WGS) has emerged as the ultimate genotyping tool, but has not yet fully crossed the divide between research method and routine clinical diagnostic microbiological technique. A clinical WGS service was officially established in 2014 as part of the Scottish Healthcare Associated Infection Prevention Institute to confirm or refute outbreaks in hospital settings from across Scotland. This article describes the authors' experiences with the aim of providing new insights into practical application of the use of WGS to investigate healthcare and public health outbreaks. Solutions to overcome barriers to implementation of this technology in a clinical environment are proposed.
暴发不仅给患者安全带来严重风险，而且调查起来既昂贵又耗时。实施有针对性的感染预防和控制措施依赖于感染预防和控制团队能够快速获得准确检测耐药性的结果以及能够提供有关分离物相关性的临床有用信息的分型结果。目前，确定是否发生了传播可能是一个重大挑战。传统的分型结果并不总是具有足够的粒度或稳健性来明确地定义菌株，而且并不总是有足够的流行病学数据来建立患者与环境之间的联系。全基因组测序 (WGS) 已成为最终的基因分型工具，但尚未完全跨越研究方法与常规临床诊断微生物学技术之间的鸿沟。2014 年，苏格兰医疗保健相关感染预防研究所正式建立了一项临床 WGS 服务，以确认或反驳苏格兰各地医院环境中的暴发。本文介绍了作者的经验，旨在为将 WGS 用于调查医疗保健和公共卫生暴发的实际应用提供新的见解。提出了解决在临床环境中实施这项技术的障碍的方法。
