Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.

中文翻译：

---

细菌病原体的全基因组测序：医院暴发分析的未来 [评论]

多重耐药细菌的爆发经常对世界各地医院中的弱势患者群体构成威胁。重症监护病房 (ICU) 患者由于血管内导管、引流管和机械通气气管插管等留置装置而特别容易发生院内感染。受感染的 ICU 患者的脆弱性日益增加，这表明制定有效的疫情管理方案的重要性。通过基因分型方法了解病原体的传播是疫情管理的重要工具。最近，病原体的全基因组测序（WGS）作为基因分型工具变得更加容易获得和负担得起。通过全基因组测序分析整个病原体基因组可以提供前所未有的分辨率，甚至可以区分高度相关的细菌谱系，并彻底改变医院的疫情分析。然而，由于早期测序平台昂贵且繁琐，临床医生长期以来一直对在疫情分析中实施全基因组测序犹豫不决。最近测序技术和分析工具的改进迅速提高了输出和分析速度，并降低了 WGS 的总体成本。在这篇综述中，我们评估了全基因组测序技术和生物信息学分析工具用于医院暴发分析的可行性，并与传统的暴发分析工作流程进行了比较。此外，我们回顾了测序技术和分析工具的优点和局限性，并提出了实施 WGS 进行抗菌药物耐药性分析的真实示例。我们旨在为医疗保健专业人员提供 WGS 疫情分析指南，强调其对医院的好处，并协助从传统的疫情分析过渡到基于 WGS 的疫情分析。