Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA.
J Clin Microbiol. 2021 Nov 18;59(12):e0013521. doi: 10.1128/JCM.00135-21. Epub 2021 Jun 2.
Advancements in comparative genomics have generated significant interest in defining applications for health care-associated pathogens. Clinical microbiology, however, relies on increasingly automated platforms to quickly identify pathogens, resistance mechanisms, and therapy options within Clinical Laboratory Improvement Amendments (CLIA)- and FDA-approved frameworks. Additionally, and most notably, health care-associated pathogens, especially those that are resistant to antibiotics, represent a diverse spectrum of genera harboring complex genetic targets, including antibiotic, biocide, and virulence determinants that can be highly transmissible and, at least for antibiotic resistance, serve as potential targets for containment efforts. U.S. public health investments have focused on rapidly detecting outbreaks and emerging resistance in health care-associated pathogens using reference, culture-based, and molecular methods that are distributed, for example, across national laboratory network infrastructures. Herein we describe the public health applications of genomic science that are built from the top-down for broad surveillance, as well as the bottom-up, starting with identification of infections and infectious clusters. For health care-associated, including antimicrobial-resistant, pathogens, we propose a combination of top-down and bottom-up genomic approaches leveraged across the public health spectrum, from local infection control, to regional and national containment efforts, to national surveillance for understanding emerging strain ecology and fitness of health care pathogens.
比较基因组学的进展引起了人们对定义与医疗保健相关病原体应用的极大兴趣。然而，临床微生物学依赖于越来越自动化的平台，以便在符合临床实验室改进修正案 (CLIA) 和 FDA 批准框架内快速识别病原体、耐药机制和治疗选择。此外，值得注意的是，与医疗保健相关的病原体，尤其是那些对抗生素耐药的病原体，代表了一个具有复杂遗传靶标的多样化属谱，其中包括抗生素、杀生物剂和毒力决定因素，这些因素具有高度传染性，至少对于抗生素耐药性而言，它们可以作为遏制努力的潜在目标。美国公共卫生投资一直专注于使用参考、基于培养和分子方法快速检测与医疗保健相关的病原体中的暴发和新出现的耐药性，这些方法分布在国家实验室网络基础设施中。在此，我们描述了从广义监测的自上而下的基因组科学的公共卫生应用，以及从识别感染和感染群开始的自下而上的应用。对于与医疗保健相关的病原体，包括抗微生物耐药性病原体，我们建议在公共卫生范围内结合使用自上而下和自下而上的基因组方法，从局部感染控制到区域和国家遏制努力，再到国家监测，以了解医疗保健病原体的新兴菌株生态和适应性。
