由于难以确定传播途径以及尽管实施了对其他重要的医院感染病原体有效的感染控制措施，但这种医院相关肠球菌感染的持续存在，使其控制成为一项艰巨的任务。本研究对2018年6月至2019年5月间从阿肯色大学医学科学大学（UAMS）的66名癌症患者中收集到的超过100个E. faecium分离株进行了全面分析。在本研究中采用的自上而下的方法不仅使用了106个E. faecium UAMS分离物，还使用了GenBank数据库中的过滤集合中的2,167个E. faecium菌株，以评估E. faecium菌种的当前种群结构，并因此确认与我们的临床分离物相关的谱系。然后，我们评估了来自物种池中的医院相关菌株的抗生素耐药性和毒力特征，重点关注最后一道防线的抗生素，以建立高危和多重耐药医院菌株的最新分类。利用全基因组测序分析方法（核心基因组多位点序列分型[CGMLST]、核心单核苷酸多态性[CoreSNP]分析和系统发育学分析）进一步对UAMS患者采集的临床分离物进行研究，并添加患者流行病学数据，揭示了三种序列类型在不同患者病房同时发生的多克隆暴发情况。整合从患者收集的基因组和流行病学数据增加了我们对E. faecium分离物的关系和传播动态的理解。我们的研究为E. faecium基因组监测提供了新的见解，以帮助监测和进一步限制多重耐药E. faecium的传播。重要性：肠球菌是肠道微生态的成员。虽然在健康的免疫能力正常的人群中，它的毒力较低，但E. faecium已成为美国医疗保健相关感染的第三大原因。本研究对阿肯色大学医学科学大学（UAMS）的癌症患者收集的超过100个E. faecium分离物进行了全面分析。我们采用从群体基因组学到分子生物学的自上而下的分析方法对临床分离株进行了遗传谱系分类，并对其抗生素耐药性和毒力特征进行了彻底评估。将患者流行病学数据添加到研究所进行的全基因组测序分析方法中，使我们能够增加对E. faecium分离物的关系和传播动态的理解。本研究提供了关于E. faecium基因组监测的新见解，以帮助监测和进一步限制多重耐药E. faecium的传播。

Control of hospital-associated Enterococcus faecium infection is a strenuous task due to the difficulty of identifying transmission routes and the persistence of this nosocomial pathogen despite the implementation of infection control measures that have been successful with other important nosocomial pathogens. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from 66 cancer patients at the University of Arkansas for Medical Sciences (UAMS) between June 2018 and May 2019. In the top-down approach used in this study, we employed, in addition to the 106 E. faecium UAMS isolates, a filtered set of 2,167 E. faecium strains from the GenBank database to assess the current population structure of E. faecium species and, consequently, to identify the lineages associated with our clinical isolates. We then evaluated the antibiotic resistance and virulence profiles of hospital-associated strains from the species pool, focusing on antibiotics of last resort, to establish an updated classification of high-risk and multidrug-resistant nosocomial clones. Further investigation of the clinical isolates collected from UAMS patients using whole-genome sequencing analytical methodologies (core genome multilocus sequence typing [cgMLST], core single nucleotide polymorphism [coreSNP] analysis, and phylogenomics), with the addition of patient epidemiological data, revealed a polyclonal outbreak of three sequence types occurring simultaneously in different patient wards. The integration of genomic and epidemiological data collected from the patients increased our understanding of the relationships and transmission dynamics of the E. faecium isolates. Our study provides new insights into genomic surveillance of E. faecium to assist in monitoring and further limiting the spread of multidrug-resistant E. faecium. IMPORTANCE Enterococcus faecium is a member of the gastrointestinal microbiota. Although its virulence is low in healthy, immunocompetent individuals, E. faecium has become the third leading cause of health care-associated infections in the United States. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from cancer patients at the University of Arkansas for Medical Sciences (UAMS). We employed a top-down analytical approach (from population genomics to molecular biology) to classify our clinical isolates into their genetic lineages and thoroughly evaluate their antibiotic resistance and virulence profiles. The addition of patient epidemiological data to the whole-genome sequencing analytical methodologies performed in the study allowed us to increase our understanding of the relationships and transmission dynamics of the E. faecium isolates. This study provides new insights into genomic surveillance of E. faecium to help monitor and further limit the spread of multidrug-resistant E. faecium.