Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas.
Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas.
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自上而下的基因组监测方法，用于调查阿肯色州癌症患者中检测到的屎肠球菌的基因组流行病学和抗生素耐药性模式。
DOI：
10.1128/spectrum.04901-22
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发表时间：
2023-06-15
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
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作者：
控制医院相关的屎肠球菌感染是一项艰巨的任务，因为难以确定传播途径，尽管实施了感染控制措施，但这种医院病原体仍持续存在，这些措施已成功地控制了其他重要的医院病原体。这项研究对2018年6月至2019年5月期间从阿肯色大学医学科学学院（UAMS）的66名癌症患者身上收集的100多株粪肠杆菌进行了全面分析。在本研究中使用的自上而下的方法中，除了106株屎肠杆菌UAMS分离株外，我们还从GenBank数据库中筛选了2167株屎肠杆菌菌株，以评估屎肠杆菌物种的当前种群结构，从而确定与我们的临床分离株相关的谱系。然后，我们评估了来自物种库的医院相关菌株的抗生素耐药性和毒力谱，重点关注最后使用的抗生素，以建立高风险和耐多药医院克隆的最新分类。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]分析和系统基因组学）对从UAMS患者收集的临床分离株进行进一步调查，并添加患者流行病学数据，发现三种序列类型的多克隆爆发同时发生在不同的患者病房。从患者收集的基因组和流行病学数据的整合增加了我们对粪肠杆菌分离株的关系和传播动力学的理解。我们的研究为粪肠杆菌的基因组监测提供了新的见解，有助于监测和进一步限制多药耐药粪肠杆菌的传播。屎肠球菌是胃肠道微生物群的一员。虽然其毒力在健康、免疫能力强的个体中较低，但在美国，粪肠杆菌已成为卫生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（UAMS）癌症患者收集的100多株粪肠杆菌进行了全面分析。我们采用自上而下的分析方法（从群体基因组学到分子生物学）对临床分离物进行遗传谱系分类，并彻底评估其抗生素耐药性和毒力谱。将患者流行病学数据添加到研究中执行的全基因组测序分析方法中，使我们能够增加对粪肠杆菌分离株的关系和传播动力学的理解。该研究为粪肠杆菌的基因组监测提供了新的见解，有助于监测和进一步限制耐多药粪肠杆菌的传播。
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.
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影响因子：
3.7
作者：
de Regt MJ;van Schaik W;van Luit-Asbroek M;Dekker HA;van Duijkeren E;Koning CJ;Bonten MJ;Willems RJ
通讯作者：
Willems RJ
影响因子：
4.9
作者：
Bortolaia, Valeria;Mander, Manuela;Guardabassi, Luca
通讯作者：
Guardabassi, Luca
影响因子：
10.7
作者：
Hoang DT;Chernomor O;von Haeseler A;Minh BQ;Vinh LS
通讯作者：
Vinh LS
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
3
作者：
Francisco AP;Vaz C;Monteiro PT;Melo-Cristino J;Ramirez M;Carriço JA
通讯作者：
Carriço JA