WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome
WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome
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DOI：
10.1093/jac/dkz118
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发表时间：
2019-07-01
影响因子：
5.2
通讯作者：
Westh, Henrik
中科院分区：
文献类型：
--
作者：
Pinholt, Mette;Bayliss, Sion C.;Westh, Henrik
目的2012年至2015年，在丹麦丹麦首都地区观察到万古霉素耐药（vanA）屎肠球菌（VREfm）突然显著增加。VREfm与万古霉素敏感E.对屎肠杆菌（VSEfm）进行了调查，确定了医院之间的传播事件，并对最大VREfm克隆群的泛基因组和质粒进行了表征。在Illumina平台上进行粪便分离物的SNP分析并鉴定泛基因组。还在PacBio平台上对一个分离株进行了测序，以关闭基因组。结果892株VREfm和166株VSEfm的系统发育均为多克隆结构，其中ST 80型占40%。VREfm和VSEfm共同发生在许多克隆组，但是，没有VSEfm相关的优势VREfm组。一个类似的vanA质粒被确定在>= 99%的菌株属于优势组和69%的剩余VREfm。在完整的基因组中鉴定出10个质粒，其中约29%的基因组由辅助基因组成。泛基因组之间的优势组的大小是5905 genes.Conclusions，VREfm出现由于进口的成功VREfm克隆，迅速传播到该地区的大多数医院，同时传播vanA质粒预先存在的VSEfm。获得一个异质性的辅助基因组可能是这个克隆成功的原因，因为它有助于适应新的环境挑战。
Objectives From 2012 to 2015, a sudden significant increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycin-susceptible E. faecium (VSEfm) was investigated, transmission events between hospitals were identified and the pan-genome and plasmids from the largest VREfm clonal group were characterized.Methods WGS of 1058 E. faecium isolates was carried out on the Illumina platform to perform SNP analysis and to identify the pan-genome. One isolate was also sequenced on the PacBio platform to close the genome. Epidemiological data were collected from laboratory information systems.Results Phylogeny of 892 VREfm and 166 VSEfm revealed a polyclonal structure, with a single clonal group (ST80) accounting for 40% of the VREfm isolates. VREfm and VSEfm co-occurred within many clonal groups; however, no VSEfm were related to the dominant VREfm group. A similar vanA plasmid was identified in >= 99% of isolates belonging to the dominant group and 69% of the remaining VREfm. Ten plasmids were identified in the completed genome, and similar to 29% of this genome consisted of dispensable accessory genes. The size of the pan-genome among isolates in the dominant group was 5905 genes.Conclusions Most probably, VREfm emerged owing to importation of a successful VREfm clone which rapidly transmitted to the majority of hospitals in the region whilst simultaneously disseminating a vanA plasmid to pre-existing VSEfm. Acquisition of a heterogeneous accessory genome may account for the success of this clone by facilitating adaptation to new environmental challenges.