Background: Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and especially to vancomycin, a first-line antibiotic to treat infections with multidrug-resistant Gram-positive pathogens, has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or Tn1546 transposition between different genomic locations. Here, we reconstructed all nested genetic elements (clone, plasmid,transposon) to study how the dissemination of vanA-type vancomycin-resistance occurred in Dutch hospitals (2012-2015). Methods: We performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012-2015). Genomic information regarding clonality and Tn1546 characterisation was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. This allowed determining all nested genomic elements (clone, plasmid and transposon) involved in the dissemination of the vanA gene cluster. Next, we conducted an "all vs. all" pairwise comparison between isolates sharing a potential epidemiological link to elucidate whether clonal, plasmid or Tn1546 spread accounted for the dissemination of vanA resistance. Results: The 309 VRE isolates belonged to 18 different SCs of which SC13 (n = 102, 33%), SC17 (n = 52,16.8%) and SC18 (n = 42, 13.6%) were predominant. We identified seven different plasmid types bearing the vanA gene cluster, four of which were highly similar (identity ~99%, coverage ~84%) to previously described complete plasmid sequences. We estimated that clonal dissemination contributed most (~45%) to the spread of vancomycin-resistance in Dutch hospitals, followed by Tn1546 mobilisation (~12%) and plasmid dissemination (~6%). Conclusions: The dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of Tn1546 transposition and/or plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides one of the first quantitative assessments to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type vancomycin-resistance cluster.

中文翻译：

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荷兰医院中vanA型万古霉素耐药性传播的模式和动力学

背景： 粪肠球菌是动物和人类胃肠道的代名词，也是医院获得性感染的致病因子。对糖肽的耐药性，尤其是对万古霉素的耐药性，万古霉素是治疗多重耐药性革兰氏阳性病原体感染的一线抗生素，已促使粪肠球菌被列入世界卫生组织全球优先清单。可以通过转座子Tn 1546上的vanA基因簇赋予万古霉素抗性，后者通常存在于质粒中。所述VANA基因簇可以通过质粒传播或TN被克隆同时也传播水平要么1546不同基因组位置之间的转座。在这里，我们重构了所有嵌套的遗传元件（克隆，质粒，转座子），以研究vanA型耐万古霉素耐药性在荷兰医院中的传播过程（2012-2015年）。方法：我们对荷兰32家医院（2012-2015年）的309株耐万古霉素的粪肠球菌（VRE）分离株的基因组流行病学进行了回顾性研究。有关克隆性和Tn 1546的基因组信息分别使用hierBAPS序列簇（SC）和TETyper提取特征。使用gplas结合基于共有k-mer含量的网络方法预测质粒。这样就可以确定与vanA基因簇的传播有关的所有嵌套基因组元件（克隆，质粒和转座子）。接下来，我们在具有潜在流行病学联系的分离株之间进行了“全部对所有”的成对比较，以阐明克隆，质粒还是Tn 1546传播是vanA传播的原因抵抗性。结果：309个VRE分离株属于18个不同的SC，其中SC13（n = 102，33％），SC17（n = 52,16.8％）和SC18（n = 42，13.6％）占优势。我们鉴定了带有vanA基因簇的七种不同质粒类型，其中四种与先前描述的完整质粒序列高度相似（同一性为99％，覆盖度为84％）。我们估计，在荷兰医院中，无性传播对万古霉素耐药性的传播贡献最大（约占45％），其次是Tn 1546动员（约占12％）和质粒的传播（约占6％）。结论：2012年至2015年间，vanA基因簇在荷兰医院中的传播以克隆传播为主导。但是，我们还确定了Tn发生频率高的爆发设置1546转座和/或质粒传播，其中抗性传播主要由水平基因转移（HGT）驱动。这项研究证明了用短读数据区分传播模式的可行性，并提供了最早的定量评估之一，以评估嵌套基因组元件在vanA型耐万古霉素抗性簇的传播中的相对贡献。