对 600 株万古霉素耐药粪肠球菌的基因组分析表明，在爱尔兰不同遗传谱系中，ST80 菌株的流行率很高，并且通过 IS1216E 和质粒转移传播了类似的 vanA 区。
Genomic analysis of 600 vancomycin-resistant Enterococcus faecium reveals a high prevalence of ST80 and spread of similar vanA regions via IS1216E and plasmid transfer in diverse genetic lineages in Ireland.
机构信息
Microbiology Research Unit, Division of Oral Biosciences, Dublin Dental University Hospital, University of Dublin, Trinity College, Lincoln Place, Dublin 2, Ireland.
Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark.
出版信息
J Antimicrob Chemother. 2022 Feb 2;77(2):320-330. doi: 10.1093/jac/dkab393.
BACKGROUND
Vancomycin-resistant Enterococcus faecium (VREfm) cause a wide range of hospital infections. Ireland has had one of the highest invasive VREfm infection rates in Europe over the last decade, yet little is known about Irish VREfm.
OBJECTIVES
To investigate the population structure of Irish VREfm, explore diversity by analysing the vanA transposon region and compare Irish, Danish and global isolates.
METHODS
E. faecium (n = 648) from five Irish hospitals were investigated, including VREfm [547 rectal screening and 53 bloodstream infection (BSI)] isolates and 48 vancomycin-susceptible (VSEfm) BSI isolates recovered between June 2017 and December 2019. WGS and core-genome MLST (cgMLST) were used to assess population structure. Genetic environments surrounding vanA were resolved by hybrid assembly of short-read (Illumina) and long-read (Oxford Nanopore Technologies) sequences.
RESULTS
All isolates belonged to hospital-adapted clade A1 and the majority (435/648) belonged to MLST ST80. The population structure was highly polyclonal; cgMLST segregated 603/648 isolates into 51 clusters containing mixtures of screening and BSI isolates, isolates from different hospitals, and VREfm and VSEfm. Isolates within clusters were closely related (mean average ≤16 allelic differences). The majority (96.5%) of VREfm harboured highly similar vanA regions located on circular or linear plasmids with multiple IS1216E insertions, variable organization of vanA operon genes and 78.6% harboured a truncated tnpA transposase. Comparison of 648 Irish isolates with 846 global E. faecium from 30 countries using cgMLST revealed little overlap.
CONCLUSIONS
Irish VREfm are polyclonal, yet harbour a characteristic plasmid-located vanA region with multiple IS1216E insertions that may facilitate spread.
背景
万古霉素耐药粪肠球菌（VREfm）可引起多种医院感染。在过去十年中，爱尔兰的侵袭性 VREfm 感染率一直是欧洲最高的国家之一，但对爱尔兰的 VREfm 知之甚少。
目的
研究爱尔兰 VREfm 的种群结构，通过分析 vanA 转座子区域来探索多样性，并比较爱尔兰、丹麦和全球的分离株。
方法
研究了来自爱尔兰五家医院的 648 株屎肠球菌，包括 547 例直肠筛查和 53 例血流感染（BSI）VREfm 分离株和 2017 年 6 月至 2019 年 12 月期间恢复的 48 例万古霉素敏感（VSEfm）BSI 分离株。使用 WGS 和核心基因组 MLST（cgMLST）来评估种群结构。通过 Illumina 短读和 Oxford Nanopore Technologies 长读序列的混合组装来解析 vanA 周围的遗传环境。
结果
所有分离株均属于医院适应的 clade A1，其中大多数（435/648）属于 MLST ST80。种群结构高度多态性；cgMLST 将 648 个分离株中的 603 个分为 51 个聚类，这些聚类包含了筛查和 BSI 分离株、来自不同医院的分离株以及 VREfm 和 VSEfm 的混合物。聚类内的分离株密切相关（平均平均≤16 个等位基因差异）。大多数（96.5%）VREfm 携带位于圆形或线性质粒上的高度相似的 vanA 区域，这些质粒上有多个 IS1216E 插入，vanA 操纵子基因的组织多样，78.6%携带截断的 tnpA 转座酶。使用 cgMLST 将 648 株爱尔兰分离株与来自 30 个国家的 846 株全球屎肠球菌进行比较，发现重叠很少。
结论
爱尔兰 VREfm 呈多态性，但携带具有多个 IS1216E 插入的特征性质粒定位 vanA 区域，这可能促进了传播。
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