Microbiology Research Unit, Dublin Dental University Hospital, University of Dublin, Trinity College Dublin, Dublin, Ireland.
Department of Clinical Microbiology, St James's Hospital, Dublin, Ireland; National MRSA Reference Laboratory, St James's Hospital, Dublin, Ireland.
J Hosp Infect. 2024 Sep;151:11-20. doi: 10.1016/j.jhin.2024.06.002. Epub 2024 Jun 27.
Vancomycin-resistant Enterococcus faecium (VREfm) are significant nosocomial pathogens. Sequence type (ST) 80 vanA-encoding VREfm predominate in Irish hospitals, but their transmission is poorly understood.
To investigate transmission and persistence of predominant complex type (CT) VREfm in two wards of an Irish hospital (H1) using whole-genome sequencing, and their intra- and inter-hospital dissemination.
Rectal screening (N = 330, September 2019 to December 2022) and environmental (N = 48, November 2022 to December 2022) E. faecium were investigated. Isolate relatedness was assessed by core-genome multi-locus sequence typing (cgMLST) and core-genome single nucleotide polymorphism (cgSNP) analysis. Likely transmission chains were identified using SeqTrack (https://graphsnp.fordelab.com/graphsnp) using cgSNP data and recovery location. Well-characterized E. faecium (N = 908) from seven Irish hospitals including H1 (June 2017 to July 2022) were also investigated.
Conventional MLST assigned isolates to nine STs (ST80, 82%). cgMLST identified three predominant ST80 CTs (CT2933, CT2932 and CT1916) (55% of isolates) of related isolates (≤20 allelic differences). cgSNP analysis differentiated these CTs into multiple distinct closely related genomic clusters (≤10 cgSNPs). Parisimonious network construction identified 55 likely inter- and intra-ward transmissions with epidemiological support between patients ≤30 days involving 73 isolates (≤10 cgSNPs) from seven genomic clusters. Numerous other likely transmissions over longer time periods without evident epidemiological links were identified, suggesting persistence and unidentified reservoirs contribute to dissemination. The three CTs predominated among E. faecium (N = 1286) in seven hospitals, highlighting inter-hospital spread without known epidemiological links.
This study revealed the long-term intra- and inter-hospital dominance of three major CT ST80 VREfm lineages, widespread transmission and persistence, implicating unidentified reservoirs.
耐万古霉素粪肠球菌（VREfm）是重要的医院获得性病原体。在爱尔兰的医院中，主要流行的是携带 vanA 基因的序列型 80（ST80）型 vanA 编码的 VREfm，但对其传播方式了解甚少。
使用全基因组测序研究爱尔兰一家医院（H1）的两个病房中主要复合类型（CT）VREfm 的传播和持续情况，并研究其在医院内和医院间的传播情况。
对 2019 年 9 月至 2022 年 12 月期间的 330 名直肠筛查患者（N=330）和 2022 年 11 月至 12 月期间的 48 名环境 E. faecium 进行了调查。使用核心基因组多位点序列分型（cgMLST）和核心基因组单核苷酸多态性（cgSNP）分析评估分离株的亲缘关系。使用 SeqTrack（https://graphsnp.fordelab.com/graphsnp），通过 cgSNP 数据和恢复位置，使用 cgSNP 数据识别可能的传播链。还对包括 H1 在内的爱尔兰七家医院的 908 株特征明确的粪肠球菌（2017 年 6 月至 2022 年 7 月）进行了调查。
传统 MLST 将分离株分为 9 种 ST（80、82%）。cgMLST 确定了三种主要的 ST80 CT（CT2933、CT2932 和 CT1916）（55%的分离株），这些 CT 相关的分离株（≤20 个等位基因差异）。cgSNP 分析将这些 CT 分为多个密切相关的基因组簇（≤10 个 cgSNPs）。通过最小生成树网络构建，在≤30 天的患者之间，识别出 55 个可能的病房内和病房间传播事件，涉及来自七个基因组簇的 73 个分离株（≤10 个 cgSNPs），这些传播事件有流行病学支持。还发现了许多其他可能的长时间传播事件，没有明显的流行病学联系，这表明持续性和未识别的储源可能会导致传播。这三种 CT 在七家医院的 1286 株粪肠球菌中占优势，突显了无已知流行病学联系的医院间传播。
本研究揭示了三种主要 CT ST80 VREfm 谱系在医院内和医院间的长期优势、广泛传播和持续存在，提示存在未识别的储源。
