Abstract：
BACKGROUND: 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.
OBJECTIVE: 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.
METHODS: Rectal screening (N=330, September 2019-December 2022) and environmental (N=48, November 2022-December 2022) E. faecium were investigated. Isolate relatedness was assessed by core-genome multilocus 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-characterised E. faecium (N=908) from seven Irish hospitals including H1 (June 2017-July 2022) were also investigated.
RESULTS: 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=1,286) in seven hospitals, highlighting inter-hospital spread without known epidemiological links.
CONCLUSIONS: 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.
OBJECTIVE: 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.
METHODS: Rectal screening (N=330, September 2019-December 2022) and environmental (N=48, November 2022-December 2022) E. faecium were investigated. Isolate relatedness was assessed by core-genome multilocus 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-characterised E. faecium (N=908) from seven Irish hospitals including H1 (June 2017-July 2022) were also investigated.
RESULTS: 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=1,286) in seven hospitals, highlighting inter-hospital spread without known epidemiological links.
CONCLUSIONS: 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.
摘要：
背景：耐万古霉素的屎肠球菌（VREfm）是重要的院内病原体。序列类型（ST）80vanA编码VREfm在爱尔兰医院中占主导地位，但是对它们的传播知之甚少。
目的：使用全基因组测序研究爱尔兰医院（H1）的两个病房中主要复合型（CT）VREfm的传播和持久性，以及它们在医院内和医院间的传播。
方法：进行直肠筛查（N=330，2019年9月-2022年12月）和环境（N=48，2022年11月-2022年12月）。通过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）分析评估分离株的相关性。可能的传输链是使用SeqTrack(https://graphsnp。fordelab.com/graphsnp)使用cgSNP数据和恢复位置。还调查了包括H1（2017年6月至2022年7月）在内的7家爱尔兰医院的特征良好的屎肠球菌（N=908）。
结果：常规MLST将分离株分配给9个ST（ST80，82%）。cgMLST鉴定了相关分离株（≤20个等位基因差异）的三个主要ST80CT（CT2933，CT2932和CT1916）（占分离株的55％）。cgSNP分析将这些CT分成多个不同的密切相关的基因组簇(≤10个cgSNP)。Parisionious网络构建确定了55种可能的行间和行内传播，在患者≤30天之间提供流行病学支持，涉及来自7个基因组簇的73个分离株（≤10个cgSNP）。确定了许多其他可能在较长时间内传播，而没有明显的流行病学联系，表明持久性和身份不明的水库有助于传播。在七家医院中，三个CT在屎肠球菌(N=1,286)中占主导地位，强调没有已知流行病学联系的医院间传播。
结论：这项研究揭示了三种主要CTST80VREfm谱系的长期院内和院内优势，广泛传播和持久性，牵涉到身份不明的水库。
目的：使用全基因组测序研究爱尔兰医院（H1）的两个病房中主要复合型（CT）VREfm的传播和持久性，以及它们在医院内和医院间的传播。
方法：进行直肠筛查（N=330，2019年9月-2022年12月）和环境（N=48，2022年11月-2022年12月）。通过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）分析评估分离株的相关性。可能的传输链是使用SeqTrack(https://graphsnp。fordelab.com/graphsnp)使用cgSNP数据和恢复位置。还调查了包括H1（2017年6月至2022年7月）在内的7家爱尔兰医院的特征良好的屎肠球菌（N=908）。
结果：常规MLST将分离株分配给9个ST（ST80，82%）。cgMLST鉴定了相关分离株（≤20个等位基因差异）的三个主要ST80CT（CT2933，CT2932和CT1916）（占分离株的55％）。cgSNP分析将这些CT分成多个不同的密切相关的基因组簇(≤10个cgSNP)。Parisionious网络构建确定了55种可能的行间和行内传播，在患者≤30天之间提供流行病学支持，涉及来自7个基因组簇的73个分离株（≤10个cgSNP）。确定了许多其他可能在较长时间内传播，而没有明显的流行病学联系，表明持久性和身份不明的水库有助于传播。在七家医院中，三个CT在屎肠球菌(N=1,286)中占主导地位，强调没有已知流行病学联系的医院间传播。
结论：这项研究揭示了三种主要CTST80VREfm谱系的长期院内和院内优势，广泛传播和持久性，牵涉到身份不明的水库。
