Table 7_Genomic characterization of vancomycin-resistant Enterococcus faecium and van-carrying mobile genetic elements in a tertiary hospital in northeastern China.xlsx

BackgroundVancomycin resistant Enterococcus faecium (VREfm) poses a significant healthcare challenge due to its multidrug resistance and genomic plasticity. Vancomycin resistance is commonly mediated by van gene clusters located on transposons, which are often associated with plasmids. Methods19 VREfm isolates were collected from different departments of the First Hospital of Jilin University between 2019 and 2024. Whole-genome sequencing (WGS) was performed on the strains for comprehensive genomic analysis. Multilocus sequence typing (MLST) was used to determine the sequence types of the strains. Plasmids were grouped based on Mash distance, and plasmid content was analyzed using the MOB-suite tool. Genome-wide comparisons and average nucleotide identity (ANI) analysis were conducted using FastANI. The TnCentral database was used to analyze resistance-associated transposons. The objective was to characterize the genomic diversity of VREfm isolates and the genetic contexts of van-carrying plasmids and transposons. ResultsAmong the 19 VREfm isolates, vanA was detected in 16 isolates, while vanM was identified in 3 isolates. MLST analysis revealed five sequence types (ST17, ST68, ST78, ST80, and ST547) with distinct temporal distributions. ST17 and ST68 were more frequently observed among isolates collected between 2019 and 2022, whereas ST78 was more common among isolates collected in 2023–2024 and was associated with multiple plasmid types. These observations suggest differences in lineage composition and plasmid backgrounds across the sampling period. Plasmidome analysis identified 19 plasmid groups, with resistance genes mainly concentrated in four major groups, some of which were shared across different sequence types. Notably, several resistance plasmids lacked functional replicons, suggesting plasmid fragmentation events. Transposon analysis revealed substantial structural diversity among Tn1546 variants, including insertions, deletions, and rearrangements, highlighting the complexity of vanA- and vanM-associated mobile genetic elements across different plasmid and clonal backgrounds. ConclusionThis study provides genomic insights into the diversity and relatedness of VREfm isolates in a tertiary hospital over a 5-year period. The findings describe the diversity of sequence types, plasmid backbones, and van-associated mobile genetic elements within this hospital collection.背景：耐万古霉素屎肠球菌（Vancomycin resistant Enterococcus faecium, VREfm）因其多重耐药性与基因组可塑性，已成为极具挑战性的临床医疗难题。万古霉素耐药性通常由位于转座子上的van基因簇介导，而这类转座子常与质粒相关联。 方法：本研究于2019年至2024年间，从吉林大学第一医院不同科室收集了19株VREfm分离株。对所有菌株开展全基因组测序（Whole-genome sequencing, WGS）以进行全面的基因组分析；采用多位点序列分型（Multilocus sequence typing, MLST）确定菌株的序列型别。基于Mash距离对质粒进行分组，并通过MOB-suite工具分析质粒携带的遗传物质。使用FastANI工具开展全基因组比较与平均核苷酸同源性（average nucleotide identity, ANI）分析；依托TnCentral数据库分析与耐药相关的转座子。本研究旨在解析VREfm分离株的基因组多样性，以及携带van基因的质粒与转座子的遗传背景。 结果：在19株VREfm分离株中，16株检出vanA基因，3株检出vanM基因。MLST分析共鉴定出5种序列型别（ST17、ST68、ST78、ST80与ST547），且各型别呈现出明显的时间分布特征：2019年至2022年收集的分离株以ST17和ST68为主，而2023年至2024年的分离株则以ST78更为常见，且该型别与多种质粒型别相关。上述结果提示，在采样周期内，菌株的谱系组成与质粒背景存在差异。质粒组学分析共鉴定出19个质粒群，耐药基因主要集中于4个主要质粒群，其中部分质粒群可在不同序列型别的菌株中共享。值得注意的是，部分耐药质粒缺乏功能性复制子，提示存在质粒片段化事件。转座子分析显示，Tn1546变异体存在丰富的结构多样性，包括插入、缺失与重排现象，这表明不同质粒与克隆背景下，与vanA和vanM相关的移动遗传元件具有较高复杂性。 结论：本研究针对某三级医院5年间收集的VREfm分离株，从基因组层面解析了其多样性与亲缘关系。研究结果阐明了该医院分离株的序列型别、质粒骨架以及与van基因相关的移动遗传元件的多样性特征。