The role of mobile genetic elements in the typing of nosocomial VREfm outbreak isolates of a successful MLST: ST117 cluster type 24

Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The rapid emergence of specific VREfm lineages makes it challenging to distinguish outbreak isolates solely based on their core genome. Here, we explored if characterisation of mobile genetic elements could be useful for molecular epidemiology and typing of VREfm isolates belonging to the same genetic background. Materials/methods: The genomes of 39 VREfm isolates from patients and environmental samples from 2011 to 2017 were sequenced using short-read sequencing. Two representative isolates were also sequenced using long-read sequencing, to close the genome sequences. Molecular typing by core genome MLST (cgMLST) and pangenome analysis were performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins and prophages. Results: All of the investigated isolates belonged to ST117 and cluster type (CT) 24. cgMLST analysis showed that the isolates could be divided into two distinct genetic clades. The vanB-carrying transposon Tn1549 was present in all isolates. However, its genomic position differed between strains depending on the outbreak event. The pangenome analysis revealed differences in the accessory genes mainly related to prophages and bacteriocins content, while a similar profile was observed for known predicted virulence and resistance genes.Conclusions: In case of closely related isolates sharing a similar genetic background, a detailed analysis of mobile genetic elements and the integration point of the vanB-carrying transposon allows to achieve a higher discriminatory power compared to cgMLST alone. Thus, enabling identification of epidemiological links among hospitalised patients.

耐万古霉素粪肠球菌（Vancomycin-resistant Enterococcus faecium, VREfm）是一类重要的院内感染病原菌。特定VREfm克隆谱系的快速出现，使得仅通过核心基因组序列区分暴发分离株颇具挑战。本研究旨在探讨移动遗传元件的特征分析，是否可用于同一遗传背景下VREfm分离株的分子流行病学研究与分型。材料与方法：本研究对2011至2017年间采集自患者与环境样本的39株VREfm分离株进行了短读长测序；同时选取2株代表性分离株采用长读长测序，以完成全基因组的闭合组装。对从头组装的基因组序列开展核心基因组多位点序列分型（core genome MLST, cgMLST）和泛基因组分析，并筛查已知的预测毒力因子、抗菌药物耐药基因、细菌素及前噬菌体。结果：所有受试分离株均归属于ST117序列型与CT24聚类型。cgMLST分析显示，分离株可划分为两个独立的遗传进化分支。所有分离株均携带vanB基因的转座子Tn1549，但其基因组整合位点因暴发事件不同而存在差异。泛基因组分析显示，附属基因的差异主要与前噬菌体和细菌素含量相关，而已知的预测毒力基因与耐药基因则呈现相似的分布特征。结论：对于遗传背景相似的密切相关分离株，相较于单独采用cgMLST分型，对移动遗传元件及vanB携带转座子的整合位点进行详细分析，可获得更高的分型分辨能力，从而能够明确住院患者间的流行病学关联。