Background Recognition of nosocomial outbreaks with antimicrobial resistant (AMR) pathogens and appropriate infection prevention measures are essential to limit the consequences of AMR pathogens to patients in hospitals. Because unrelated, but genetically similar AMR pathogens may circulate simultaneously, rapid high-resolution molecular typing methods are needed for outbreak management. We compared amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) during a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VRE) that spanned 5 months. Methods Hierarchical clustering of AFLP profiles was performed using unweighted pair-grouping and similarity coefficients were calculated with Pearson correlation. For WGS-analysis, core single nucleotide polymorphisms (SNPs) were used to calculate the pairwise distance between isolates, construct a maximum likelihood phylogeny and establish a cut-off for relatedness of epidemiologically linked VRE isolates. SNP-variations in the vanB gene cluster were compared to increase the comparative resolution. Technical replicates of 2 isolates were sequenced to determine the number of core-SNPs derived from random sequencing errors. Results Of the 721 patients screened for VRE carriage, AFLP assigned isolates of 22 patients to the outbreak cluster. According to WGS, all 22 isolates belonged to ST117 but only 21 grouped in a tight phylogenetic cluster and carried vanB resistance gene clusters. Sequencing of technical replicates showed that 4-5 core-SNPs were derived by random sequencing errors. The cut-off for relatedness of epidemiologically linked VRE isolates was established at ≤7 core-SNPs. The discrepant isolate was separated from the index isolate by 61 core-SNPs and the vanB gene cluster was absent. In AFLP analysis this discrepant isolate was indistinguishable from the other outbreak isolates, forming a cluster with 92% similarity (cut-off for identical isolates ≥90%). The inclusion of the discrepant isolate in the outbreak resulted in the screening of 250 patients and quarantining of an entire ward. Conclusion AFLP was a rapid and affordable screening tool for characterising hospital VRE outbreaks. For in-depth understanding of the outbreak WGS was needed. Compared to AFLP, WGS provided higher resolution typing of VRE isolates with implications for outbreak management.

中文翻译：

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扩增片段长度多态性和全基因组测序：万古霉素耐药肠球菌医院暴发调查方法的比较。

背景 识别抗菌素耐药 (AMR) 病原体的医院暴发并采取适当的感染预防措施对于限制 AMR 病原体对医院患者造成的后果至关重要。由于不相关但基因相似的 AMR 病原体可能同时传播，因此需要快速高分辨率分子分型方法来进行疫情管理。我们比较了历时 5 个月的耐万古霉素屎肠球菌 (VRE) 院内爆发期间的扩增片段长度多态性 (AFLP) 和全基因组测序 (WGS)。方法使用未加权配对对 AFLP 概况进行层次聚类，并使用 Pearson 相关性计算相似系数。对于 WGS 分析，核心单核苷酸多态性 (SNP) 用于计算分离株之间的成对距离、构建最大似然系统发育并建立流行病学相关 VRE 分离株的相关性截止值。比较 vanB 基因簇中的 SNP 变异以提高比较分辨率。对 2 个分离株进行技术重复测序，以确定因随机测序错误而产生的核心 SNP 数量。结果 在筛查 VRE 携带情况的 721 名患者中，AFLP 将 22 名患者的分离株分配至爆发群。根据 WGS，所有 22 个分离株均属于 ST117，但只有 21 个分离株属于紧密的系统发育簇并携带 vanB 抗性基因簇。技术重复的测序表明，4-5 个核心 SNP 是由随机测序错误产生的。流行病学相关的 VRE 分离株的相关性截止点设定为 ≤7 个核心 SNP。差异分离株与指示分离株之间有 61 个核心 SNP，并且 vanB 基因簇不存在。在 AFLP 分析中，这种差异分离株与其他暴发分离株无法区分，形成相似度为 92% 的簇（相同分离株的截止值≥90%）。由于此次疫情中包含了不符的菌株，因此对 250 名患者进行了筛查，并对整个病房进行了隔离。结论 AFLP 是一种快速且经济实惠的筛查工具，可用于描述医院 VRE 暴发的特征。为了深入了解疫情爆发，需要进行全基因组测序。与 AFLP 相比，WGS 提供了更高分辨率的 VRE 分离株分型，对疫情管理具有重要意义。