Abstract：
BACKGROUND: vanB-carrying vancomycin-resistant Enterococcus faecium (VREfm) of the sequence types 80 (ST80) and ST117 have dominated Germany in the past. In 2020, our hospital witnessed a sharp increase in the proportion of vanA-positive VREfm.
OBJECTIVE: To attempt to understand these dynamics through whole-genome sequencing (WGS) and analysis of nosocomial transmissions.
METHODS: At our hospital, the first VREfm isolate per patient, treated during 2020, was analysed retrospectively using specific vanA/vanB PCR, WGS, multi-locus sequence typing (MLST), and core-genome (cg) MLST. Epidemiologic links between VRE-positive patients were assessed using hospital occupancy data.
RESULTS: Isolates from 319 out of 356 VREfm patients were available for WGS, of which 181 (56.7%) fulfilled the ECDC definition for nosocomial transmission. The high load of nosocomial cases is reflected in the overall high clonality rate with only three dominating sequence (ST) and complex types (CT), respectively: the new emerging strain ST1299 (100% vanA, 77.4% CT1903), and the well-known ST80 (90.0% vanB, 81.0% CT1065) and ST117 (78.0% vanB, 65.0% CT71). The ST1299 isolates overall, and the subtype CT1903 in particular, showed high isolate clonality, which demonstrates impressively high spreading potential. Overall, 152 out of 319 isolates had an allelic cgMLST difference of ≤3 to another, including 91 (59.6%) ST1299. Occupancy data identified shared rooms (3.7%), shared departments (6.2%), and VRE-colonized prior room occupants (0.6%) within 30 days before diagnosis as solid epidemiological links.
CONCLUSIONS: A new emerging VREfm clone, ST1299/CT1903/vanA, dominated our institution in 2020 and has been an important driver of the increasing VREfm rates.
OBJECTIVE: To attempt to understand these dynamics through whole-genome sequencing (WGS) and analysis of nosocomial transmissions.
METHODS: At our hospital, the first VREfm isolate per patient, treated during 2020, was analysed retrospectively using specific vanA/vanB PCR, WGS, multi-locus sequence typing (MLST), and core-genome (cg) MLST. Epidemiologic links between VRE-positive patients were assessed using hospital occupancy data.
RESULTS: Isolates from 319 out of 356 VREfm patients were available for WGS, of which 181 (56.7%) fulfilled the ECDC definition for nosocomial transmission. The high load of nosocomial cases is reflected in the overall high clonality rate with only three dominating sequence (ST) and complex types (CT), respectively: the new emerging strain ST1299 (100% vanA, 77.4% CT1903), and the well-known ST80 (90.0% vanB, 81.0% CT1065) and ST117 (78.0% vanB, 65.0% CT71). The ST1299 isolates overall, and the subtype CT1903 in particular, showed high isolate clonality, which demonstrates impressively high spreading potential. Overall, 152 out of 319 isolates had an allelic cgMLST difference of ≤3 to another, including 91 (59.6%) ST1299. Occupancy data identified shared rooms (3.7%), shared departments (6.2%), and VRE-colonized prior room occupants (0.6%) within 30 days before diagnosis as solid epidemiological links.
CONCLUSIONS: A new emerging VREfm clone, ST1299/CT1903/vanA, dominated our institution in 2020 and has been an important driver of the increasing VREfm rates.
摘要：
背景：VanB携带耐万古霉素的屎肠球菌（VREfm）的序列类型80[ST80]和ST117在过去占主导地位。2020年，我院VNA阳性VREfm比例大幅上升。我们试图通过全基因组测序（WGS）和医院传播分析来了解这些动态。
方法：在我们医院，每位患者的第一个VREfm分离株，在2020年期间接受治疗，使用特异性vanA/vanBPCR进行回顾性分析，WGS,多位点序列分型（MLST），和核心基因组(cg)MLST。使用医院入住数据评估VRE阳性患者之间的流行病学联系。
结果：来自356名VREfm患者中的319名的分离株可用于WGS，其中181人(56.7%)符合ECDC对医院传播的定义。医院病例的高负荷反映在总体克隆率高，只有三种主要序列（ST）和复杂类型（CT），分别：新出现的菌株ST1299(100%vanA，77.4%CT1903)，和著名的ST80(90.0%vanB，81.0%CT1065)和ST117(78.0%vanB，65.0%CT71）。ST1299分离整体，特别是CT1903亚型，显示出高分离克隆性，这显示了令人印象深刻的高传播潜力。总的来说,319个分离株中的152个与另一个分离株的等位基因cgMLST差异≤3，包括91（59.6%）ST1299。占用数据确定共享房间(3.7%)，共享部门(6.2%)，和VRE在诊断前30天内定植的先前房间居住者（0.6％）作为坚实的流行病学联系。
结论：一个新出现的VREfm克隆，ST1299/CT1903/vanA,在2020年主导了我们的机构，并被证明是VREfm利率上升的重要驱动力。
方法：在我们医院，每位患者的第一个VREfm分离株，在2020年期间接受治疗，使用特异性vanA/vanBPCR进行回顾性分析，WGS,多位点序列分型（MLST），和核心基因组(cg)MLST。使用医院入住数据评估VRE阳性患者之间的流行病学联系。
结果：来自356名VREfm患者中的319名的分离株可用于WGS，其中181人(56.7%)符合ECDC对医院传播的定义。医院病例的高负荷反映在总体克隆率高，只有三种主要序列（ST）和复杂类型（CT），分别：新出现的菌株ST1299(100%vanA，77.4%CT1903)，和著名的ST80(90.0%vanB，81.0%CT1065)和ST117(78.0%vanB，65.0%CT71）。ST1299分离整体，特别是CT1903亚型，显示出高分离克隆性，这显示了令人印象深刻的高传播潜力。总的来说,319个分离株中的152个与另一个分离株的等位基因cgMLST差异≤3，包括91（59.6%）ST1299。占用数据确定共享房间(3.7%)，共享部门(6.2%)，和VRE在诊断前30天内定植的先前房间居住者（0.6％）作为坚实的流行病学联系。
结论：一个新出现的VREfm克隆，ST1299/CT1903/vanA,在2020年主导了我们的机构，并被证明是VREfm利率上升的重要驱动力。
