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Abstract：
BACKGROUND: Surveillance systems revealed that the prevalence of vancomycin-resistant Enterococcus faecium (VREfm) has increased. We aim to investigate the epidemiological and genomic characteristics of VREfm in China.
METHODS: We collected 20,747 non-redundant E. faecium isolates from inpatients across 19 hospitals in six provinces between January 2018 and June 2023. VREfm was confirmed by antimicrobial susceptibility testing. The prevalence was analyzed using changepoint package in R. Genomic characteristics were explored by whole-genome sequencing.
RESULTS: 5.59% (1159/20,747) of E. faecium isolates were resistant to vancomycin. The prevalence of VREfm increased in Guangdong province from 5% before 2021 to 20-50% in 2023 (p < 0.0001), but not in the other five provinces. Two predominant clones before 2021, ST17 and ST78, were substituted by an emerging clone, ST80, from 2021 to 2023 (88.63%, 195/220). All ST80 VREfm from Guangdong formed a single lineage (SC11) and were genetically distant from the ST80 VREfm from other countries, suggesting a regional outbreak. All ST80 VREfm in SC11 carried a new type of plasmid harbouring a vanA cassette, which was embedded in a Tn1546-like structure flanked by IS1678 and ISL3. However, no conjugation-related gene was detected and no transconjugant was obtained in conjugation experiment, indicating that the outbreak of ST80 VREfm could be attributed to clonal transmission.
CONCLUSIONS: We revealed an ongoing outbreak of ST80 VREfm with a new vanA-harbouring plasmid in Guangdong, China. This clone has also been identified in other provinces and countries, foreboding a risk of wider spreading shortly. Continuous surveillance is needed to inform public health interventions.
METHODS: We collected 20,747 non-redundant E. faecium isolates from inpatients across 19 hospitals in six provinces between January 2018 and June 2023. VREfm was confirmed by antimicrobial susceptibility testing. The prevalence was analyzed using changepoint package in R. Genomic characteristics were explored by whole-genome sequencing.
RESULTS: 5.59% (1159/20,747) of E. faecium isolates were resistant to vancomycin. The prevalence of VREfm increased in Guangdong province from 5% before 2021 to 20-50% in 2023 (p < 0.0001), but not in the other five provinces. Two predominant clones before 2021, ST17 and ST78, were substituted by an emerging clone, ST80, from 2021 to 2023 (88.63%, 195/220). All ST80 VREfm from Guangdong formed a single lineage (SC11) and were genetically distant from the ST80 VREfm from other countries, suggesting a regional outbreak. All ST80 VREfm in SC11 carried a new type of plasmid harbouring a vanA cassette, which was embedded in a Tn1546-like structure flanked by IS1678 and ISL3. However, no conjugation-related gene was detected and no transconjugant was obtained in conjugation experiment, indicating that the outbreak of ST80 VREfm could be attributed to clonal transmission.
CONCLUSIONS: We revealed an ongoing outbreak of ST80 VREfm with a new vanA-harbouring plasmid in Guangdong, China. This clone has also been identified in other provinces and countries, foreboding a risk of wider spreading shortly. Continuous surveillance is needed to inform public health interventions.
摘要：
■监测系统显示，耐万古霉素屎肠球菌（VREfm）的患病率有所增加。我们的目的是调查中国VREfm的流行病学和基因组特征。
■我们在2018年1月至2023年6月期间从6个省的19家医院的住院患者中收集了20747种非冗余屎肠球菌分离株。VREfm通过抗菌药物敏感性试验证实。使用R中的变化点软件包分析患病率。通过全基因组测序探索基因组特征。
■5.59%(1159/20747)的屎肠球菌分离株对万古霉素耐药。广东省的VREfm患病率从2021年之前的5%上升到2023年的20%-50%(p<0.0001),但不是在其他五个省。2021年之前的两个主要克隆，ST17和ST78，被一个新兴的克隆所取代，ST80，从2021年到2023年（88.63%，195/220）。所有来自广东的ST80VREfm形成一个单一的谱系(SC11)，并且在遗传上与来自其他国家的ST80VREfm相距遥远，表明是区域性爆发。SC11中的所有ST80VREfm都带有一种新型的带有vanA盒的质粒，嵌入在IS1678和ISL3两侧的Tn1546结构中。然而,在接合实验中未检测到接合相关基因，也未获得跨接合体，表明ST80VREfm的爆发可能归因于克隆传播。
■我们发现在广东正在爆发带有新的vanA携带质粒的ST80VREfm，中国。在其他省份和国家也发现了这种克隆，预示着很快会有更广泛扩散的风险。需要持续监测以告知公共卫生干预措施。
■我们在2018年1月至2023年6月期间从6个省的19家医院的住院患者中收集了20747种非冗余屎肠球菌分离株。VREfm通过抗菌药物敏感性试验证实。使用R中的变化点软件包分析患病率。通过全基因组测序探索基因组特征。
■5.59%(1159/20747)的屎肠球菌分离株对万古霉素耐药。广东省的VREfm患病率从2021年之前的5%上升到2023年的20%-50%(p<0.0001),但不是在其他五个省。2021年之前的两个主要克隆，ST17和ST78，被一个新兴的克隆所取代，ST80，从2021年到2023年（88.63%，195/220）。所有来自广东的ST80VREfm形成一个单一的谱系(SC11)，并且在遗传上与来自其他国家的ST80VREfm相距遥远，表明是区域性爆发。SC11中的所有ST80VREfm都带有一种新型的带有vanA盒的质粒，嵌入在IS1678和ISL3两侧的Tn1546结构中。然而,在接合实验中未检测到接合相关基因，也未获得跨接合体，表明ST80VREfm的爆发可能归因于克隆传播。
■我们发现在广东正在爆发带有新的vanA携带质粒的ST80VREfm，中国。在其他省份和国家也发现了这种克隆，预示着很快会有更广泛扩散的风险。需要持续监测以告知公共卫生干预措施。
