Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance.
Quantifying acquisition and transmission of Enterococcus faecium using genomic surveillance.
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DOI：
10.1038/s41564-020-00806-7
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发表时间：
2021-01
影响因子：
28.3
通讯作者：
Peacock SJ
中科院分区：
文献类型：
--
作者：
Gouliouris T;Coll F;Ludden C;Blane B;Raven KE;Naydenova P;Crawley C;Török ME;Enoch DA;Brown NM;Harrison EM;Parkhill J;Peacock SJ
医院内获得和传播耐万古霉素屎肠球菌 (VREfm) 是住院患者携带屎肠球菌的驱动因素，而这又是免疫功能低下患者侵袭性感染的危险因素。在这里，我们使用序列驱动的方法提供了整个样本患者群体中屎肠球菌传播的全面情况。我们前瞻性地识别并跟踪了英国一家医院收治的 149 名血液病患者 6 个月。定期采集患者粪便（n=376）和环境拭子（n=922）并培养屎肠球菌。我们对 1,560 个分离株（1,001 个粪便、559 个环境）进行了测序，并将基因组分析重点放在医院适应型 A1 分支中的 1,477 个分离株（95%）上。在提供 ≥2 个粪便样本的 101 名患者中，根据培养结果，有 40 名患者 (40%) 在入院后出现了粪肠球菌携带，而根据基因组分析 (73% VREfm)，有 64 名患者 (63%) 出现了粪肠球菌携带。 922 份环境拭子中有一半（447 份，48%）呈 VREfm 阳性。网络分析显示，在 111 名 A1 分支呈阳性的患者中，有 67 名患者与至少 1 名其他患者和/或其直接环境有很强的流行病学和基因组联系，支持医院内传播。六名患者 (3.4%) 因自身肠道定植菌株而发生侵袭性屎肠球菌感染，其中一半患者在医院内获得了感染分离株。两种信息学方法（定义系统发育簇的亚型分类和传播 SNP 截止点的开发）是我们分析的核心，这两种方法都将为将来将屎肠球菌测序转化为常规疫情检测和调查提供信息。总之，我们表明，医院适应的屎肠球菌谱系的携带和环境污染在我们的研究人群中是高度流行的，需要改进感染控制措施来降低医院感染率。
Nosocomial acquisition and transmission of vancomycin-resistant Enterococcus faecium (VREfm) is the driver for E. faecium carriage in hospitalized patients which, in turn, is a risk factor for invasive infection in immune-compromised patients. Here, we provide a comprehensive picture of E. faecium transmission in an entire sampled patient population using a sequence-driven approach. We prospectively identified and followed 149 hematology patients admitted to a hospital in England for 6 months. Patient stools (n=376) and environmental swabs (n=922) were taken at intervals and cultured for E. faecium. We sequenced 1,560 isolates (1,001 stool, 559 environment) and focused our genomic analyses on 1,477 isolates (95%) in the hospital-adapted clade A1. Out of 101 patients who provided ≥2 stool samples, forty (40%) developed E. faecium carriage after admission based on culture, compared with 64 patients (63%) based on genomic analysis (73% VREfm). Half of 922 environmental swabs (447, 48%) were positive for VREfm. Network analysis showed that, out of 111 patients positive for the A1 clade, 67 had strong epidemiological and genomic links with at least 1 other patient and/or their direct environment, supporting nosocomial transmission. Six patients (3.4%) developed an invasive E. faecium infection from their own gut-colonizing strain, which was preceded by nosocomial acquisition of the infecting isolate in half of these. Two informatics approaches (subtype categorization to define phylogenetic clusters and the development of a SNP cut-off for transmission) were central to our analyses, both of which will inform the future translation of E. faecium sequencing into routine outbreak detection and investigation. In conclusion, we showed that carriage and environmental contamination by the hospital-adapted E. faecium lineage was hyperendemic in our study population and that improved infection control measures will be needed to reduce hospital acquisition rates.
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影响因子：
14.9
作者：
Tonkin-Hill, Gerry;Lees, John A.;Corander, Jukka
通讯作者：
Corander, Jukka
影响因子：
17.1
作者：
Pidot, Sacha J.;Gao, Wei;Stinear, Timothy P.
通讯作者：
Stinear, Timothy P.
影响因子：
4.9
作者：
Liese, Jan;Schuele, Leonard;Peter, Silke
通讯作者：
Peter, Silke
DOI：
10.1093/bioinformatics/btq675
发表时间：
2011-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Smoot ME;Ono K;Ruscheinski J;Wang PL;Ideker T
通讯作者：
Ideker T
影响因子：
5.2
作者：
Pinholt, Mette;Bayliss, Sion C.;Westh, Henrik
通讯作者：
Westh, Henrik