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Precision identification of diverse bloodstream pathogens in the gut microbiome.
Nature Medicine ( IF 82.9 ) Pub Date : 2018-Dec-01 , DOI: 10.1038/s41591-018-0202-8
Fiona B. Tamburini , Tessa M. Andermann , Ekaterina Tkachenko , Fiona Senchyna , Niaz Banaei , Ami S. Bhatt

A comprehensive evaluation of every patient with a bloodstream infection includes an attempt to identify the infectious source. Pathogens can originate from various places, such as the gut microbiota, skin and the external environment. Identifying the definitive origin of an infection would enable precise interventions focused on management of the source1,2. Unfortunately, hospital infection control practices are often informed by assumptions about the source of various specific pathogens; if these assumptions are incorrect, they lead to interventions that do not decrease pathogen exposure3. Here, we develop and apply a streamlined bioinformatic tool, named StrainSifter, to match bloodstream pathogens precisely to a candidate source. We then leverage this approach to interrogate the gut microbiota as a potential reservoir of bloodstream pathogens in a cohort of hematopoietic cell transplantation recipients. We find that patients with Escherichia coli and Klebsiella pneumoniae bloodstream infections have concomitant gut colonization with these organisms, suggesting that the gut may be a source of these infections. We also find cases where typically nonenteric pathogens, such as Pseudomonas aeruginosa and Staphylococcus epidermidis, are found in the gut microbiota, thereby challenging the existing informal dogma of these infections originating from environmental or skin sources. Thus, we present an approach to distinguish the source of various bloodstream infections, which may facilitate more accurate tracking and prevention of hospital-acquired infections.

中文翻译:

精确鉴定肠道微生物组中各种血液病原体。

对每位患有血流感染的患者进行全面评估包括尝试确定感染源。病原体可以来自各个地方,例如肠道菌群,皮肤和外部环境。确定感染的确切来源将使专注于源1,2的管理的精确干预成为可能。不幸的是,医院感染控制措施通常是基于各种特定病原体来源的假设而得出的。如果这些假设不正确,则将导致干预措施不会减少病原体的暴露3。在这里,我们开发并应用了名为StrainSifter的简化的生物信息学工具,以将血液中的病原体精确匹配到候选来源。然后,我们利用这种方法来询问肠道菌群,将其作为造血细胞移植受者队列中潜在的血流病原体库。我们发现大肠埃希菌和肺炎克雷伯菌血流感染的患者伴有这些生物体的肠道定植,表明肠道可能是这些感染的来源。我们还发现在肠道菌群中发现典型的非肠胃病原体,例如铜绿假单胞菌和表皮葡萄球菌的情况,从而挑战了源自环境或皮肤来源的这些感染的现有非正式教条。因此,
更新日期:2018-10-16
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