Abstract：
Understanding the role of fecal microbiota transplantation (FMT) in the decolonization of multidrug-resistant organisms (MDRO) is critical. Specifically, little is known about virome changes in MDRO-infected subjects treated with FMT. Using shotgun metagenomic sequencing, we characterized longitudinal dynamics of the gut virome and bacteriome in three recipients who successfully decolonized carbapenem-resistant Enterobacteriaceae (CRE), including Klebsiella spp. and Escherichia coli, after FMT. We observed large shifts of the fecal bacterial microbiota resembling a donor-like community after transfer of a fecal microbiota dominated by the genus Ruminococcus. We found a substantial expansion of Klebsiella phages after FMT with a concordant decrease of Klebsiella spp. and striking increase of Escherichia phages in CRE E. coli carriers after FMT. We also observed the CRE elimination and similar evolution of Klebsiella phage in mice, which may play a role in the collapse of the Klebsiella population after FMT. In summary, our pilot study documented bacteriome and virome alterations after FMT which mediate many of the effects of FMT on the gut microbiome community. IMPORTANCE Fecal microbiota transplantation (FMT) is an effective treatment for multidrug-resistant organisms; however, introducing a complex mixture of microbes also has unknown consequences for landscape features of gut microbiome. We sought to understand bacteriome and virome alterations in patients undergoing FMT to treat infection with carbapenem-resistant Enterobacteriaceae. This finding indicates that transkingdom interactions between the virome and bacteriome communities may have evolved in part to support efficient FMT for treating CRE.
摘要：
了解粪便微生物群移植（FMT）在多药耐药生物（MDRO）的去定植中的作用至关重要。具体来说,对FMT治疗的MDRO感染受试者的病毒学变化知之甚少。使用鸟枪宏基因组测序，我们描述了成功脱色耐碳青霉烯的肠杆菌（CRE）的三个接受者的肠道病毒体和细菌群的纵向动力学，包括克雷伯菌属。和大肠杆菌，FMT之后。我们观察到，在转移了以Ruminococus属为主的粪便微生物区后，粪便细菌微生物区有很大的变化，类似于供体样群落。我们发现FMT后克雷伯菌噬菌体的大量扩张，克雷伯菌属的数量也随之减少。FMT后CRE大肠杆菌携带者中大肠杆菌噬菌体的急剧增加。我们还观察到克雷伯菌噬菌体在小鼠中的CRE消除和类似进化，这可能在FMT后克雷伯氏菌种群的崩溃中起作用。总之,我们的初步研究记录了FMT后细菌组和病毒组的改变,这些改变介导了FMT对肠道微生物群落的许多影响.重要性粪便微生物移植（FMT）是一种有效的治疗多药耐药生物;然而，引入复杂的微生物混合物对肠道微生物组的景观特征也有未知的后果。我们试图了解接受FMT治疗耐碳青霉烯类肠杆菌感染的患者的细菌组和病毒学改变。这一发现表明，病毒体和细菌群落之间的越界相互作用可能已经进化，以部分支持有效的FMT治疗CRE。
