Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae

mSystems

Fen Zhang¹  Wenyi Zhu¹  Tao Zuo¹  Wenqi Lu¹  Siew C. Ng¹  Qi Su¹  Qin Liu¹  Chun Pan Cheung¹  Paul K. S. Chan¹  Francis K. L. Chan¹  Keli Yang¹  Yun Kit Yeoh¹  Whitney Tang¹  Zhilu Xu¹  Grace C. Lui²  Rashid N. S. Lui²  Rity Wong²  Louis H. S. Lau²  Miu Ling Chin³ 

[1] Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, China;Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, China;Department of Microbiology, The Chinese University of Hong Kong, Hong Kong, China;

关键词: CRE;    FMT;    bacteriome;    virome;   

DOI  :  10.1128/msystems.01510-21

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown