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

Qin Liu, Tao Zuo, Wenqi Lu, Yun Kit Yeoh, Qi Su, Zhilu Xu, Whitney Tang, Keli Yang, Fen Zhang, Louis H S Lau, Rashid N S Lui, Miu Ling Chin, Rity Wong, Chun Pan Cheung, Wenyi Zhu, Paul K S Chan, Francis K L Chan, Grace C Lui, Siew C Ng*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

4 Citations (Scopus)


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.

Original languageEnglish
Article numbere0151021
Number of pages16
Issue number3
Early online date1 Jun 2022
Publication statusPublished - 28 Jun 2022

User-Defined Keywords

  • Animals
  • Mice
  • Fecal Microbiota Transplantation
  • Carbapenem-Resistant Enterobacteriaceae
  • Virome
  • Escherichia coli
  • Pilot Projects
  • Bacteriophages
  • CRE
  • FMT
  • bacteriome
  • virome


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