Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae
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 l...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2022-06-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.01510-21 |
| _version_ | 1818249317270421504 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Qin Liu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-12T15:34:34Z |
| format | Article |
| id | doaj.art-ad3803a9cef04d1ea331a5dd4c5fd0b6 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-12T15:34:34Z |
| publishDate | 2022-06-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-ad3803a9cef04d1ea331a5dd4c5fd0b62022-12-22T00:20:03ZengAmerican Society for MicrobiologymSystems2379-50772022-06-017310.1128/msystems.01510-21Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant EnterobacteriaceaeQin Liu0Tao Zuo1Wenqi Lu2Yun Kit Yeoh3Qi Su4Zhilu Xu5Whitney Tang6Keli Yang7Fen Zhang8Louis H. S. Lau9Rashid N. S. Lui10Miu Ling Chin11Rity Wong12Chun Pan Cheung13Wenyi Zhu14Paul K. S. Chan15Francis K. L. Chan16Grace C. Lui17Siew C. Ng18Center for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Microbiology, The Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaDepartment of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, ChinaCenter for Gut Microbiota Research, The Chinese University of Hong Kong, Hong Kong, ChinaABSTRACT 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.https://journals.asm.org/doi/10.1128/msystems.01510-21CREFMTbacteriomevirome |
| spellingShingle | 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 Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae mSystems CRE FMT bacteriome virome |
| title | Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae |
| title_full | Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae |
| title_fullStr | Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae |
| title_full_unstemmed | Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae |
| title_short | Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae |
| title_sort | longitudinal evaluation of gut bacteriomes and viromes after fecal microbiota transplantation for eradication of carbapenem resistant enterobacteriaceae |
| topic | CRE FMT bacteriome virome |
| url | https://journals.asm.org/doi/10.1128/msystems.01510-21 |
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