The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans
Open accessAbstract
Bloodstream infection by highly antibiotic-resistant bacteria, such as vancomycin-resistant Enterococcus (VRE), is a growing clinical problem that increasingly defies medical intervention. Identifying patients at high risk for bacterial sepsis remains an important clinical challenge. Recent studies have shown that antibiotics can alter microbial diversity in the intestine. Here, we characterized these effects using 16s rDNA pyrosequencing and demonstrated that antibiotic treatment of mice enabled exogenously administered VRE to efficiently and nearly completely displace the normal microbiota of the small and large intestine. In the clinical setting, we found that intestinal domination by VRE preceded bloodstream infection in patients undergoing allogeneic hematopoietic stem cell transplantation. Our results demonstrate that antibiotics perturb the normal commensal microbiota and set the stage for intestinal domination by bacteria associated with hospital-acquired infections. Thus, high-throughput DNA sequencing of the intestinal microbiota could identify patients at high risk of developing bacterial sepsis.
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“Each of these outcomes, as well as overall survival, has been associated in single-center studies with features of the intestinal microbiota in the period after hematopoietic-cell transplantation.2–4,8–15”
From Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation (2020) · cites this paper as [13]
In the citing paper
“Gram− commensals can be depleted by vancomycin, which is a Gram+-targeting drug [83].”
From Antibiotic-Induced Changes in the Intestinal Microbiota and Disease (2016) · cites this paper as [83]
In the citing paper
“VRE colonizes the intestine following antibiotic treatment, prior to spreading to the bloodstream, and thus, represents a major threat for hospitalized patients [83].”
From Antibiotic-Induced Changes in the Intestinal Microbiota and Disease (2016) · cites this paper as [83]
In the citing paper
“The taxonomic composition of the gut microbiota changes throughout the gastrointestinal tract, according to nutrient availability, mucus structure, pH and oxygen availability [1–6].”
From Role of the gut microbiota in nutrient competition and protection against intestinal pathogen colonization (2023) · cites this paper as [3]
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Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 21,481
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 20,145
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785
Diversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913
A core gut microbiome in obese and lean twins
Turnbaugh, P. J., Hamady, M., Yatsunenko, T., Cantarel, B. L., Duncan, A., Ley, R. E., Sogin, M. L., Jones, W. J., Roe, B. A., Affourtit, J. P., et al. (2009) · Nature · doi:10.1038/nature07540 · Cited by 7,823
Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,682
The gut microbiota as an environmental factor that regulates fat storage
Bäckhed, F., Ding, H., Wang, T., Hooper, L. V., Koh, G. Y., Nagy, A., Semenkovich, C. F., & Gordon, J. I. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407076101 · Cited by 6,245
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix
Price, M. N., Dehal, P. S., & Arkin, A. P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp077 · Cited by 5,602
Host-Bacterial Mutualism in the Human Intestine
Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277
Recognition of Commensal Microflora by Toll-Like Receptors Is Required for Intestinal Homeostasis
Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., Edberg, S., & Medzhitov, R. (2004) · Cell · doi:10.1016/j.cell.2004.07.002 · Cited by 4,251
Microbial diversity in the deep sea and the underexplored “rare biosphere”
Sogin, M. L., Morrison, H. G., Huber, J. A., Welch, D. B. M., Huse, S. M., Neal, P. R., Arrieta, J. M., & Herndl, G. J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0605127103 · Cited by 3,803
Ecological and Evolutionary Forces Shaping Microbial Diversity in the Human Intestine
Ley, R. E., Peterson, D. A., & Gordon, J. I. (2006) · Cell · doi:10.1016/j.cell.2006.02.017 · Cited by 3,358
Dethlefsen, L., Huse, S., Sogin, M. L., & Relman, D. A. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060280 · Cited by 2,361
A microbial symbiosis factor prevents intestinal inflammatory disease
Mazmanian, S. K., Round, J. L., & Kasper, D. L. (2008) · Nature · doi:10.1038/nature07008 · Cited by 2,340
Nod2-Dependent Regulation of Innate and Adaptive Immunity in the Intestinal Tract
Kobayashi, K. S., Chamaillard, M., Ogura, Y., Henegariu, O., Inohara, N., Núñez, G., & Flavell, R. A. (2005) · Science · doi:10.1126/science.1104911 · Cited by 1,834
H OW H OST -M ICROBIAL I NTERACTIONS S HAPE THE N UTRIENT E NVIRONMENT OF THE M AMMALIAN I NTESTINE
Hooper, L. V., Midtvedt, T., & Gordon, J. I. (2002) · Annual Review of Nutrition · doi:10.1146/annurev.nutr.22.011602.092259 · Cited by 1,623
UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context
Lozupone, C., Hamady, M., & Knight, R. D. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-371 · Cited by 1,454
Symbiotic bacteria direct expression of an intestinal bactericidal lectin
Cash, H. L., Whitham, C. V., Behrendt, C. L., & Hooper, L. V. (2006) · Science · doi:10.1126/science.1127119 · Cited by 1,432
Gewirtz, A. T., Navas, T. A., Lyons, S., Godowski, P. J., & Madara, J. (2001) · The Journal of Immunology · doi:10.4049/jimmunol.167.4.1882 · Cited by 1,345
Molecular analysis of the bacterial microbiota in the human stomach
Bik, E. M., Eckburg, P. B., Gill, S. R., Nelson, K. E., Purdom, E. A., François, F., Perez-Perez, G., Blaser, M. J., & Relman, D. A. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506655103 · Cited by 1,160
Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells
Stappenbeck, T. S., Hooper, L. V., & Gordon, J. I. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202604299 · Cited by 1,095
Secretion of microbicidal α-defensins by intestinal Paneth cells in response to bacteria
Ayabe, T., Satchell, D. P., Wilson, C. L., Parks, W. C., Selsted, M. E., & Ouellette, A. J. (2000) · Nature Immunology · doi:10.1038/77783 · Cited by 1,060
Stecher, B., Robbiani, R., Walker, A. W., Westendorf, A. M., Barthel, M., Kremer, M., Chaffron, S., Macpherson, A. J., Buer, J., Parkhill, J., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050244 · Cited by 1,048
Vaishnava, S., Behrendt, C. L., Ismail, A. S., Eckmann, L., & Hooper, L. V. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0808723105 · Cited by 1,019
Moderated statistical tests for assessing differences in tag abundance
Robinson, M. D., & Smyth, G. K. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm453 · Cited by 856
Influences of microbiota on intestinal immune system development.
Cebra, J. (1999) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/69.5.1046s · Cited by 819
Vancomycin-resistant enterococci exploit antibiotic-induced innate immune deficits
Brandl, K., Plitas, G., Mihu, C. N., Ubeda, C., Jia, T., Fleisher, M., Schnabl, B., DeMatteo, R. P., & Pamer, E. G. (2008) · Nature · doi:10.1038/nature07250 · Cited by 631
Self-citationNarrative Review: The New Epidemic of Clostridium difficile–Associated Enteric Disease
Bartlett, J. G. (2006) · Annals of Internal Medicine · doi:10.7326/0003-4819-145-10-200611210-00008 · Cited by 592
Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation
Antonopoulos, D. A., Huse, S. M., Morrison, H. G., Schmidt, T. M., Sogin, M. L., & Young, V. B. (2009) · Infection and Immunity · doi:10.1128/iai.01520-08 · Cited by 564
Sekirov, I., Tam, N. M., Jogova, M., Robertson, M. L., Li, Y., Lupp, C., & Finlay, B. B. (2008) · Infection and Immunity · doi:10.1128/iai.00319-08 · Cited by 500
Vollaard, E. J., & Clasener, H. A. (1994) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.38.3.409 · Cited by 478
Hill, D. A., Hoffmann, C., Abt, M. C., Du, Y., Kobuley, D. E., Kirn, T. J., Bushman, F. D., & Artis, D. (2009) · Mucosal Immunology · doi:10.1038/mi.2009.132 · Cited by 439
Genomic and Metabolic Studies of the Impact of Probiotics on a Model Gut Symbiont and Host
Sonnenburg, J. L., Chen, C. T. L., & Gordon, J. I. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040413 · Cited by 423
van Baarlen, P., Troost, F. J., van Hemert, S., van Kraaij, C., de Vos, W. M., de Groot, P. J., Hooiveld, G. J. E. J., Brummer, R. J., & Kleerebezem, M. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809919106 · Cited by 395
Antimicrobial resistance in gram-positive bacteria
Rice, L. B. (2006) · American Journal of Infection Control · doi:10.1016/j.ajic.2006.05.220 · Cited by 393
Brandl, K., Plitas, G., Schnabl, B., DeMatteo, R. P., & Pamer, E. G. (2007) · The Journal of Experimental Medicine · doi:10.1084/jem.20070563 · Cited by 385
Self-citationβ-Defensin-2 Expression Is Regulated by TLR Signaling in Intestinal Epithelial Cells
Vora, P., Youdim, A., Thomas, L. S., Fukata, M., Tesfay, S., Lukasek, K., Michelsen, K. S., Wada, A., Hirayama, T., Arditi, M., et al. (2004) · The Journal of Immunology · doi:10.4049/jimmunol.173.9.5398 · Cited by 358
Lawley, T. D., Clare, S., Walker, A. W., Goulding, D., Stabler, R. A., Croucher, N., Mastroeni, P., Scott, P., Raisen, C., Mottram, L., et al. (2009) · Infection and Immunity · doi:10.1128/iai.00558-09 · Cited by 349
Antimicrobial Resistance in Gram-Positive Bacteria
Rice, L. B. (2006) · The American Journal of Medicine · doi:10.1016/j.amjmed.2006.03.012 · Cited by 330
Croswell, A., Amir, E., Teggatz, P., Barman, M., & Salzman, N. H. (2009) · Infection and Immunity · doi:10.1128/iai.00006-09 · Cited by 279
Kinnebrew, M. A., Ubeda, C., Zenewicz, L. A., Smith, N., Flavell, R. A., & Pamer, E. G. (2010) · The Journal of Infectious Diseases · doi:10.1086/650203 · Cited by 236
Self-citationWeinstock, D. M., Conlon, M., Iovino, C. S., Aubrey, T., Gudiol, C., Riedel, E., Young, J. W., Kiehn, T. E., & Zuccotti, G. (2007) · Transplantation and Cellular Therapy · doi:10.1016/j.bbmt.2007.01.078 · Cited by 209
Immune responses to commensal and environmental microbes
Pamer, E. G. (2007) · Nature Immunology · doi:10.1038/ni1526 · Cited by 173
Self-citationAntibiotic Regimens and Intestinal Colonization with Antibiotic-Resistant Gram-Negative Bacilli
Donskey, C. J. (2006) · Clinical Infectious Diseases · doi:10.1086/504481 · Cited by 152
Garner, C. D., Antonopoulos, D. A., Wagner, B., Duhamel, G. E., Keresztes, I., Ross, D. A., Young, V. B., & Altier, C. (2009) · Infection and Immunity · doi:10.1128/iai.01570-08 · Cited by 140
Donskey, C. J., Hanrahan, J., Hutton, R. A., & Rice, L. B. (1999) · The Journal of Infectious Diseases · doi:10.1086/314874 · Cited by 139
Kingsley, R. A., Amsterdam, K. V., Kramer, N. E., & Bäumler, A. J. (2000) · Infection and Immunity · doi:10.1128/iai.68.5.2720-2727.2000 · Cited by 128
TLR signaling at the intestinal epithelial interface
Abreu, M. T., Thomas, L. S., Arnold, E. T., Lukasek, K., Michelsen, K. S., & Arditi, M. (2003) · Journal of Endotoxin Research · doi:10.1179/096805103225002593 · Cited by 107
Role of the Innate Immune System and Host-Commensal Mutualism
Rakoff-Nahoum, S., & Medzhitov, R. M. (2006) · Springer eBooks · doi:10.1007/3-540-30657-9_1 · Cited by 90
Zirakzadeh, A. A., Gastineau, D. A., Mandrekar, J. N., Burke, J. P., Johnston, P. B., & Patel, R. (2007) · Bone Marrow Transplantation · doi:10.1038/sj.bmt.1705912 · Cited by 73
How Bacterial Communities Expand Functional Repertoires
Versalovic, J. A., & Relman, D. A. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040430 · Cited by 15
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- Abreu, 2003, J Endotoxin Res., 9, 322, 10.1177/09680519030090050901 · DOI
- Rakoff-Nahoum, 2006, Curr Top Microbiol Immunol., 308, 1
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Metadata
- Authors
- Ubeda, C., Taur, Y., Jenq, R. R., Equinda, M. J., Son, T., Samstein, M., Viale, A., Socci, N. D., van den Brink, M. R. M., Kamboj, M., & Pamer, E. G.
- Affiliations
- Memorial Sloan Kettering Cancer Center (US)
- Venue
- Journal of Clinical Investigation
- Published
- 2010-12-01
- Volume
- 120
- Issue
- 12
- Pages
- 4332-4341
- ISSN
- 0021-9738 (ISSN-L)
- PMC
- PMC2993598
- OpenAlex
- W1979573684
- Cited by
- 943
- References
- 51
- Citations by year
- 2026: 52 · 2025: 48 · 2024: 55 · 2023: 58 · 2022: 94 · 2021: 72 · 2020: 76 · 2019: 90 · 2018: 64 · 2017: 66 · 2016: 56 · 2015: 49 · 2014: 44 · 2013: 51 · 2012: 46
- FWCI
- 15.49
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Clinical Investigation (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Cancer Research Institute
- National Institutes of Health (4r37ai039031-21, CA023766)
- National Cancer Institute (P01CA023766, R01CA107096, P30CA008748)
- National Institute of General Medical Sciences (T32GM007739)
- National Institute of Allergy and Infectious Diseases (R37-AI039031, R01AI080455, K23AI083880, R01AI042135)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Microbiology (medical) › Antibiotic Resistance in Bacteria
- Health Sciences › Medicine › Infectious Diseases › Clostridium difficile and Clostridium perfringens research
- Keywords
- vancomycin-resistant enterococci, antibiotic-induced dysbiosis, gut microbiota, bacterial sepsis, bloodstream infection, allogeneic hematopoietic stem cell transplantation, nosocomial infections, sepsis risk prediction
- MeSH terms
- Animals, Anti-Bacterial Agents, Base Sequence, Cross Infection, DNA, Bacterial, DNA, Ribosomal, Humans, Intestines, Mice, Inbred C57BL, Bacteremia, Gram-Positive Bacterial Infections, Enterococcus, Hematopoietic Stem Cell Transplantation, Vancomycin Resistance, Mice, Metagenome
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