Compositional Flux Within the Intestinal Microbiota and Risk for Bloodstream Infection With Gram-negative Bacteria
Open accessAbstract
Background: Gram-negative bloodstream infections (BSIs) represent a significant complication facing allogeneic hematopoietic cell transplant (allo-HCT) recipients, as a result of intestinal translocation during neutropenia. In this study we sought to better understand how the composition of the intestinal microbiota is connected to risk of gram-negative BSIs, expanding on our prior work in these patients. Methods: Fecal specimens were collected from recipients of allo-HCT and analyzed using 16S ribosomal RNA gene sequencing. Samples and clinical data extending from the pretransplant conditioning period through stem cell engraftment were used in the analysis. Intestinal domination (relative abundance ≥ 30%) by gram-negative bacteria was used as predictor of gram-negative BSI using Cox proportional hazards modeling. Further analysis of microbiota composition was performed at the genus level. Results: Seven hundred eight allo-HCT subjects were studied (7.5% developed gram-negative infection), with 4768 fecal samples for analysis. Gram-negative intestinal domination was associated with subsequent BSI, which was observed overall and individually at the genus level: Escherichia, Klebsiella, Enterobacter, Pseudomonas, and Stenotrophomonas. Fluoroquinolone prophylaxis was associated with decreased BSI and intestinal colonization by gram-negative microbes. In fluoroquinolone-prophylaxed patients, Escherichia coli was more frequently observed as breakthrough, both in terms of intestinal colonization and BSIs, compared with nonprophylaxed patients. Initial colonization by members of Ruminococcaceae and Bacteroidetes were associated with protection against gram-negative BSI. Conclusions: Gram-negative intestinal colonization is highly predictive of BSI in the setting of allo-HCT. Fluoroquinolones appear to reduce these infections by influencing gut colonization.
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Allogeneic HCT patients show microbiota disruption, including overgrowth of potential pathogens and reduced alpha diversity.
“We and others have reported that patients undergoing allogeneic hematopoietic-cell transplantation have microbiota disruption that is characterized by expansions of potentially pathogenic bacteria and loss of alpha diversity — a variable that reflects the number of unique bacterial taxa present and their relative frequencies.2–5”
From Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation (2020) · cites this paper as [5]
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Basic local alignment search tool
Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
DADA2: High–resolution sample inference from Illumina amplicon data
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,013 · see citing works
Metagenomic biomarker discovery and explanation
Segata, N., Izard, J., Waldron, L., Gevers, D., Miropolsky, L., Garrett, W. S., & Huttenhower, C. (2011) · Genome Biology · doi:10.1186/gb-2011-12-6-r60 · Cited by 16,192 · see citing works
Freifeld, A. G., Bow, E. J., Sepkowitz, K. A., Boeckh, M. J., Ito, J. I., Mullen, C. A., Raad, I. I., Rolston, K. V., Young, J.-A. H., & Wingard, J. R. (2011) · Clinical Infectious Diseases · doi:10.1093/cid/cir073 · Cited by 3,463 · see citing works
The first 1000 cultured species of the human gastrointestinal microbiota
Rajilić-Stojanović, M., & de Vos, W. M. (2014) · FEMS Microbiology Reviews · doi:10.1111/1574-6976.12075 · Cited by 1,182 · see citing works
Taur, Y., Xavier, J. B., Lipuma, L., Ubeda, C., Goldberg, J., Gobourne, A., Lee, Y. J., Dubin, K. A., Socci, N. D., Viale, A., et al. (2012) · Clinical Infectious Diseases · doi:10.1093/cid/cis580 · Cited by 1,020 · see citing works
Self-citationTaur, Y., Jenq, R. R., Perales, M.-A., Littmann, E. R., Morjaria, S., Ling, L., No, D., Gobourne, A., Viale, A., Dahi, P. B., et al. (2014) · Blood · doi:10.1182/blood-2014-02-554725 · Cited by 885 · see citing works
Self-citationLevofloxacin to Prevent Bacterial Infection in Patients with Cancer and Neutropenia
Bucaneve, G., Micozzi, A., Menichetti, F., Martino, P., Dionisi, M., Martinelli, G., Allione, B., D’Antonio, D., Buelli, M., Nosari, A., et al. (2005) · New England Journal of Medicine · doi:10.1056/nejmoa044097 · Cited by 643 · see citing works
RefSeq microbial genomes database: new representation and annotation strategy
Tatusova, T. A., Ciufo, S. A., Fedorov, B., O’Neill, K. E., & Tolstoy, I. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1274 · Cited by 483 · see citing works
Averbuch, D., Tridello, G., Hoek, J., Mikulska, M., Akan, H., Yáñez, L., Pabst, T., Özçelik, T., Klyasova, G. A., Donnini, I., et al. (2017) · Clinical Infectious Diseases · doi:10.1093/cid/cix646 · Cited by 274 · see citing works
Haak, B. W., Littmann, E. R., Chaubard, J.-L., Pickard, A. J., Fontana, E., Adhi, F., Gyaltshen, Y., Ling, L., Morjaria, S. M., Peled, J. U., et al. (2018) · Blood · doi:10.1182/blood-2018-01-828996 · Cited by 273 · see citing works
Self-citationSorbara, M. T., Dubin, K., Littmann, E. R., Moody, T. U., Fontana, E., Seok, R., Leiner, I. M., Taur, Y., Peled, J. U., van den Brink, M. R. M., et al. (2019) · Journal of Experimental Medicine · doi:10.1084/jem.20181639 · Cited by 259 · see citing works
Self-citationTrecarichi, E. M., Pagano, L., Candoni, A., Pastore, D., Cattaneo, C. M., Fanci, R., Nosari, A., Caira, M., Spadea, A., Busca, A., et al. (2014) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2014.11.022 · Cited by 247 · see citing works
Caballero, S., Carter, R. A., Ke, X., Sušac, B., Leiner, I. M., Kim, G. J., Miller, L., Ling, L., Katia, M., & Pamer, E. G. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1005132 · Cited by 116 · see citing works
Self-citationLee, Y. J., Argüello, E., Jenq, R. R., Littmann, E. R., Kim, G. J., Miller, L., Ling, L., Figueroa, C. J., Robilotti, E. V., Perales, M., et al. (2017) · The Journal of Infectious Diseases · doi:10.1093/infdis/jix011 · Cited by 83 · see citing works
Self-citationСтома, И. О., Karpov, I., Milanovich, N., et al. (2016) · Blood Research · doi:10.5045/br.2016.51.2.102 · Cited by 54 · see citing works
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Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation
Peled, J. U., Gomes, A. L. C., Devlin, S. M., Littmann, E. R., Taur, Y., Sung, A. D., Weber, D., Hashimoto, D., Slingerland, A. E., Slingerland, J. B., et al. (2020) · New England Journal of Medicine · doi:10.1056/nejmoa1900623 · Cited by 765 · see citing works
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- Authors
- Stoma, I., Littmann, E. R., Peled, J. U., Giralt, S., van den Brink, M. R. M., Pamer, E. G., & Taur, Y.
- Affiliations
- Center for Microbes, Inflammation and Cancer, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Memorial Sloan Kettering Cancer Center (US)
- Adult Bone Marrow Transplantation Service, Memorial Hospital, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Corresponding author
- Taur, Ying
- Venue
- Clinical Infectious Diseases
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-01-24
- Volume
- 73
- Issue
- 11
- Pages
- e4627-e4635
- ISSN
- 1058-4838 (ISSN-L)
- 1537-6591
- PMC
- PMC8662789
- OpenAlex
- W3000837182
- Cited by
- 142
- References
- 17
- Citations by year
- 2026: 22 · 2025: 19 · 2024: 23 · 2023: 26 · 2022: 23 · 2021: 18 · 2020: 10
- FWCI
- 6.32
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Clinical Infectious Diseases (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of Allergy and Infectious Diseases
- National Institutes of Health (U01 Al124275, R01 AI137269, P30 CA008748)
- National Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Medicine › Oncology › Neutropenia and Cancer Infections
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- gram-negative bacteremia, allogeneic hematopoietic stem cell transplantation, gut microbiota, intestinal colonization, fluoroquinolone prophylaxis, Escherichia coli, Klebsiella, Enterobacter, Pseudomonas, Stenotrophomonas, Ruminococcaceae, Bacteroidetes, neutropenia, intestinal translocation, infection risk prediction
- MeSH terms
- Gastrointestinal Microbiome, Gram-Negative Bacteria, Humans, Retrospective Studies, Bacteremia, Hematopoietic Stem Cell Transplantation, Sepsis
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