Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection

Genome Medicine

Volumn 8, Issue 1, 2016, Pages

  Montassier, Emmanuel ^a,b   Al Ghalith, Gabriel A ^b,c   Ward, Tonya ^c   Corvec, Stephane ^a,d   Gastinne, Thomas ^d   Potel, Gilles ^a   Moreau, Phillipe ^d   de la Cochetiere, Marie France ^a   Batard, Eric ^a   Knights, Dan ^b,c  

^a UNIVERSITÉ DE NANTES   (France)

^b University of Minnesota   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

^d NANTES UNIVERSITY HOSPITAL   (France)

Author keywords

Bloodstream infection; Chemotherapy; Intestinal microbiome; Prediction

Indexed keywords

COTRIMOXAZOLE; PENICILLIN V; RNA 16S; ANTINEOPLASTIC AGENT;

ADULT; ALLOGENEIC HEMATOPOIETIC STEM CELL TRANSPLANTATION; ANTIBIOTIC PROPHYLAXIS; AREA UNDER THE CURVE; ARTICLE; BACTERIUM; BACTEROIDES; BARNESIELLACEAE; BLOODSTREAM INFECTION; CHEMOTHERAPY RELATED BLOODSTREAM INFECTION; CHRISTENSENELLA; CLINICAL ARTICLE; CONTROLLED STUDY; CORIOBACTERIACEAE; DEHALOBACTERIUM; DESULFOVIBRIO; DIAGNOSTIC TEST ACCURACY STUDY; FAECALIBACTERIUM; FECES ANALYSIS; FECES MICROFLORA; FEMALE; FIRMICUTES; GENERAL PATHOLOGICAL PARAMETERS; HIGH RISK PATIENT; HIGH THROUGHPUT DNA SEQUENCING; HIGH THROUGHPUT SEQUENCING; HUMAN; INFECTION RISK; INTESTINE FLORA; MACHINE LEARNING; MALE; NONHODGKIN LYMPHOMA; NONHUMAN; PREDICTION; PREDICTIVE ACCURACY; PRIORITY JOURNAL; PROTEOBACTERIA; RECEIVER OPERATING CHARACTERISTIC; RISK ASSESSMENT; SENSITIVITY AND SPECIFICITY; SUTTERELLA; BACTEREMIA; CLASSIFICATION; FECES; GENETIC VARIATION; GENETICS; HEMATOPOIETIC STEM CELL TRANSPLANTATION; INCIDENCE; LYMPHOMA, NON-HODGKIN; MICROBIOLOGY; MIDDLE AGED; PROCEDURES; RETROSPECTIVE STUDY; RISK FACTOR; SEQUENCE ANALYSIS;

ANTINEOPLASTIC AGENTS; BACTEREMIA; BACTERIA; FECES; FEMALE; GASTROINTESTINAL MICROBIOME; GENETIC VARIATION; HEMATOPOIETIC STEM CELL TRANSPLANTATION; HUMANS; INCIDENCE; LYMPHOMA, NON-HODGKIN; MACHINE LEARNING; MALE; MIDDLE AGED; RETROSPECTIVE STUDIES; RISK FACTORS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA;

EID: 84964514022     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-016-0301-4     Document Type: Article

References (40)

1. Tuncer HH, Rana N, Milani C, Darko A, Al-Homsi SA. Gastrointestinal and hepatic complications of hematopoietic stem cell transplantation. World J Gastroenterol. 2012;18:1851-60.
2. Keefe DM, Schubert MM, Elting LS, Sonis ST, Epstein JB, Raber-Durlacher JE, et al. Updated clinical practice guidelines for the prevention and treatment of mucositis. Cancer. 2007;109:820-31.
3. Sonis ST. The pathobiology of mucositis. Nat Rev Cancer. 2004;4:277-84.
4. Berg RD. Bacterial translocation from the gastrointestinal tract. Adv Exp Med Biol. 1999;473:11-30.
5. Blennow O, Ljungman P, Sparrelid E, Mattsson J, Remberger M. Incidence, risk factors, and outcome of bloodstream infections during the pre-engraftment phase in 521 allogeneic hematopoietic stem cell transplantations. Transpl Infect Dis. 2014;16:106-14.
6. Åttman E, Aittoniemi J, Sinisalo M, Vuento R, Lyytikäinen O, Kärki T, et al. Etiology, clinical course and outcome of healthcare-associated bloodstream infections in patients with hematological malignancies: a retrospective study of 350 patients in a Finnish tertiary care hospital. Leuk Lymphoma. 2015;56:3370-7.
7. Marin M, Gudiol C, Ardanuy C, Garcia-Vidal C, Calvo M, Arnan M, et al. Bloodstream infections in neutropenic patients with cancer: differences between patients with haematological malignancies and solid tumours. J Infect. 2014;69:417-23.
8. Poutsiaka DD, Price LL, Ucuzian A, Chan GW, Miller KB, Snydman DR. Blood stream infection after hematopoietic stem cell transplantation is associated with increased mortality. Bone Marrow Transplant. 2007;40:63-70.
9. van Vliet MJ, Harmsen HJM, de Bont ESJM, Tissing WJE. The role of intestinal microbiota in the development and severity of chemotherapy-induced mucositis. PLoS Pathog. 2010;6:e1000879.
10. Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, et al. Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clin Infect Dis. 2012;55:905-14.
11. Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley Des Varannes S, Massart S, et al. Chemotherapy-driven dysbiosis in the intestinal microbiome. Aliment Pharmacol Ther. 2015;42:515-28.
12. Andersson AF, Lindberg M, Jakobsson H, Bäckhed F, Nyrén P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PloS One. 2008;3:e2836.
13. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335-6.
14. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72:5069-72.
15. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol. 2013;31:814-21.
16. Breiman L. Random forests. Mach Learn. 2001;45:5-32.
17. He Y, Caporaso JG, Jiang XT, Sheng HF, Huse SM, Rideout JR, et al. Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. Microbiome. 2015;3:20.
18. Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60.
19. Dinh DM, Volpe GE, Duffalo C, Bhalchandra S, Tai AK, Kane AV, et al. Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection. J Infect Dis. 2015;211:19-27.
20. Zenewicz LA, Yin X, Wang G, Elinav E, Hao L, Zhao L, et al. IL-22 deficiency alters colonic microbiota to be transmissible and colitogenic. J Immunol 1950. 2013;190:5306-12.
21. Giannelli V, Di Gregorio V, Iebba V, Giusto M, Schippa S, Merli M, et al. Microbiota and the gut-liver axis: bacterial translocation, inflammation and infection in cirrhosis. World J Gastroenterol. 2014;20:16795-810.
22. Lam YY, Ha CWY, Campbell CR, Mitchell AJ, Dinudom A, Oscarsson J, et al. Increased gut permeability and microbiota change associate with mesenteric fat inflammation and metabolic dysfunction in diet-induced obese mice. PloS One. 2012;7:e34233.
23. Taur Y, Jenq RR, Perales M-A, Littmann ER, Morjaria S, Ling L, et al. The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation. Blood. 2014;124:1174-82.
24. Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014;15:382-92.
25. Craven M, Egan CE, Dowd SE, McDonough SP, Dogan B, Denkers EY, et al. Inflammation drives dysbiosis and bacterial invasion in murine models of ileal Crohn's disease. PloS One. 2012;7:e41594.
26. Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207-14.
27. Ubeda C, Bucci V, Caballero S, Djukovic A, Toussaint NC, Equinda M, et al. Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infect Immun. 2013;81:965-73.
28. Montassier E, Batard E, Gastinne T, Potel G, de La Cochetière MF. Recent changes in bacteremia in patients with cancer: a systematic review of epidemiology and antibiotic resistance. Eur J Clin Microbiol Infect Dis. 2013;32:841-50.
29. Mutlu EA, Keshavarzian A, Losurdo J, Swanson G, Siewe B, Forsyth C, et al. A compositional look at the human gastrointestinal microbiome and immune activation parameters in HIV infected subjects. PLoS Pathog. 2014;10:e1003829.
30. Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. Human genetics shape the gut microbiome. Cell. 2014;159:789-99.
31. Wong JMW, de Souza R, Kendall CWC, Emam A, Jenkins DJA. Colonic health: fermentation and short chain fatty acids. J Clin Gastroenterol. 2006;40:235-43.
32. Rajilić-Stojanović M, Shanahan F, Guarner F, de Vos WM. Phylogenetic analysis of dysbiosis in ulcerative colitis during remission. Inflamm Bowel Dis. 2013;19:481-8.
33. Jalanka-Tuovinen J, Salojärvi J, Salonen A, Immonen O, Garsed K, Kelly FM, et al. Faecal microbiota composition and host-microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome. Gut. 2014;63:1737-45.
34. Rey FE, Gonzalez MD, Cheng J, Wu M, Ahern PP, Gordon JI. Metabolic niche of a prominent sulfate-reducing human gut bacterium. Proc Natl Acad Sci. 2013;110:13582-7.
35. Bhargava P, Mowry EM. Gut microbiome and multiple sclerosis. Curr Neurol Neurosci Rep. 2014;14:492.
36. Bibbò S, Lopetuso LR, Ianiro G, Di Rienzo T, Gasbarrini A, Cammarota G. Role of microbiota and innate immunity in recurrent Clostridium difficile infection. J Immunol Res. 2014;2014:462740.
37. Palm NW, de Zoete MR, Cullen TW, Barry NA, Stefanowski J, Hao L, et al. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell. 2014;158:1000-10.
38. Zackular JP, Baxter NT, Iverson KD, Sadler WD, Petrosino JF, Chen GY, et al. The gut microbiome modulates colon tumorigenesis. mBio. 2013;4:e00692-00613.
39. Pamer EG. Fecal microbiota transplantation: effectiveness, complexities, and lingering concerns. Mucosal Immunol. 2014;7:210-4.
40. Kuczynski J, Costello EK, Nemergut DR, Zaneveld J, Lauber CL, Knights D, et al. Direct sequencing of the human microbiome readily reveals community differences. Genome Biol. 2010;11:210.