Skip to main content
×
×
Home

Research Agenda for Microbiome Based Research for Multidrug-resistant Organism Prevention in the Veterans Health Administration System

  • Ashley E. Kates (a1) (a2), Jessica S. Tischendorf (a1) (a2), Marin Schweizer (a3) (a4) (a5), Loreen Herwaldt (a3) (a4), Matthew Samore (a6) (a7), Kimberly C. Dukes (a5) (a8), Dale N. Gerding (a9) (a10), Daniel J. Diekema (a4) (a11) (a12) and Nasia Safdar (a1) (a2)...
  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure no-reply@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Research Agenda for Microbiome Based Research for Multidrug-resistant Organism Prevention in the Veterans Health Administration System
      Available formats
      ×
      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      Research Agenda for Microbiome Based Research for Multidrug-resistant Organism Prevention in the Veterans Health Administration System
      Available formats
      ×
      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      Research Agenda for Microbiome Based Research for Multidrug-resistant Organism Prevention in the Veterans Health Administration System
      Available formats
      ×
Abstract
Copyright
Corresponding author
Address correspondence to Ashley Kates, PhD, 5th Floor, UW Medical Foundation Centennial Bldg, 1685 Highland Ave, Madison, WI 53705 (akates@medicine.wisc.edu).
References
Hide All
1. Ravel J, Blaser MJ, Braun J, et al. Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013. Microbiome 2014;2:16.
2. Tang WHW, Wang Z, Levison BS, et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med 2013;368:15751584.
3. Pascal V, Pozuelo M, Borruel N, et al. A microbial signature for Crohn’s disease. Gut 2017;66:813822.
4. Pedamallu CS, Bhatt AS, Bullman S, et al. Metagenomic characterization of microbial communities in situ within the deeper layers of the ileum in Crohn’s disease. Cell Molec Gastroenterol Hepatol 2016;2:563566.e565.
5. Schubert AM, Rogers MAM, Ring C, et al. Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile–associated diarrhea from healthy controls. mBio 2014;5:e0102101014.
6. Ferreyra JA, Wu KJ, Hryckowian AJ, Bouley DM, Weimer BC, Sonnenburg JL. Gut microbiota-produced succinate promotes C. difficile infection after antibiotic treatment or motility disturbance. Cell Host Microbe 2014;16:770777.
7. Human Microbiome Project: overview. National Institutes of Health website. http://commonfund.nih.gov/hmp/overview. Published 2014. Accessed January 4, 2018.
8. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:5965.
9. Raising standards in microbiome research. Nature Microbiol 2016;1:16112.
10. International Human Microbiome Standards website. http://www.microbiome-standards.org/. Published 2015. Accessed February 27, 2017.
11. The microbiome and innovations to slow antibiotic resistance. Centers for Disease Control and Prevention website. https://www.cdc.gov/drugresistance/solutions-initiative/microbiome-innovations.html. Published 2017. Accessed January 4, 2018.
12. Gajer P, Brotman RM, Bai G, et al. Temporal dynamics of the human vaginal microbiota. Science Translat Med 2012;4:132ra152132ra152.
13. Kuczynski J, Lauber CL, Walters WA, et al. Experimental and analytical tools for studying the human microbiome. Nat Rev Genet 2012;13:4758.
14. Caporaso JG, Kuczynski J, Stombaugh J, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods 2010;7:335336.
15. Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Applied Environ Microbiol 2009;75:75377541.
16. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Meth 2013;10:996998.
17. R: A language and environment for statistical computing. 2010. R Development Core Team website. http://www.r-project.org/. Published 2010. Accessed January 4, 2018.
18. The Wellcome Trust. Sharing Data from Large-scale Biological Research Projects: A System of Tripartite Responsibility. 2003; Fort Lauderdale: FL.
19. Kociolek LK, Gerding DN. Breakthroughs in the treatment and prevention of Clostridium difficile infection. Nature Rev Gastroenterol Hepatol 2016;13:150160.
20. Halpin AL, McDonald LC. Editorial commentary: the dawning of microbiome remediation for addressing antibiotic resistance. Clin infect Dis 2016;62:14871488.
21. Forslund K, Hildebrand F, Nielsen T, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature 2015;528:262266.
22. Hanson BM, Weinstock GM. The importance of the microbiome in epidemiologic research. Ann Epidemiol 2016;26:301305.
23. Gaziano JM, Concato J, Brophy M, et al. Million Veteran Program: a mega-biobank to study genetic influences on health and disease. J Clin Epidemiol 2016;70:214223.
24. US Department of Veterans Affairs Office of Research and Development. Million Veteran Program: for researchers and research partners. Department of Veterans Affairs website. https://www.research.va.gov/MVP/researchers.cfm. Published 2017. Accessed January 4, 2017.
25. Cohen SH, Gerding DN, Johnson S, et al. Clinical practice guidelines for Clostridium difficile infection in adults: 2010 update by the society for healthcare epidemiology of America (SHEA) and the infectious diseases society of America (IDSA). Infect Control Hosp Epidemiol 2010;31:431455.
26. Crook DW, Walker AS, Kean Y, et al. Fidaxomicin versus vancomycin for Clostridium difficile infection: meta-analysis of pivotal randomized controlled trials. Clin Infect Dis 2012;55:S93S103.
27. Chang JY, Antonopoulos DA, Kalra A, et al. Decreased diversity of the fecal microbiome in recurrent Clostridium difficile—associated diarrhea. J Infect Dis 2008;197:435438.
28. Kyne L, Warny M, Qamar A, Kelly CP. Association between antibody response to toxin A and protection against recurrent Clostridium difficile diarrhoea. Lancet 2001;357:189193.
29. Abou Chakra CN, Pepin J, Sirard S, Valiquette L. Risk factors for recurrence, complications and mortality in Clostridium difficile infection: a systematic review. PLoS ONE 2014;9:e98400.
30. Chapman BC, Moore HB, Overbey DM, et al. Fecal microbiota transplant in patients with Clostridium difficile infection: a systematic review. J Trauma Acute Care Surg 2016;81:756764.
31. Silverman MS, Davis I, Pillai DR. Success of self-administered home fecal transplantation for chronic Clostridium difficile infection. Clin Gastroenterol Hepatol 2010;8:471473.
32. Bakken JS, Borody T, Brandt LJ, et al. Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol 2011;9:10441049.
33. Youngster I, Russell GH, Pindar C, Ziv-Baran T, Sauk J, Hohmann EL. Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridium difficile infection. JAMA 2014;312:17721778.
34. Cammarota G, Masucci L, Ianiro G, et al. Randomised clinical trial: faecal microbiota transplantation by colonoscopy vs. vancomycin for the treatment of recurrent Clostridium difficile infection. Aliment Pharmacol Therapeut 2015;41:835843.
35. van Nood E, Vrieze A, Nieuwdorp M, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile . N Engl J Med 2013;368:407415.
36. Lofgren ET, Moehring RW, Anderson DJ, Weber DJ, Fefferman NH. A mathematical model to evaluate the routine use of fecal microbiota transplantation to prevent incident and recurrent Clostridium difficile infection. Infect Control Hosp Epidemiol 2013;35:1827.
37. Lagier JC, Delord M, Million M, et al. Dramatic reduction in Clostridium difficile ribotype 027-associated mortality with early fecal transplantation by the nasogastric route: a preliminary report. Eur Soc Clin Microbiol 2015;34:15971601.
38. Neemann K, Eichele DD, Smith PW, Bociek R, Akhtari M, Freifeld A. Fecal microbiota transplantation for fulminant Clostridium difficile infection in an allogeneic stem cell transplant patient. Transplant . Infect Dis 2012;14:E161E165.
39. Trubiano JA, Gardiner B, Kwong JC, Ward P, Testro AG, Charles PGP. Faecal microbiota transplantation for severe Clostridium difficile infection in the intensive care unit. Eur J Gastroenterol Hepatol 2013;25:255257.
40. Gallegos-Orozco J, Paskvan-Gawryletz C, Gurudu S, Orenstein R. Successful colonoscopic fecal transplant for severe acute Clostridium difficile pseudomembranous colitis. Rev Gastroenterol Mex 2011;77:4042.
41. You DM, Franzos MA, Holman RP. Successful treatment of fulminant Clostridium difficile infection with fecal bacteriotherapy. Ann Intern Med 2008;148:632633.
42. Drekonja D, Reich J, Gezahegn S, et al. VA Evidence-based Synthesis Program reports. Fecal Microbiota Transplantation for Clostridium Difficile Infection: A Systematic Review of the Evidence. Washington, DC: Department of Veterans Affairs; 2014.
43. Zipursky JS, Sidorsky TI, Freedman CA, Sidorsky MN, Kirkland KB. Patient attitudes toward the use of fecal microbiota transplantation in the treatment of recurrent Clostridium difficile infection. Clin Infect Dis 2012;55:16521658.
44. Zipursky JS, Sidorsky TI, Freedman CA, Sidorsky MN, Kirkland KB. Physician attitudes toward the use of fecal microbiota transplantation for the treatment of recurrent Clostridium difficile infection. Can J Gastroenterol Hepatol 2014;28:319324.
45. Caballero S, Carter R, Ke X, et al. Distinct but spatially overlapping intestinal niches for vancomycin-resistant enterococcus faecium and carbapenem-resistant Klebsiella pneumoniae . PLoS Pathogens 2015;11:e1005132.
46. Ubeda C, Bucci V, Caballero S, et al. Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infect Immun 2013;81:965973.
47. Halpin AL, de Man TJ, Kraft CS, et al. Intestinal microbiome disruption in patients in a long-term acute care hospital: a case for development of microbiome disruption indices to improve infection prevention. Am J Infect Control 2016;44:830836.
48. Stripling J, Kumar R, Baddley JW, et al. Loss of vancomycin-resistant enterococcus fecal dominance in an organ transplant patient with Clostridium difficile colitis after fecal microbiota transplant. Open Forum Infect Dis 2015;2:ofv078.
49. Davido B, Batista R, Michelon H, et al. Is faecal microbiota transplantation an option to eradicate highly drug-resistant enteric bacteria carriage? J Hosp Infect 2017;95:433437.
50. Lagier JC, Million M, Fournier PE, Brouqui P, Raoult D. Faecal microbiota transplantation for stool decolonization of OXA-48 carbapenemase-producing Klebsiella pneumoniae . J Hosp Infect 2015;90:173174.
51. Millan B, Park H, Hotte N, et al. Fecal microbial transplants reduce antibiotic-resistant genes in patients with recurrent Clostridium difficile infection. Clin Infect Dis 2016;62:14791486.
52. Sawin EA, De Wolfe TJ, Aktas B, et al. Glycomacropeptide is a prebiotic that reduces Desulfovibrio bacteria, increases cecal short-chain fatty acids, and is anti-inflammatory in mice. Am J Physio . Gastrointestin Liver Physiol 2015;309:G590G601.
53. Johnston BC, Ma SY, Goldenberg JZ, et al. Probiotics for the prevention of clostridium difficile–associated diarrhea: a systematic review and meta-analysis. Ann Intern Med 2012;157:878888.
54. Shen NT, Maw A, Tmanova LL, et al. Timely use of probiotics in hospitalized adults prevents Clostridium difficile infection: a systematic review with meta-regression analysis. Gastroenterol 2017;152:18891900.e1889.
55. Gerding DN, Meyer T, Lee C, et al. Administration of spores of nontoxigenic Clostridium difficile strain M3 for prevention of recurrent C. difficile infection: a randomized clinical trial. JAMA 2015;313:17191727.
56. Bessesen MT, Kotter CV, Wagner BD, et al. MRSA colonization and the nasal microbiome in adults at high risk of colonization and infection. J Infect 2015;71:649657.
57. Ramsey MM, Freire MO, Gabrilska RA, Rumbaugh KP, Lemon KP. Staphylococcus aureus shifts toward commensalism in response to Corynebacterium species. Front Microbiol 2016;7:1230.
58. Uehara Y, Nakama H, Agematsu K, et al. Bacterial interference among nasal inhabitants: eradication of Staphylococcus aureus from nasal cavities by artificial implantation of Corynebacterium sp. J Hosp Infect 2000;44:127133.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

Infection Control & Hospital Epidemiology
  • ISSN: 0899-823X
  • EISSN: 1559-6834
  • URL: /core/journals/infection-control-and-hospital-epidemiology
Please enter your name
Please enter a valid email address
Who would you like to send this to? *
×

Metrics

Altmetric attention score

Full text views

Total number of HTML views: 4
Total number of PDF views: 94 *
Loading metrics...

Abstract views

Total abstract views: 277 *
Loading metrics...

* Views captured on Cambridge Core between 8th February 2018 - 21st February 2018. This data will be updated every 24 hours.