-
1
-
-
84923775846
-
Burden of Clostridium difficile infection in the United States
-
Lessa FC, Mu Y, Bamberg WM, Beldavs ZG, Dumyati GK, Dunn JR, Farley MM, Holzbauer SM, Meek JI, Phipps EC, Wilson LE, Winston LG, Cohen JA, Limbago BM, Fridkin SK, Gerding DN, McDonald LC. 2015. Burden of Clostridium difficile infection in the United States. N Engl J Med 372:825-834. http://dx.doi.org/10.1056/NEJMoa1408913.
-
(2015)
N Engl J Med
, vol.372
, pp. 825-834
-
-
Lessa, F.C.1
Mu, Y.2
Bamberg, W.M.3
Beldavs, Z.G.4
Dumyati, G.K.5
Dunn, J.R.6
Farley, M.M.7
Holzbauer, S.M.8
Meek, J.I.9
Phipps, E.C.10
Wilson, L.E.11
Winston, L.G.12
Cohen, J.A.13
Limbago, B.M.14
Fridkin, S.K.15
Gerding, D.N.16
McDonald, L.C.17
-
2
-
-
19344364596
-
Relatively poor outcome after treatment of Clostridium difficile colitis with metronidazole
-
Musher DM, Aslam S, Logan N, Nallcheru S, Bhaila I, Borchert F, Hamill RJ. 2005. Relatively poor outcome after treatment of Clostridium difficile colitis with metronidazole. Clin Infect Dis 40:1586-1590. http://dx.doi.org/10.1086/430311.
-
(2005)
Clin Infect Dis
, vol.40
, pp. 1586-1590
-
-
Musher, D.M.1
Aslam, S.2
Logan, N.3
Nallcheru, S.4
Bhaila, I.5
Borchert, F.6
Hamill, R.J.7
-
3
-
-
78651111353
-
Clostridium difficile infection: epidemiology, risk factors and management
-
Ananthakrishnan AN. 2011. Clostridium difficile infection: epidemiology, risk factors and management. Nat Rev Gastroenterol Hepatol 8:17-26. http://dx.doi.org/10.1038/nrgastro.2010.190.
-
(2011)
Nat Rev Gastroenterol Hepatol
, vol.8
, pp. 17-26
-
-
Ananthakrishnan, A.N.1
-
4
-
-
0024418767
-
The ecology of the human intestine and its consequences for overgrowth by pathogens such as Clostridium difficile
-
van der Waaji D. 1989. The ecology of the human intestine and its consequences for overgrowth by pathogens such as Clostridium difficile. Annu Rev Microbiol 43:69-87. http://dx.doi.org/10.1146/annurev.mi.43.100189.000441.
-
(1989)
Annu Rev Microbiol
, vol.43
, pp. 69-87
-
-
van der Waaji, D.1
-
5
-
-
84892894991
-
Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection
-
Theriot CM, Koenigsknecht MJ, Carlson PE, Jr, Hatton GE, Nelson AM, Li B, Huffnagle GBZLJ, Young VB. 2014. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun 5:3114. http://dx.doi.org/10.1038/ncomms4114.
-
(2014)
Nat Commun
, vol.5
, pp. 3114
-
-
Theriot, C.M.1
Koenigsknecht, M.J.2
Carlson, P.E.3
Hatton, G.E.4
Nelson, A.M.5
Li, B.6
Huffnagle, G.B.Z.L.J.7
Young, V.B.8
-
6
-
-
84904012195
-
Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls
-
e01021-14
-
Schubert AM, Rogers MA, Ring C, Mogle J, Petrosino JP, Young VB, AronoffDM, Schloss PD. 2014. Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. mBio 5:e01021-14. http://dx.doi.org/10.1128/mBio.01021-14.
-
(2014)
mBio
, vol.5
-
-
Schubert, A.M.1
Rogers, M.A.2
Ring, C.3
Mogle, J.4
Petrosino, J.P.5
Young, V.B.6
Aronoff, D.M.7
Schloss, P.D.8
-
7
-
-
84882779621
-
Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea
-
Antharam VC, Li EC, Ishmael A, Sharma A, Mai V, Rand KH, Wang GP. 2013. Intestinal dysbiosis and depletion of butyrogenic bacteria in Clostridium difficile infection and nosocomial diarrhea. J Clin Microbiol 51:2884-2892. http://dx.doi.org/10.1128/JCM.00845-13.
-
(2013)
J Clin Microbiol
, vol.51
, pp. 2884-2892
-
-
Antharam, V.C.1
Li, E.C.2
Ishmael, A.3
Sharma, A.4
Mai, V.5
Rand, K.H.6
Wang, G.P.7
-
8
-
-
84898662818
-
Alteration of the murine gastrointestinal microbiota by tigecycline leads to increased susceptibility to Clostridium difficile infection
-
Bassis CM, Theriot CM, Young VB. 2014. Alteration of the murine gastrointestinal microbiota by tigecycline leads to increased susceptibility to Clostridium difficile infection. Antimicrob Agents Chemother 58:2767-2774. http://dx.doi.org/10.1128/AAC.02262-13.
-
(2014)
Antimicrob Agents Chemother
, vol.58
, pp. 2767-2774
-
-
Bassis, C.M.1
Theriot, C.M.2
Young, V.B.3
-
9
-
-
39749120072
-
Antimicrobial-associated risk factors for Clostridium difficile infection
-
Owens RC, Jr, Donskey CJ, Gaynes RP, Loo VG, Muto CA. 2008. Antimicrobial-associated risk factors for Clostridium difficile infection. Clin Infect Dis 46(Suppl 1):S19-S31. http://dx.doi.org/10.1086/521859.
-
(2008)
Clin Infect Dis
, vol.46
, pp. S19-S31
-
-
Owens, R.C.1
Donskey, C.J.2
Gaynes, R.P.3
Loo, V.G.4
Muto, C.A.5
-
10
-
-
84907553520
-
Clostridium difficile and the microbiota
-
Seekatz AM, Young VB. 2014. Clostridium difficile and the microbiota. J Clin Invest 124:4182-4189. http://dx.doi.org/10.1172/JCI72336.
-
(2014)
J Clin Invest
, vol.124
, pp. 4182-4189
-
-
Seekatz, A.M.1
Young, V.B.2
-
11
-
-
84923240963
-
The effects of tigecycline and vancomycin administration on established Clostridium difficile infection
-
Theriot CM, Schumacher CA, Bassis CM, Seekatz AM, Young VB. 2014. The effects of tigecycline and vancomycin administration on established Clostridium difficile infection. Antimicrob Agents Chemother 59:1596-1604. http://dx.doi.org/10.1128/AAC.04296-14.
-
(2014)
Antimicrob Agents Chemother
, vol.59
, pp. 1596-1604
-
-
Theriot, C.M.1
Schumacher, C.A.2
Bassis, C.M.3
Seekatz, A.M.4
Young, V.B.5
-
12
-
-
39349107697
-
Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea
-
Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, Schmidt TM, Young VB. 2008. Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. J Infect Dis 197:435-438. http://dx.doi.org/10.1086/525047.
-
(2008)
J Infect Dis
, vol.197
, pp. 435-438
-
-
Chang, J.Y.1
Antonopoulos, D.A.2
Kalra, A.3
Tonelli, A.4
Khalife, W.T.5
Schmidt, T.M.6
Young, V.B.7
-
13
-
-
80054736926
-
Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection
-
Gough E, Shaikh H, Manges AR. 2011. Systematic review of intestinal microbiota transplantation (fecal bacteriotherapy) for recurrent Clostridium difficile infection. Clin Infect Dis 53:994-1002. http://dx.doi.org/10.1093/cid/cir632.
-
(2011)
Clin Infect Dis
, vol.53
, pp. 994-1002
-
-
Gough, E.1
Shaikh, H.2
Manges, A.R.3
-
14
-
-
84903954202
-
Recovery of the gut microbiome following fecal microbiota transplantation
-
e00893-14
-
Seekatz AM, Aas J, Gessert CE, Rubin TA, Saman DM, Bakken JS, Young VB. 2014. Recovery of the gut microbiome following fecal microbiota transplantation. mBio 5:e00893-14. http://dx.doi.org/10.1128/mBio.00893-14.
-
(2014)
mBio
, vol.5
-
-
Seekatz, A.M.1
Aas, J.2
Gessert, C.E.3
Rubin, T.A.4
Saman, D.M.5
Bakken, J.S.6
Young, V.B.7
-
15
-
-
84874737205
-
High-throughputDNAsequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria
-
Hamilton MJ, Weingarden AR, Unno T, Khoruts A, Sadowsky MJ. 2013. High-throughputDNAsequence analysis reveals stable engraftment of gut microbiota following transplantation of previously frozen fecal bacteria. Gut Microbes 4:125-135. http://dx.doi.org/10.4161/gmic.23571.
-
(2013)
Gut Microbes
, vol.4
, pp. 125-135
-
-
Hamilton, M.J.1
Weingarden, A.R.2
Unno, T.3
Khoruts, A.4
Sadowsky, M.J.5
-
16
-
-
84896708902
-
Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection
-
Song Y, Garg S, Girotra M, Maddox C, von Rosenvinge EC, Dutta A, Dutta S, Fricke FW. 2013. Microbiota dynamics in patients treated with fecal microbiota transplantation for recurrent Clostridium difficile infection. PLoS One 8:e81330. http://dx.doi.org/10.1371/journal.pone.0081330.
-
(2013)
PLoS One
, vol.8
-
-
Song, Y.1
Garg, S.2
Girotra, M.3
Maddox, C.4
von Rosenvinge, E.C.5
Dutta, A.6
Dutta, S.7
Fricke, F.W.8
-
17
-
-
84867598881
-
Cefoperazone-treated mice as an experimental platform to assess differential virulence of Clostridium difficile strains
-
Theriot CM, Koumpouras CC, Carlson PE, Bergin II, AronoffDM, Young VB. 2011. Cefoperazone-treated mice as an experimental platform to assess differential virulence of Clostridium difficile strains. Gut Microbes 2:326-334. http://dx.doi.org/10.4161/gmic.19142.
-
(2011)
Gut Microbes
, vol.2
, pp. 326-334
-
-
Theriot, C.M.1
Koumpouras, C.C.2
Carlson, P.E.3
Bergin, I.I.4
Aronoff, D.M.5
Young, V.B.6
-
18
-
-
80051717743
-
The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile infection
-
Reeves AE, Theriot CM, Bergin IL, Huffnagle GB, Schloss PD, Young VB. 2011. The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile infection. Gut Microbes 2:145-158. http://dx.doi.org/10.4161/gmic.2.3.16333.
-
(2011)
Gut Microbes
, vol.2
, pp. 145-158
-
-
Reeves, A.E.1
Theriot, C.M.2
Bergin, I.L.3
Huffnagle, G.B.4
Schloss, P.D.5
Young, V.B.6
-
19
-
-
84922971911
-
Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract
-
Koenigsknecht MJ, Theriot CM, Bergin IL, Schumacher CA, Schloss PD, Young VB. 2015. Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract. Infect Immun 83:934-941. http://dx.doi.org/10.1128/IAI.02768-14.
-
(2015)
Infect Immun
, vol.83
, pp. 934-941
-
-
Koenigsknecht, M.J.1
Theriot, C.M.2
Bergin, I.L.3
Schumacher, C.A.4
Schloss, P.D.5
Young, V.B.6
-
20
-
-
84884251320
-
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform
-
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. 2013. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79:5112-5120. http://dx.doi.org/10.1128/AEM.01043-13.
-
(2013)
Appl Environ Microbiol
, vol.79
, pp. 5112-5120
-
-
Kozich, J.J.1
Westcott, S.L.2
Baxter, N.T.3
Highlander, S.K.4
Schloss, P.D.5
-
21
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537-7541. http://dx.doi.org/10.1128/AEM.01541-09.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
Hall, J.R.4
Hartmann, M.5
Hollister, E.B.6
Lesniewski, R.A.7
Oakley, B.B.8
Parks, D.H.9
Robinson, C.J.10
Sahl, J.W.11
Stres, B.12
Thallinger, G.G.13
Van Horn, D.J.14
Weber, C.F.15
-
22
-
-
37549027613
-
SILVA: a comprehensive online resource for quality checked and aligned rRNA sequence data compatible with ARB
-
Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glockner FO. 2007. SILVA: a comprehensive online resource for quality checked and aligned rRNA sequence data compatible with ARB. Nucleic Acids Res 35:7188-7196. http://dx.doi.org/10.1093/nar/gkm864.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 7188-7196
-
-
Pruesse, E.1
Quast, C.2
Knittel, K.3
Fuchs, B.M.4
Ludwig, W.5
Peplies, J.6
Glockner, F.O.7
-
23
-
-
79961181125
-
UCHIME improves sensitivity and speed of chimera detection
-
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27:2194-2200. http://dx.doi.org/10.1093/bioinformatics/btr381.
-
(2011)
Bioinformatics
, vol.27
, pp. 2194-2200
-
-
Edgar, R.C.1
Haas, B.J.2
Clemente, J.C.3
Quince, C.4
Knight, R.5
-
24
-
-
34548293679
-
Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
-
Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261-5267. http://dx.doi.org/10.1128/AEM.00062-07.
-
(2007)
Appl Environ Microbiol
, vol.73
, pp. 5261-5267
-
-
Wang, Q.1
Garrity, G.M.2
Tiedje, J.M.3
Cole, J.R.4
-
25
-
-
27744480824
-
A similarity measure based on species proportions
-
Yue JC, Clayton MK. 2005. A similarity measure based on species proportions. Commun Stat Theory Methods 34:2123-2131. http://dx.doi.org/10.1080/STA-200066418.
-
(2005)
Commun Stat Theory Methods
, vol.34
, pp. 2123-2131
-
-
Yue, J.C.1
Clayton, M.K.2
-
26
-
-
84944466599
-
-
Community Ecology Package, v2.0-10.
-
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, Simpson GL, Solymos P, Stevens MH, Wagner H. 2013. Community Ecology Package, v2.0-10. https://cran.r-project.org/.
-
(2013)
-
-
Oksanen, J.1
Blanchet, F.G.2
Kindt, R.3
Legendre, P.4
Minchin, P.R.5
O'Hara, R.B.6
Simpson, G.L.7
Solymos, P.8
Stevens, M.H.9
Wagner, H.10
-
27
-
-
84944466600
-
-
gplots: various R programming tools for plotting data (v2.12.1)
-
Warnes GR, Bolker B, Bonebakker L, Gentleman R, Liaw WH, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B. 2013. gplots: various R programming tools for plotting data (v2.12.1). http://cran.r-project.org/web/packages/gplots/gplots.pdf.
-
(2013)
-
-
Warnes, G.R.1
Bolker, B.2
Bonebakker, L.3
Gentleman, R.4
Liaw, W.H.5
Lumley, T.6
Maechler, M.7
Magnusson, A.8
Moeller, S.9
Schwartz, M.10
Venables, B.11
-
28
-
-
0026681074
-
Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data
-
Excoffier L, Smouse PE, Quattro JM. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491.
-
(1992)
Genetics
, vol.131
, pp. 479-491
-
-
Excoffier, L.1
Smouse, P.E.2
Quattro, J.M.3
-
29
-
-
69049108796
-
Antibiotic treatment of Clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts
-
Lawley TD, Clare S, Walker AW, Goulding D, Stabler RA, Croucher N, Mastroeni P, Scott P, Raisen C, Mottram L, Fairweather NF, Wren BW, Parkhill J, Dougan G. 2009. Antibiotic treatment of Clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect Immun 77:3661-3669. http://dx.doi.org/10.1128/IAI.00558-09.
-
(2009)
Infect Immun
, vol.77
, pp. 3661-3669
-
-
Lawley, T.D.1
Clare, S.2
Walker, A.W.3
Goulding, D.4
Stabler, R.A.5
Croucher, N.6
Mastroeni, P.7
Scott, P.8
Raisen, C.9
Mottram, L.10
Fairweather, N.F.11
Wren, B.W.12
Parkhill, J.13
Dougan, G.14
-
30
-
-
57249086250
-
A mouse model of Clostridium difficile-associated disease
-
Chen X, Katchar K, Goldsmith JD, Nanthakumar N, Cheknis A, Gerding DN, Kelly CP. 2008. A mouse model of Clostridium difficile-associated disease. Gastroenterology 135:1984-1992. http://dx.doi.org/10.1053/j.gastro.2008.09.002.
-
(2008)
Gastroenterology
, vol.135
, pp. 1984-1992
-
-
Chen, X.1
Katchar, K.2
Goldsmith, J.D.3
Nanthakumar, N.4
Cheknis, A.5
Gerding, D.N.6
Kelly, C.P.7
-
31
-
-
84857067037
-
Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis
-
Buffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, Viale A, Ubeda C, Xavier J, Pamer EG. 2012. Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to Clostridium difficile-induced colitis. Infect Immun 80:62-73. http://dx.doi.org/10.1128/IAI.05496-11.
-
(2012)
Infect Immun
, vol.80
, pp. 62-73
-
-
Buffie, C.G.1
Jarchum, I.2
Equinda, M.3
Lipuma, L.4
Gobourne, A.5
Viale, A.6
Ubeda, C.7
Xavier, J.8
Pamer, E.G.9
-
32
-
-
77951026738
-
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)
-
Cohen SH, Gerding DN, Johnson S, Kelly CP, Loo VG, McDonald LC, Pepin J, Wilcox MH. 2010. 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 31:431-455. http://dx.doi.org/10.1086/651706.
-
(2010)
Infect Control Hosp Epidemiol
, vol.31
, pp. 431-455
-
-
Cohen, S.H.1
Gerding, D.N.2
Johnson, S.3
Kelly, C.P.4
Loo, V.G.5
McDonald, L.C.6
Pepin, J.7
Wilcox, M.H.8
-
33
-
-
84925500413
-
Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile
-
Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E, van den Brink MR, Jenq RR, Taur Y, Sander C, Cross JR, Toussaint NC, Xavier JB, Pamer EG. 2015. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 517:205-208. http://dx.doi.org/10.1038/nature13828.
-
(2015)
Nature
, vol.517
, pp. 205-208
-
-
Buffie, C.G.1
Bucci, V.2
Stein, R.R.3
McKenney, P.T.4
Ling, L.5
Gobourne, A.6
No, D.7
Liu, H.8
Kinnebrew, M.9
Viale, A.10
Littmann, E.11
van den Brink, M.R.12
Jenq, R.R.13
Taur, Y.14
Sander, C.15
Cross, J.R.16
Toussaint, N.C.17
Xavier, J.B.18
Pamer, E.G.19
-
34
-
-
84922764903
-
Fecal microbiota transplantation for the management of Clostridium difficile infection
-
Rao K, Young VB. 2015. Fecal microbiota transplantation for the management of Clostridium difficile infection. Infect Dis Clin North Am 29:109-122. http://dx.doi.org/10.1016/j.idc.2014.11.009.
-
(2015)
Infect Dis Clin North Am
, vol.29
, pp. 109-122
-
-
Rao, K.1
Young, V.B.2
-
35
-
-
84868158515
-
Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice
-
Lawley TD, Clare S, Walker AW, Stares MD, Connor TR, Raisen C, Goulding D, Rad R, Schreiber F, Brandt C, Deakin LJ, Pickard DJ, Duncan SH, Flint HJ, Clark TG, Parkhill J, Dougan G. 2012. Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog 8:e1002995. http://dx.doi.org/10.1371/journal.ppat.1002995.
-
(2012)
PLoS Pathog
, vol.8
-
-
Lawley, T.D.1
Clare, S.2
Walker, A.W.3
Stares, M.D.4
Connor, T.R.5
Raisen, C.6
Goulding, D.7
Rad, R.8
Schreiber, F.9
Brandt, C.10
Deakin, L.J.11
Pickard, D.J.12
Duncan, S.H.13
Flint, H.J.14
Clark, T.G.15
Parkhill, J.16
Dougan, G.17
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