Recurrent Clostridium difficile infection associates with distinct bile acid and microbiome profiles

Alimentary Pharmacology and Therapeutics

Volumn 43, Issue 11, 2016, Pages 1142-1153

  Allegretti, J R ^a   Kearney, S ^b   Li, N ^a   Bogart, E ^a   Bullock, K ^c   Gerber, G K ^a   Bry, L ^a   Clish, C B ^c   Alm, E ^b   Korzenik, J R ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL BILE SALT HYDROLASE; BACTERIAL ENZYME; BILE ACID; BILE SALT; BIOLOGICAL MARKER; DEOXYCHOLIC ACID; GLYCOURSODEOXYCHOLATE; HYDROLASE; RIBOSOME RNA; UNCLASSIFIED DRUG; ANTIINFECTIVE AGENT; RNA 16S;

ADULT; AGED; ARTICLE; BACTERIAL GENE; BILE ACID BLOOD LEVEL; BILE ACID METABOLISM; BLOOD ANALYSIS; BSH GENE; CLINICAL ARTICLE; CLOSTRIDIUM DIFFICILE INFECTION; CONTROLLED STUDY; DISEASE ASSOCIATION; FECES ANALYSIS; FEMALE; HUMAN; MALE; METABOLOMICS; MICROBIOME; PRIORITY JOURNAL; RNA SEQUENCE; CASE CONTROL STUDY; CLOSTRIDIUM INFECTION; CROSS-SECTIONAL STUDY; FECES; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MICROFLORA; MIDDLE AGED; PEPTOCLOSTRIDIUM DIFFICILE; RECURRENT DISEASE; VERY ELDERLY;

ADULT; AGED; AGED, 80 AND OVER; ANTI-BACTERIAL AGENTS; BILE ACIDS AND SALTS; CASE-CONTROL STUDIES; CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM INFECTIONS; CROSS-SECTIONAL STUDIES; FECES; FEMALE; HUMANS; MALE; METABOLOMICS; MICROBIOTA; MIDDLE AGED; RECURRENCE; RNA, RIBOSOMAL, 16S;

EID: 84963891450     PISSN: 02692813     EISSN: 13652036     Source Type: Journal    
DOI: 10.1111/apt.13616     Document Type: Article

References (40)

1. Bartlett JG,. Narrative review: the new epidemic of Clostridium difficile-associated enteric disease. Ann Intern Med 2006; 145: 758-64.
2. O'Connor JR, Johnson S, Gerding DN,. Clostridium difficile infection caused by the epidemic BI/NAP1/027 strain. Gastroenterology 2009; 136: 1913-24.
3. Kassam Z, Cribb Fabersunne C, Smith MB, et al,. Clostridium difficile associated risk of death score (CARDS): a novel severity score to predict mortality among hospitalised patients with C. difficile infection. Aliment Pharmacol Ther 2016; 43: 725-33.
4. Shivashankar R, Khanna S, Kammer PP, et al,. Clinical predictors of recurrent Clostridium difficile infection in out-patients. Aliment Pharmacol Ther 2014; 40: 518-22.
5. Sorg JA, Sonenshein AL,. Bile salts and glycine as cogerminants for Clostridium difficile spores. J Bacteriol 2008; 190: 2505-12.
6. Rupnik M,. Is Clostridium difficile-associated infection a potentially zoonotic and foodborne disease? Clin Microbiol Infect 2007; 13: 457-9.
7. Leffler DA, Lamont JT,. Clostridium difficile infection. N Engl J Med 2015; 373: 287-8.
8. Ridlon JM, Kang DJ, Hylemon PB,. Bile salt biotransformations by human intestinal bacteria. J Lipid Res 2006; 47: 241-59.
9. Hashimoto S, Igimi H, Uchida K, Satoh T, Benno Y, Takeuchi N,. Effects of beta-lactam antibiotics on intestinal microflora and bile acid metabolism in rats. Lipids 1996; 31: 601-9.
10. Sorg JA, Sonenshein AL,. Chenodeoxycholate is an inhibitor of Clostridium difficile spore germination. J Bacteriol 2009; 191: 1115-7.
11. Sorg JA, Sonenshein AL,. Inhibiting the initiation of Clostridium difficile spore germination using analogs of chenodeoxycholic acid, a bile acid. J Bacteriol 2010; 192: 4983-90.
12. Giel JL, Sorg JA, Sonenshein AL, Zhu J,. Metabolism of bile salts in mice influences spore germination in Clostridium difficile. PLoS ONE 2010; 5: e8740.
13. Buffie CG, Bucci V, Stein RR, et al,. Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. Nature 2015; 517: 205-8.
14. Bakken JS, Borody T, Brandt LJ, et al,. Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol 2011; 9: 1044-9.
15. Murphy S, Churchill S, Bry L, et al,. Instrumenting the health care enterprise for discovery research in the genomic era. Genome Res 2009; 19: 1675-81.
16. Pecora ND, Li N, Allard M, et al,. Genomically Informed Surveillance for Carbapenem-resistant Enterobacteriaceae in a Health Care System. MBio 2015; 6: e01030-15.
17. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD,. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 2013; 79: 5112-20.
18. Schloss PD, Westcott SL, Ryabin T, et al,. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009; 75: 7537-41.
19. Matsen FA, Kodner RB, Armbrust EV,. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 2010; 11: 538.
20. Cole JR, Wang Q, Fish JA, et al,. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 2014; 42: D633-42.
21. David LA, Maurice CF, Carmody RN, et al,. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014; 505: 559-63.
22. Shannon CE,. The mathematical theory of communication. 1963. MD Comput 1997; 14: 306-17.
23. Bauer DF,. Circular triads when not all paired comparisons are made. Biometrics 1978; 34: 458-61.
24. Lozupone C, Knight R,. UniFrac: a new phylogenetic method for comparing microbial communities. Appl Environ Microbiol 2005; 71: 8228-35.
25. Excoffier L, Smouse PE, Quattro JM,. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 1992; 131: 479-91.
26. Baxter NT, Zackular JP, Chen GY, Schloss PD,. Structure of the gut microbiome following colonization with human feces determines colonic tumor burden. Microbiome 2014; 2: 20.
27. McMurdie PJ, Holmes S,. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 2013; 8: e61217.
28. Hochberg Y, Benjamini Y,. More powerful procedures for multiple significance testing. Stat Med 1990; 9: 811-8.
29. DeSantis TZ, Hugenholtz P, Larsen N, et al,. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72: 5069-72.
30. Langille MG, Zaneveld J, Caporaso JG, et al,. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 2013; 31: 814-21.
31. Cutler DR, Edwards TC Jr, Beard KH, et al,. Random forests for classification in ecology. Ecology 2007; 88: 2783-92.
32. Hirano S, Masuda N,. Epimerization of the 7-hydroxy group of bile acids by the combination of two kinds of microorganisms with 7 alpha- and 7 beta-hydroxysteroid dehydrogenase activity, respectively. J Lipid Res 1981; 22: 1060-8.
33. Hirano S, Masuda N,. Characterization of NADP-dependent 7 beta-hydroxysteroid dehydrogenases from Peptostreptococcus productus and Eubacterium aerofaciens. Appl Environ Microbiol 1982; 43: 1057-63.
34. Theriot CM, Koenigsknecht MJ, Carlson PE Jr, et al,. Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection. Nat Commun 2014; 5: 3114.
35. Theriot CM, Young VB,. Microbial and metabolic interactions between the gastrointestinal tract and Clostridium difficile infection. Gut Microbes 2014; 5: 86-95.
36. Weingarden AR, Chen C, Bobr A, et al,. Microbiota transplantation restores normal fecal bile acid composition in recurrent Clostridium difficile infection. Am J Physiol Gastrointest Liver Physiol 2014; 306: G310-9.
37. Varier RU, Biltaji E, Smith KJ, et al,. Cost-effectiveness analysis of treatment strategies for initial Clostridium difficile infection. Clin Microbiol Infect 2014; 20: 1343-51.
38. Sorg JA,. Microbial bile acid metabolic clusters: the bouncers at the bar. Cell Host Microbe 2014; 16: 551-2.
39. Doerner KC, Takamine F, LaVoie CP, Mallonee DH, Hylemon PB,. Assessment of fecal bacteria with bile acid 7 alpha-dehydroxylating activity for the presence of bai-like genes. Appl Environ Microbiol 1997; 63: 1185-8.
40. Kitahara M, Takamine F, Imamura T, Benno Y,. Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7alpha-dehydroxylating activity to Clostridium scindens and proposal of Clostridium hylemonae sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2000; 50 (Pt 3): 971-8.