Gut Microbiota Patterns Associated with Colonization of Different Clostridium difficile Ribotypes

PLoS ONE

Volumn 8, Issue 2, 2013, Pages

  Skraban, Jure ^a,c   Dzeroski, Saso ^c,d   Zenko, Bernard ^c,d   Mongus, Domen ^a   Gangl, Simon ^a   Rupnik, Maja ^a,b,c  

^a UNIVERSITY OF MARIBOR   (Slovenia)

^b Institute of Public Health Maribor   (Slovenia)

^c Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins   (Slovenia)

^d JO EF STEFAN INSTITUTE   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA 16S;

ADOLESCENT; ADULT; AGED; ARTICLE; BACTERIAL COLONIZATION; BACTERIUM CARRIER; BACTERIUM CULTURE; BACTERIUM DETECTION; BACTERIUM ISOLATION; BACTEROIDES UNIFORMIS; BACTEROIDES VULGATUS; BIFIDOBACTERIUM LONGUM; CANDIDA ALBICANS; CANDIDA GLABRATA; CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM DIFFICILE INFECTION; COMPUTER PROGRAM; CONTROLLED STUDY; DENATURING HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; DNA EXTRACTION; ENTEROBACTERIACEAE; ESCHERICHIA; FAECALIBACTERIUM; FECES ANALYSIS; FEMALE; HUMAN; INTESTINE FLORA; MACHINE LEARNING; MAJOR CLINICAL STUDY; MALE; METHANOBREVIBACTER SMITHII; MICROBIAL DIVERSITY; PEPTOSTREPTOCOCCACEAE; POLYMERASE CHAIN REACTION; PREDICTION; PREVOTELLA; RIBOTYPING; RUMINOCOCCUS; RUMINOCOCCUS BROMII; SHIGELLA;

ADOLESCENT; ADULT; AGED; ARCHAEA; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CLOSTRIDIUM DIFFICILE; FECES; FEMALE; FUNGI; HUMANS; INTESTINES; MALE; METAGENOME; MIDDLE AGED; POLYMERASE CHAIN REACTION; PRINCIPAL COMPONENT ANALYSIS; RIBOTYPING; YOUNG ADULT;

EID: 84874556536     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0058005     Document Type: Article

References (46)

1. Rupnik M, Wilcox MH, Gerding DN, (2009) Clostridium difficile infection: new developments in epidemiology and pathogenesis. Nat Rev Microbiol 7: 526-536.
2. Johnson S, Samore MH, Farrow KA, Killgore GE, Tenover FC, et al. (1999) Epidemics of diarrhea caused by a clindamycin-resistant strain of Clostridium difficile in four hospitals. N Engl J Med 341: 1645-1651.
3. Graul T, Cain AM, Karpa KD, (2009) Lactobacillus and bifidobacteria combinations: a strategy to reduce hospital-acquired Clostridium difficile diarrhea incidence and mortality. Med Hypotheses 73: 194-198.
4. Mattila E, Uusitalo-Seppala R, Wuorela M, Lehtola L, Nurmi H, et al. (2012) Fecal Transplantation, Through Colonoscopy, Is Effective Therapy for Recurrent Clostridium difficile Infection. Gastroenterology 142: 490-496.
5. Mellow MH, Kanatzar A, (2011) Colonoscopic fecal bacteriotherapy in the treatment of recurrent Clostridium difficile infection--results and follow-up. J Okla State Med Assoc 104: 89-91.
6. Ho N, Prasad V, (2011) Clostridium difficile diarrhea and fecal transplantation. J Clin Gastroenterol 45: 742-743.
7. Buffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, et al. (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.
8. Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, et al. (2008) Decreased diversity of the fecal Microbiome in recurrent Clostridium difficile-associated diarrhea. J Infect Dis 197: 435-438.
9. De La Cochetiere MF, Durand T, Lalande V, Petit JC, Potel G, et al. (2008) Effect of antibiotic therapy on human fecal microbiota and the relation to the development of Clostridium difficile. Microb Ecol 56: 395-402.
10. Rousseau C, Lemee L, Le Monnier A, Poilane I, Pons JL, et al. (2011) Prevalence and diversity of Clostridium difficile strains in infants. J Med Microbiol 60: 1112-1118.
11. Rea MC, O'Sullivan O, Shanahan F, O'Toole PW, Stanton C, et al. (2012) Clostridium difficile Carriage in Elderly Subjects and Associated Changes in the Intestinal Microbiota. J Clin Microbiol 50: 867-875.
12. Goldenberg O, Herrmann S, Marjoram G, Noyer-Weidner M, Hong G, et al. (2007) Molecular monitoring of the intestinal flora by denaturing high performance liquid chromatography. Journal of Microbiological Methods 68: 94-105.
13. Wagner AO, Malin C, Illmer P, (2009) Application of denaturing high-performance liquid chromatography in microbial ecology: fermentor sludge, compost, and soil community profiling. Appl Environ Microbiol 75: 956-964.
14. Domann E, Hong G, Imirzalioglu C, Turschner S, Kuhle J, et al. (2003) Culture-independent identification of pathogenic bacteria and polymicrobial infections in the genitourinary tract of renal transplant recipients. Journal of Clinical Microbiology 41: 5500-5510.
15. Rouge C, Goldenberg O, Ferraris L, Berger B, Rochat F, et al. (2010) Investigation of the intestinal microbiota in preterm infants using different methods. Anaerobe 16: 362-370.
16. Peterfreund GL, Vandivier LE, Sinha R, Marozsan AJ, Olson WC, et al. (2012) Succession in the Gut Microbiome following Antibiotic and Antibody Therapies for Clostridium difficile. PLoS One 7: e46966.
17. Zidaric V, Zemljic M, Janezic S, Kocuvan A, Rupnik M, (2008) High diversity of Clostridium difficile genotypes isolated from a single poultry farm producing replacement laying hens. Anaerobe 14: 325-327.
18. Bidet P, Barbut F, Lalande V, Burghoffer B, Petit JC, (1999) Development of a new PCR-ribotyping method for Clostridium difficile based on ribosomal RNA gene sequencing. FEMS Microbiol Lett 175: 261-266.
19. Rupnik M, Avesani V, Janc M, von Eichel-Streiber C, Delmee M, (1998) A novel toxinotyping scheme and correlation of toxinotypes with serogroups of Clostridium difficile isolates. J Clin Microbiol 36: 2240-2247.
20. Thompson JR, Marcelino LA, Polz MF, (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res 30: 2083-2088.
21. Ovreas L, Forney L, Daae FL, Torsvik V, (1997) Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA. Appl Environ Microbiol 63: 3367-3373.
22. Borneman J, Hartin RJ, (2000) PCR primers that amplify fungal rRNA genes from environmental samples. Appl Environ Microbiol 66: 4356-4360.
23. White TJ, Bruns T, Lee S, Taylor J (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: a guide to methods and applications Academic Press, New York, USA: 315-322.
24. Turenne CY, Sanche SE, Hoban DJ, Karlowsky JA, Kabani AM, (1999) Rapid identification of fungi by using the ITS2 genetic region and an automated fluorescent capillary electrophoresis system. J Clin Microbiol 37: 1846-1851.
25. Goldenberg O, Herrmann S, Adam T, Marjoram G, Hong G, et al. (2005) Use of denaturing high-performance liquid chromatography for rapid detection and identification of seven Candida species. J Clin Microbiol 43: 5912-5915.
26. Quinlan JR (1993) C4.5: Programs for Machine Learning. Morgan Kaufman, San Francisco, CA, USA.
27. Breiman L, Friedman J, Olshen R, Stone C (1984) Classification and Regression Trees. Wadsworth, Belmont, CA.
28. Witten IH, Frank E, Hall MA (2011) Data mining: Practical Machine Learning Tools and Techniques. Morgan Kaufman, San Francisco, CAUSA, third edition.
29. Blockeel H, De Raedt L, Ramon J (1998) Top-down induction of clustering trees. In: Proceedings of the Fifteenth International Conference on Machine Learning (ICML 98) Morgan Kaufmann: 55-63.
30. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, et al. (2006) Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 55: 205-211.
31. Carroll IM, Ringel-Kulka T, Siddle JP, Ringel Y, (2012) Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Neurogastroenterol Motil24: 521-530, e248.
32. Zwielehner J, Lassl C, Hippe B, Pointner A, Switzeny OJ, et al. (2011) Changes in human fecal microbiota due to chemotherapy analyzed by TaqMan-PCR, 454 sequencing and PCR-DGGE fingerprinting. PLoS One 6: e28654.
33. De La Cochetiere MF, Durand T, Lepage P, Bourreille A, Galmiche JP, et al. (2005) Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J Clin Microbiol 43: 5588-5592.
34. Lofmark S, Jernberg C, Jansson JK, Edlund C, (2006) Clindamycin-induced enrichment and long-term persistence of resistant Bacteroides spp. and resistance genes. J Antimicrob Chemother 58: 1160-1167.
35. Hopkins MJ, Macfarlane GT, (2002) Changes in predominant bacterial populations in human faeces with age and with Clostridium difficile infection. J Med Microbiol 51: 448-454.
36. Manges AR, Labbe A, Loo VG, Atherton JK, Behr MA, et al. (2010) Comparative metagenomic study of alterations to the intestinal microbiota and risk of nosocomial Clostridum difficile-associated disease. J Infect Dis 202: 1877-1884.
37. Rousseau C, Levenez F, Fouqueray C, Dore J, Collignon A, et al. (2011) Clostridium difficile colonization in early infancy is accompanied by changes in intestinal microbiota composition. J Clin Microbiol 49: 858-865.
38. Ozaki E, Kato H, Kita H, Karasawa T, Maegawa T, et al. (2004) Clostridium difficile colonization in healthy adults: transient colonization and correlation with enterococcal colonization. J Med Microbiol 53: 167-172.
39. Fujitani S, George WL, Morgan MA, Nichols S, Murthy AR, (2011) Implications for vancomycin-resistant Enterococcus colonization associated with Clostridium difficile infections. Am J Infect Control 39: 188-193.
40. Scanlan PD, Marchesi JR, (2008) Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and-independent analysis of faeces. Isme Journal 2: 1183-1193.
41. Ott SJ, Kuhbacher T, Musfeldt M, Rosenstiel P, Hellmig S, et al. (2008) Fungi and inflammatory bowel diseases: Alterations of composition and diversity. Scand J Gastroenterol 43: 831-841.
42. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
43. Samuel BS, Gordon JI, (2006) A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism. Proc Natl Acad Sci U S A 103: 10011-10016.
44. Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, et al. (2009) Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci U S A 106: 2365-2370.
45. Eckburg PB, Lepp PW, Relman DA, (2003) Archaea and their potential role in human disease. Infect Immun 71: 591-596.
46. Barbut F, Rupnik M, (2012) Editorial commentary: 027, 078, and others: going beyond the numbers (and away from the hypervirulence). Clin Infect Dis 55: 1669-1672.