Effects of b-lactam antibiotics and fluoroquinolones on human gut microbiota in relation to clostridium difficile associated diarrhea

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Knecht, Henrik ^a   Neulinger, Sven C ^a   Heinsen, Femke Anouska ^a   Knecht, Carolin ^a   Schilhabel, Anke ^a   Schmitz, Ruth A ^a   Zimmermann, Alexandra ^a   Dos Santos, Vitor Martins ^b,c   Ferrer, Manuel ^d   Rosenstiel, Philip C ^a   Schreiber, Stefan ^a,e   Friedrichs, Anette K ^a,e   Ott, Stephan J ^a,e  

^a UNIVERSITY OF KIEL   (Germany)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c LIFEGLIMMER GMBH   (Germany)

^d INSTITUTO DE CATÁLISIS Y PETROLEOQUÍMICA   (Spain)

^e UNIVERSITY HOSPITAL SCHLESWIG HOLSTEIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BETA LACTAM ANTIBIOTIC; CEPHALOSPORIN; COMPLEMENTARY DNA; QUINOLINE DERIVED ANTIINFECTIVE AGENT; RNA 16S; SULTAMICILLIN; AMPICILLIN; BETA LACTAM; CEPHALOSPORIN DERIVATIVE; QUINOLONE DERIVATIVE; SULBACTAM;

AGED; AMPLICON; ANTIBIOTIC THERAPY; ARTICLE; BACTERIAL COLONIZATION; CLINICAL ARTICLE; CLOSTRIDIUM DIFFICILE INFECTION; CONTROLLED STUDY; DISEASE SEVERITY; DNA DETERMINATION; DOWN REGULATION; DRUG EFFECT; FECES ANALYSIS; HUMAN; INTESTINE FLORA; MICROBIAL DIVERSITY; NONHUMAN; RNA ANALYSIS; RNA SEQUENCE; SPECIES COMPOSITION; SPECIES DISTRIBUTION; UPREGULATION; CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM INFECTION; DIARRHEA; GASTROINTESTINAL TRACT; GENETICS; MICROBIOLOGY; MICROFLORA; PATHOGENICITY;

AMPICILLIN; BETA-LACTAMS; CEPHALOSPORINS; CLOSTRIDIUM DIFFICILE; CLOSTRIDIUM INFECTIONS; DIARRHEA; FLUOROQUINOLONES; GASTROINTESTINAL TRACT; HUMANS; MICROBIOTA; RNA, RIBOSOMAL, 16S; SULBACTAM;

EID: 84896520726     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0089417     Document Type: Article

References (52)

1. Kyne L, Hamel MB, Polavaram R, Kelly CP (2002) Health care costs and mortality associated with nosocomial diarrhea due to C. difficile. Clin Infect Dis 23: 653-9.
2. Lawley TD, Walker AW (2013) Intestinal colonization resistance. Immunology 138: 1-11.
3. Thomas V, Rochet V, Boureau H, Ekstrand C, Bulteau S, et al. (2002) Molecular characterization and spatial analysis of a simplified gut microbiota displaying colonization resistance against Clostridium difficile. Microbial ecology in Health and Disease 14: 203-210. (Pubitemid 36222180)
4. Pepin J, Alary ME, Valiquette L, Raiche E, Ruel J, et al. (2005) Increasing risk of relapse after treatment of Clostridium difficile colitis in Quebec, Canada. Clin Infect Dis 40: 1591-7. (Pubitemid 40720808)
5. McDonald LC (2006) Confronting C. difficile in inpatient health care facilities. Clin Infect Dis 45: 1274-6.
6. Cloud J, Kelly CP (2007) Update on C. difficile associated diseases. Curr Opin Gastroenterol 23: 4-9.
7. Bartlett JG (2006) Narrative review: the new epidemic of C. difficile-associated enteric diseases. Ann Intern Med 145:758-64.
8. Loo VG, Poirier L, Miller MA, Oughton M, Libman MD, et al. (2005) A predominant clonal multi-institutional outbreak of C. difficile-associated diarrhea with high morbidity and mortality. N Engl J Med 353: 2442-9. (Pubitemid 41770165)
9. Gerding DN (2004) Clindamycine, cephalosporins, fluoroquinolones, and C. difficile-associated diarrhea: this is an antimicrobial resistance problem. Clin Infect Dis 38: 646-648. (Pubitemid 38333859)
10. Sullivan A, Edlund C, Nord C (2001) Effect of antimicrobial agents on the ecological balance of human microflora. Lancet Infect Dis 1: 101-114. (Pubitemid 33586045)
11. Jernberg C, Lo fmark S, Edlund C, Jansson JK (2007) Long-term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 1:56-66. (Pubitemid 46717132)
12. Freeman HJ (2008) Recent developments on the role of C. difficile in inflammatory bowel disease. World J Gastroenterol 14: 2794-2796.
13. Wilson K (1993) The microecology of C. difficile. Clin Infect Dis 16:214-218.
14. Manges A, Labbe A, Loo V, Atherton J, Behr M, et al. (2010) Comparative metagenomic study of alterations to the intestinal microbiota and risk of nosocomial C. difficile-associated disease. J Infect Dis 202: 1877-1884.
15. Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, et al. (2008) Decreased diversity of the fecal Microbiome in recurrent C. difficile-associated diarrhea. J Infect Dis 197: 435-8. (Pubitemid 351263426)
16. Barc MC, Bourlioux F, Rigottier-Gois L, Charrin-Sarnel C, Janoir C, et al. (2004) Effect of amoxicillin-clavulanic acid on human fecal flora in gnotobiotic mouse model assessed with fluorescence hybridization using group-specific 16S rRNA probes in combination with flow cytrometry. Antimicrob Agents Chemother 48:1365-8. (Pubitemid 38405497)
17. Tvade M, Rask Madsen J (1989) Bacteriotherapy for chronic relapsing C. difficile diarrhea in six patients. Lancet 1: 1156-1160.
18. Rosseau C, Lemee L, Le Monnier A, Poilane I, Pons JL, et al. (2011) Prevalence and diversity of C. difficile strains in infants. J Med Microbiol 60: 1112-8.
19. Blazewicz SJ, Barnard RL, Daly RA, Firestone MK (2013) Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses. ISME 7: 2061-8
20. Reeves AE, Theriot SM, Bergin IL, Huffnagle GB, Schloss PD, et al. (2011) The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile infection. Gut Microbes 2: 145-58.
21. Blondeau JM (2009) What have we learned about antimicrobial use and the risks for Clostridium difficile-associated diarrhea? Journal of Antimicrobial Chemotherapy 63: 238-242.
22. Hove H, Tvede M, Mortensen PB (1996) Antibiotic-associated diarrhea, Clostridium difficile, and short-chain fatty acids. Scand J Gastroenterol 31: 688-93. (Pubitemid 26290933)
23. Rolfe RD (1984) Role of volatile fatty acids in colonization resistance to Clostridium difficile. Infect. Immun 45: 185-191. (Pubitemid 14078938)
24. Cotta M, Forster R (2006) The family Lachnospiraceae, including the genera Butyrivibrio, Lachnospira and Roseburia. Prokaryotes 4: 1002-1021.
25. Hill DA, Hoffmann C, Abt MC, Du Y, Kobuley D, et al. (2010) Metagenomic analysis reveal antibiotic-induced temporal and spatial changes in the intestinal microbiota with associated alterations in immune cell homeostasis. Mucosa Immunology 3; 148-158.
26. Fujimoto T, Imaeda H, Takahashi K, Kasumi E, Bamba S, et al. (2013) Decreased abundance of Faecalibacterium prausnitzii in the gut microbiota of Crohn's disease. J Gastroenterol Hepatol 28: 613-9.
27. Duboc H, Rainteau D, Rajca S, Humbert L, Farabos D, et al. (2012) Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome. Neurogastroenterol Motil 24:513-20.
28. Bajaj JS, Hylemon PB, Ridlon JM, Heuman DM, Daita K, et al. (2012) Colonic mucosal microbiome differs from stool microiome in cirrhosis and hepatic encephalopathy and is linked to cognition and inflammation. Am J Physiol Gastrointest Liver Physiol 303: G675-85.
29. Chen W, Liu F, Ling Z, Tong X, Xiang C (2012) Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PloS One 7: e39743.
30. Kassinen A, Krogius-Kurikka L, Makivuokko H, Rinttila T, Paulin L, et al. (2007) The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133: 24-33. (Pubitemid 47031125)
31. Lau S, Woo PC, Fung AM, Chan KM, Woo GK, et al. (2004) Anaerobic, nonsporulating, Gram-positive bacilli bacteraemia characterized by 16S rRNA gene sequencing. J Med Microbiol 53: 1247-1253. (Pubitemid 40052481)
32. Lau S, Woo PC, Woo GK, Fung AM, Wong MK, et al. (2004). Eggerthella hongkongensis sp. nov. and Eggerthella sinensis sp. nov., two novel Eggerthella species, account for half of the cases of Eggerthella bacteremia. Diagn Microbiol Infect Dis 49: 255-263. (Pubitemid 39094616)
33. Rajeshwair DS, Basappa BK (2011) Vancomycin Resistance Genes in Various Organisms-An Insilico Study. IJBB 5(2).
34. Coates P, Vyakrnam S, Eady EA, Jones CE, Cove JH, et al. (2002) Prevalence of antibiotic-resistant propionibacteria on the skin of acne patients: 10-year surveillance data and snapshot distribution study. Br J Dermatol 146: 840-8. (Pubitemid 34539195)
35. Tzellos T, Zampelli V, Makrantonaki E, Zouboulis CC (2011) Treating acne with antibiotic-resistant bacterial colonization. Expert Opin Pharmacother 12: 1233-47.
36. Mutschler E, Geisslinger HK, Kroemer P (2008) Arzneitmittelwirkungen. Lehrbuch der Pharmakologie und Toxikologie p794.
37. Kohler W, Eggers HJ, Fleischer B (2001) Medizinische Mikrobiologie. 8. Auflage, Elsevier, Munick, p.200.
38. Antonopoulos DA, Huse SM, Morrison HG, Schmidt TM, Sogin ML, et al. (2009) Reproducible community dynamics of the gastrointestinal microbiota following antibiotic perturbation. Infect Immun; 77: 2367-75.
39. Croswell A, Amir E, Teggatz P, Barman M, Salzman NH (2009) Prolonged impact of antibiotics on intestinal microbial ecology and susceptibility to enteric Salmonella infection. Infect Immun 77: 2741-2753.
40. De La Cochetiere MF, Durand T, Lepage P, Bourreille A, Galmiche JP (2005) Resilience of the dominant human faecal microbiota upon short-course antibiotic challenge. L Clin Microbiol 43: 5588-92. (Pubitemid 41612335)
41. Dethlefsen L, Huse S, Sogin ML, Relman DA (2008) The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 6:e280.
42. Rehman A, Sina C, Gavrilova O, Ha sler R, Ott S, et al. (2011) Nod2 is essentiell for temporal development of intestinal microbial communities. Gut 60: 1354-62.
43. Stratil SB, Neulinger SC, Knecht H, Friedrichs AK, Wahl M (2013) Temperature-driven shifts in the epibiotic bacterial community of the brown macroalgae Fucus vesiculosus. Microbiologyopen 2: 338-49.
44. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-41.
45. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing J R Statist Soc B 57: 289-300.
46. Borcard D, Gillet F, Legendre P (2011) Numerical ecology with R. New York : Springer. 319 p.
47. Oksanen J, Blanchet FG, Kindt R, Legendre O, Minchin PR, et al. (2013) Vegan: Community ecology package. R package version 2.0-7 ed.
48. Legendre P, Gallagher ED (2001) Ecologically meaningful transformation for ordination of species data. Oecologia 129: 271-280. (Pubitemid 32996572)
49. Jost L (2006) Entropy and diversity. Oikos 113: 363-375. (Pubitemid 43781677)
50. Jost L (2007) Partitioning diversity into independent alpha and beta components. Ecology 88: 2427-2439. (Pubitemid 351345099)
51. Zhu M, Ghodsi A (2006) Automatic dimensionality selection from the scree plot vial the use of profile likelihood. Computitional Statistics & Data Analysis 51: 918-930. (Pubitemid 44635870)
52. De Caceres M, Legendre P (2009) Association between species and groups of sites: indices and statistical interference. Ecology 90: 3566-3574.