Real-time PCR analysis of enteric pathogens from fecal samples of irritable bowel syndrome subjects

Gut Pathogens

Volumn 3, Issue 1, 2011, Pages

  Rinttilä, Teemu ^a,b   Lyra, Anna ^a,c   Krogius Kurikka, Lotta ^a   Palva, Airi ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b Alimetrics Ltd   (Finland)

^c Danisco Finland Oy   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80053602622     PISSN: None     EISSN: 17574749     Source Type: Journal    
DOI: 10.1186/1757-4749-3-6     Document Type: Article

References (66)

1. Functional bowel disorders. Longstreth GF, Thompson WG, Chey WD, Houghton LA, Mearin F, Spiller RC, Gastroenterology 2006 130 5 1480 1491 10.1053/j.gastro.2005.11.061 16678561
2. Irritable bowel syndrome. Mertz HR, N Engl J Med 2003 349 22 2136 2146 10.1056/NEJMra035579 14645642 (Pubitemid 37464539)
3. A national survey of practice patterns of gastroenterologists with comparison to the past two decades. Russo MW, Gaynes BN, Drossman DA, J Clin Gastroenterol 1999 29 4 339 10.1097/00004836-199912000-00009 10599638
4. Rome II-The functional gastrointestinal disorders. Drossman DA, Corazziari E, Talley NJ, Thompson WG, Whitehead WE, Virginia: Degnon Associates Second 2000
5. A systematic review of alternative therapies in the irritable bowel syndrome. Spanier JA, Howden CW, Jones MP, Arch Intern Med 2003 163 3 265 274 10.1001/archinte.163.3.265 12578506 (Pubitemid 36183854)
6. Functional bowel disorders and functional abdominal pain. Thompson WG, Longstreth GF, Drossman DA, Heaton KW, Irvine EJ, Muller-Lissner SA, Gut 1999 45 Suppl 2 I43 7 10457044
7. The functional gastrointestinal disorders and the Rome III process. Drossman DA, Gastroenterology 2006 130 5 1377 1390 10.1053/j.gastro.2006.03.008 16678553
8. Review article: the psycho-neuro-immunology of irritable bowel syndrome-an exploration of interactions between psychological, neurological and immunological observations. Arebi N, Gurmany S, Bullas D, Hobson A, Stagg A, Kamm M, Aliment Pharmacol Ther 2008 28 7 830 840 10.1111/j.1365-2036.2008.03801. x 18637004
9. New pathophysiological mechanisms in irritable bowel syndrome. Barbara G, De Giorgio R, Stanghellini V, Cremon C, Salvioli B, Corinaldesi R, Aliment Pharmacol Ther 2004 20 1 9 15496213 (Pubitemid 39237523)
10. AGA technical review on irritable bowel syndrome. Drossman DA, Camilleri M, Mayer EA, Whitehead WE, Gastroenterology 2002 123 6 2108 2131 10.1053/gast.2002.37095 12454866 (Pubitemid 35408332)
11. Postinfectious irritable bowel syndrome. Spiller R, Garsed K, Gastroenterology 2009 136 6 1979 1988 10.1053/j.gastro.2009.02.074 19457422
12. The incidence of irritable bowel syndrome among community subjects with previous acute enteric infection. Borgaonkar MR, Ford DC, Marshall JK, Churchill E, Collins SM, Dig Dis Sci 2006 51 5 1026 1032 10.1007/s10620-006-9348-1 16758307 (Pubitemid 44030833)
13. Irritable bowel syndrome-Post salmonella infection. McKendrick MW, Read NW, J Infect 1994 29 1 1 3 10.1016/S0163-4453(94)94871-2 7963621 (Pubitemid 24243103)
14. Prognosis in post-infective irritable bowel syndrome: a six year follow up study. Neal KR, Barker L, Spiller RC, Gut 2002 51 3 410 413 10.1136/gut.51.3.410 12171965
15. Prevalence of gastrointestinal symptoms six months after bacterial gastroenteritis and risk factors for development of the irritable bowel syndrome: postal survey of patients. Neal KR, Hebden J, Spiller R, BMJ 1997 314 7083 779 782 9080994 (Pubitemid 27117047)
16. Does bacterial gastroenteritis predispose people to functional gastrointestinal disorders? A prospective, community-based, case-control study. Parry SD, Stansfield R, Jelley D, Gregory W, Phillips E, Barton JR, Welfare MR, Am J Gastroenterol 2003 98 9 1970 1975 14499773 (Pubitemid 37185791)
17. Increased risk of irritable bowel syndrome after bacterial gastroenteritis: cohort study. Rodriguez LA, Ruigomez A, BMJ 1999 318 7183 565 566 10037630 (Pubitemid 29188957)
18. Bacillary dysentery as a causative factor of irritable bowel syndrome and its pathogenesis. Wang LH, Fang XC, Pan GZ, Gut 2004 53 8 1096 10.1136/gut.2003.021154 15247174 (Pubitemid 38961961)
19. Postinfectious Irritable Bowel Syndrome. Gwee KA, Curr Treat Options Gastroenterol 2001 4 4 287 291 10.1007/s11938-001-0053-z 11469986
20. Disease burden of post-infectious irritable bowel syndrome in The Netherlands. Haagsma JA, Siersema PD, DE Wit NJ, Havelaar AH, Epidemiol Infect 2010 138 11 1650 1656 10.1017/S0950268810000531 20223049
21. Is irritable bowel syndrome more common in patients presenting with bacterial gastroenteritis? A community-based, case-control study. Parry SD, Stansfield R, Jelley D, Gregory W, Phillips E, Barton JR, Welfare MR, Am J Gastroenterol 2003 98 2 327 331 10.1111/j.1572-0241.2003.07242.x 12591050 (Pubitemid 36232381)
22. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Zoetendal EG, Rajili -Stojanovi M, de Vos WM, Gut 2008 57 11 1605 1615 10.1136/gut.2007.133603 18941009
23. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Higuchi R, Fockler C, Dollinger G, Watson R, Biotechnology (N Y) 1993 11 9 1026 1030 10.1038/nbt0993-1026 (Pubitemid 23254023)
24. The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Kassinen A, Krogius-Kurikka L, Mäkivuokko H, Rinttilä T, Paulin L, Corander J, Malinen E, Apajalahti J, Palva A, Gastroenterology 2007 133 1 24 33 10.1053/j.gastro.2007.04.005 17631127 (Pubitemid 47031125)
25. Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers. Krogius-Kurikka L, Lyra A, Malinen E, Aarnikunnas J, Tuimala J, Paulin L, Mäkivuokko H, Kajander K, Palva A, BMC Gastroenterol 2009 9 95 10.1186/1471-230X-9-95 20015409
26. Diarrhoea-predominant irritable bowel syndrome distinguishable by 16S rRNA gene phylotype quantification. Lyra A, Rinttilä T, Nikkilä J, Krogius-Kurikka L, Kajander K, Malinen E, Mättö J, Mäkelä L, Palva A, World J Gastroenterol 2009 15 47 5936 5945 10.3748/wjg.15.5936 20014457
27. Effect of a multispecies probiotic supplement on quantity of irritable bowel syndrome-related intestinal microbial phylotypes. Lyra A, Krogius-Kurikka L, Nikkilä J, Malinen E, Kajander K, Kurikka K, Korpela R, Palva A, BMC Gastroenterology 2010 10 1 110 10.1186/1471-230X-10-110 20849659
28. Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. Malinen E, Krogius-Kurikka L, Lyra A, Nikkilä J, Jääskeläinen A, Rinttilä T, Vilpponen-Salmela T, von Wright AJ, Palva A, World J Gastroenterol 2010 16 36 4532 4540 10.3748/wjg.v16.i36.4532 20857523
29. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Malinen E, Rinttilä T, Kajander K, Mättö J, Kassinen A, Krogius L, Saarela M, Korpela R, Palva A, Am J Gastroenterol 2005 100 2 373 382 10.1111/j.1572-0241.2005.40312.x 15667495 (Pubitemid 40314522)
30. Functional bowel disorders and functional abdominal pain. Thompson WG, Creed FH, Drossman DA, Heaton KW, Mazzacca G, Gastroenterol Int 1992 5 75 91
31. Effects of multispecies probiotic supplementation on intestinal microbiota in irritable bowel syndrome. Kajander K, Krogius-Kurikka L, Rinttilä T, Karjalainen H, Palva A, Korpela R, Aliment Pharmacol Ther 2007 26 3 463 473 10.1111/j.1365-2036.2007.03391.x 17635381 (Pubitemid 47063154)
32. Sequence analysis of percent G+C fraction libraries of human faecal bacterial DNA reveals a high number of Actinobacteria. Krogius-Kurikka L, Kassinen A, Paulin L, Corander J, Mäkivuokko H, Tuimala J, Palva A, BMC Microbiol 2009 9 1 68 10.1186/1471-2180-9-68 19351420
33. Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome - a longitudinal study in IBS and control subjects. Mättö J, Maunuksela L, Kajander K, Palva A, Korpela R, Kassinen A, Saarela M, FEMS Immunol Med Microbiol 2005 43 2 213 222 10.1016/j.femsim.2004. 08.009 15747442 (Pubitemid 40170291)
34. Effective recovery of bacterial DNA and percent-guanine-plus-cytosine- based analysis of community structure in the gastrointestinal tract of broiler chickens. Apajalahti JH, Särkilahti LK, Mäki BR, Heikkinen JP, Nurminen PH, Holben WE, Appl Environ Microbiol 1998 64 10 4084 4088 9758849 (Pubitemid 28463022)
35. Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, J Mol Biol 1990 215 3 403 410 2231712
36. R: A Language and Environment for Statistical Computing. R Development Core Team, 2009
37. The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM, Nucleic Acids Res 2003 31 1 442 443 10.1093/nar/gkg039 12520046 (Pubitemid 36150424)
38. A Molecular Analysis of Fecal and Mucosal Bacterial Communities in Irritable Bowel Syndrome. Codling C, O'Mahony L, Shanahan F, Quigley EM, Marchesi JR, Dig Dis Sci 2009 55 2 392 397 19693670
39. Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. Maukonen J, Satokari R, Mättö J, Söderlund H, Mattila-Sandholm T, Saarela M, J Med Microbiol 2006 55 Pt 5 625 633 16585652
40. Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome. Tana C, Umesaki Y, Imaoka A, Handa T, Kanazawa M, Fukudo S, Neurogastroenterology & Motility 2010 22 5 512 519 21519375
41. Staphylococcal food poisoning (Staphylococcal enterotoxicosis). Tortora GJ, Microbiology. An Introduction Benjamin Cummings Publishing Company, Inc, Tortora GJ, Funke BR, Case CL, 1 1995 616 618
42. Current perspectives on detection of staphylococcal enterotoxins. Su YC, Wong L, Amy C, J Food Prot 1997 60 2 195 202
43. Identification and typing of food-borne Staphylococcus aureus by PCR-based techniques. Pinto B, Chenoll E, Aznar R, Syst Appl Microbiol 2005 28 4 340 352 10.1016/j.syapm.2005.01.002 15997707 (Pubitemid 40726080)
44. Postinfectious irritable bowel syndrome: a long-term consequence of bacterial gastroenteritis. Smith JL, Bayles D, J Food Prot 2007 70 7 1762 1769 17685356 (Pubitemid 47076120)
45. Relative importance of enterochromaffin cell hyperplasia, anxiety, and depression in postinfectious IBS. Dunlop SP, Jenkins D, Neal KR, Spiller RC, Gastroenterology 2003 125 6 1651 1659 10.1053/j.gastro.2003.09.028 14724817 (Pubitemid 37500429)
46. Dyspepsia and irritable bowel syndrome after a Salmonella gastroenteritis outbreak: one-year follow-up cohort study. Mearin F, Perez-Oliveras M, Perello A, Vinyet J, Ibanez A, Coderch J, Perona M, Gastroenterology 2005 129 1 98 104 10.1053/j.gastro.2005.04.012 16012939 (Pubitemid 41002046)
47. The association between Helicobacter pylori infection and functional dyspepsia in patients with irritable bowel syndrome. Su YC, Wang WM, Wang SY, Lu SN, Chen LT, Wu DC, Chen CY, Jan CM, Horowitz M, Am J Gastroenterol 2000 95 8 1900 1905 10.1111/j.1572-0241.2000.02252.x 10950033
48. The putative role of inflammation in the irritable bowel syndrome. Collins SM, Piche T, Rampal P, Gut 2001 49 6 743 745 10.1136/gut.49.6.743 11709500 (Pubitemid 33096023)
49. The rapid identification of Clostridium perfringens as the possible aetiology of a diarrhoeal outbreak using PCR. Loh JP, Liu YC, Chew SW, Ong ES, Fam JM, Ng YY, Taylor MB, Ooi EE, Epidemiol Infect 2008 136 08 1142 1146 17961281 (Pubitemid 351982939)
50. Characterization of an outbreak of Clostridium perfringens food poisoning by quantitative fecal culture and fecal enterotoxin measurement. Birkhead G, Vogt RL, Heun EM, Snyder JT, McClane BA, J Clin Microbiol 1988 26 3 471 474 2895776 (Pubitemid 18062103)
51. The evaluation of a fluorogenic polymerase chain reaction assay for the detection of Salmonella species in food commodities. Chen S, Yee A, Griffiths M, Larkin C, Yamashiro CT, Behari R, Paszko-Kolva C, Rahn K, De Grandis SA, Int J Food Microbiol 1997 35 3 239 250 10.1016/S0168-1605(97)01241-5 9105933 (Pubitemid 27148437)
52. Removal of PCR inhibitors from human faecal samples through the use of an aqueous two-phase system for sample preparation prior to PCR. Lantz PG, Matsson M, Wadström T, Rådström P, J Microbiol Methods 1997 28 3 159 167 10.1016/S0167-7012(97)00979-2 (Pubitemid 27244800)
53. Detection of Helicobacter pylori DNA in human feces by PCR: DNA stability and removal of inhibitors. Monteiro L, Gras N, Vidal R, Cabrita J, Megraud F, J Microbiol Methods 2001 45 2 89 94 10.1016/S0167-7012(01)00225-1 11311393 (Pubitemid 32322649)
54. Capacity of nine thermostable DNA polymerases to mediate DNA amplification in the presence of PCR-inhibiting samples. Abu Al-Soud W, Rådström P, Appl Environ Microbiol 1998 64 10 3748 3753 9758794 (Pubitemid 28462967)
55. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. Rinttilä T, Kassinen A, Malinen E, Krogius L, Palva A, J Appl Microbiol 2004 97 6 1166 1177 10.1111/j.1365-2672.2004.02409.x 15546407 (Pubitemid 39573940)
56. Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. Salonen A, Nikkilä J, Jalanka-Tuovinen J, Immonen O, Rajili -Stojanovi M, Kekkonen RA, Palva A, de Vos WM, J Microbiol Methods 2010 81 2 127 134 10.1016/j.mimet.2010.02.007 20171997
57. PCR detection, characterization, and distribution of virulence genes in Aeromonas spp. Kingombe CI, Huys G, Tonolla M, Albert MJ, Swings J, Peduzzi R, Jemmi T, Appl Environ Microbiol 1999 65 12 5293 5302 10583979 (Pubitemid 129520612)
58. Detection of Bacillus cereus group bacteria from cardboard and paper with real-time PCR. Priha O, Hallamaa K, Saarela M, Raaska L, J Ind Microbiol Biotechnol 2004 31 4 161 169 15064974 (Pubitemid 38916389)
59. Multiplex PCR for identification of Campylobacter coli and Campylobacter jejuni from pure cultures and directly on stool samples. Persson S, Olsen KE, J Med Microbiol 2005 54 Pt 11 1043 1047 16192435 (Pubitemid 41566774)
60. Detection of enterotoxigenic Clostridium perfringens in food and fecal samples with a duplex PCR and the slide latex agglutination test. Fach P, Popoff MR, Appl Environ Microbiol 1997 63 11 4232 4236 9361409 (Pubitemid 27485744)
61. Duplex real-time SYBR green PCR assays for detection of 17 species of food- or waterborne pathogens in stools. Fukushima H, Tsunomori Y, Seki R, J Clin Microbiol 2003 41 11 5134 5146 10.1128/JCM.41.11.5134-5146.2003 14605150 (Pubitemid 37429927)
62. Detection in Escherichia coli of the genes encoding the major virulence factors, the genes defining the O157:H7 serotype, and components of the type 2 Shiga toxin family by multiplex PCR. Wang G, Clark CG, Rodgers FG, J Clin Microbiol 2002 40 10 3613 3619 10.1128/JCM.40.10.3613-3619.2002 12354854
63. Detection and quantification of the iap gene of Listeria monocytogenes and Listeria innocua by a new real-time quantitative PCR assay. Hein I, Klein D, Lehner A, Bubert A, Brandl E, Wagner M, Res Microbiol 2001 152 1 37 46 10.1016/S0923-2508(00)01166-9 11281324 (Pubitemid 32168116)
64. Amplification of an invA gene sequence of Salmonella typhimurium by polymerase chain reaction as a specific method of detection of Salmonella. Rahn K, De Grandis SA, Clarke RC, McEwen SA, Galan JE, Ginocchio C, Curtiss R, Gyles CL, Mol Cell Probes 1992 6 4 271 279 10.1016/0890-8508(92)90002-F 1528198
65. Detection of Staphylococcus aureus by polymerase chain reaction amplification of the nuc gene. Brakstad OG, Aasbakk K, Maeland JA, J Clin Microbiol 1992 30 7 1654 1660 1629319
66. Development of a fluorogenic 5′ nuclease PCR assay for detection of the ail gene of pathogenic Yersinia enterocolitica. Jourdan AD, Johnson SC, Wesley IV, Appl Environ Microbiol 2000 66 9 3750 3755 10.1128/AEM.66.9.3750- 3755.2000 10966386