IGEM:IMPERIAL/2007/Projects/Biofilm Detector/References

Infector Detector: References

• Introduction
• Specifications
• Design
• Modelling
• Fabrication
• Testing
• Data Analysis
• Validation
• Notes
• References

Publications

• Introductions and reviews

1. Costerton JW, Lewandowski Z, DeBeer D, Caldwell D, Korber D, and James G. Biofilms, the customized microniche. J Bacteriol. 1994 Apr;176(8):2137-42. DOI:10.1128/jb.176.8.2137-2142.1994 |
2. Jackson DW, Suzuki K, Oakford L, Simecka JW, Hart ME, and Romeo T. Biofilm formation and dispersal under the influence of the global regulator CsrA of Escherichia coli. J Bacteriol. 2002 Jan;184(1):290-301. DOI:10.1128/JB.184.1.290-301.2002 |
3. Lu TK and Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proc Natl Acad Sci U S A. 2007 Jul 3;104(27):11197-202. DOI:10.1073/pnas.0704624104 |

Heterogeneity of phenotypes

4. Xu KD, Stewart PS, Xia F, Huang CT, and McFeters GA. Spatial physiological heterogeneity in Pseudomonas aeruginosa biofilm is determined by oxygen availability. Appl Environ Microbiol. 1998 Oct;64(10):4035-9. DOI:10.1128/AEM.64.10.4035-4039.1998 |
5. MacLeod FA, Guiot SR, and Costerton JW. Layered structure of bacterial aggregates produced in an upflow anaerobic sludge bed and filter reactor. Appl Environ Microbiol. 1990 Jun;56(6):1598-607. DOI:10.1128/aem.56.6.1598-1607.1990 |
6. Sternberg C, Christensen BB, Johansen T, Toftgaard Nielsen A, Andersen JB, Givskov M, and Molin S. Distribution of bacterial growth activity in flow-chamber biofilms. Appl Environ Microbiol. 1999 Sep;65(9):4108-17. DOI:10.1128/AEM.65.9.4108-4117.1999 |

Experimental techniques

7. Harmsen HJ, Kengen HM, Akkermans AD, Stams AJ, and de Vos WM. Detection and localization of syntrophic propionate-oxidizing bacteria in granular sludge by in situ hybridization using 16S rRNA-based oligonucleotide probes. Appl Environ Microbiol. 1996 May;62(5):1656-63. DOI:10.1128/aem.62.5.1656-1663.1996 |

Diffusion and flow in biofilms

8. Stewart PS. A review of experimental measurements of effective diffusive permeabilities and effective diffusion coefficients in biofilms. Biotechnol Bioeng. 1998 Aug 5;59(3):261-72. DOI:10.1002/(sici)1097-0290(19980805)59:3<261::aid-bit1>3.0.co;2-9 |
9. Stoodley P, Debeer D, and Lewandowski Z. Liquid flow in biofilm systems. Appl Environ Microbiol. 1994 Aug;60(8):2711-6. DOI:10.1128/aem.60.8.2711-2716.1994 |
10. Wood BD, Quintard M, and Whitaker S. Calculation of effective diffusivities for biofilms and tissues. Biotechnol Bioeng. 2002 Mar 5;77(5):495-516. DOI:10.1002/bit.10075 |
11. Nilsson P, Olofsson A, Fagerlind M, Fagerström T, Rice S, Kjelleberg S, and Steinberg P. Kinetics of the AHL regulatory system in a model biofilm system: how many bacteria constitute a "quorum"?. J Mol Biol. 2001 Jun 8;309(3):631-40. DOI:10.1006/jmbi.2001.4697 |

[Biofilm Mechanics]

Modelling biofilms

12. Picioreanu C, van Loosdrecht MC, and Heijnen JJ. Mathematical modeling of biofilm structure with a hybrid differential-discrete cellular automaton approach. Biotechnol Bioeng. 1998 Apr 5;58(1):101-16. DOI:10.1002/(sici)1097-0290(19980405)58:1<101::aid-bit11>3.0.co;2-m |
13. Kreft JU, Picioreanu C, Wimpenny JW, and van Loosdrecht MC. Individual-based modelling of biofilms. Microbiology (Reading). 2001 Nov;147(Pt 11):2897-912. DOI:10.1099/00221287-147-11-2897 |
14. Hermanowicz SW. A simple 2D biofilm model yields a variety of morphological features. Math Biosci. 2001 Jan;169(1):1-14. DOI:10.1016/s0025-5564(00)00049-3 |
15. Dockery JD and Keener JP. A mathematical model for quorum sensing in Pseudomonas aeruginosa. Bull Math Biol. 2001 Jan;63(1):95-116. DOI:10.1006/bulm.2000.0205 |
16. Nilsson P, Olofsson A, Fagerlind M, Fagerström T, Rice S, Kjelleberg S, and Steinberg P. Kinetics of the AHL regulatory system in a model biofilm system: how many bacteria constitute a "quorum"?. J Mol Biol. 2001 Jun 8;309(3):631-40. DOI:10.1006/jmbi.2001.4697 |

1. Programmed Population control by Cell-Cell Communication and Regulated Killing

Cell signalling

15. Redfield RJ. Is quorum sensing a side effect of diffusion sensing?. Trends Microbiol. 2002 Aug;10(8):365-70. DOI:10.1016/s0966-842x(02)02400-9 |
17. Davies DG, Parsek MR, Pearson JP, Iglewski BH, Costerton JW, and Greenberg EP. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science. 1998 Apr 10;280(5361):295-8. DOI:10.1126/science.280.5361.295 |
18. O'Toole GA, Gibbs KA, Hager PW, Phibbs PV Jr, and Kolter R. The global carbon metabolism regulator Crc is a component of a signal transduction pathway required for biofilm development by Pseudomonas aeruginosa. J Bacteriol. 2000 Jan;182(2):425-31. DOI:10.1128/JB.182.2.425-431.2000 |

Gene expression

19. Whiteley M, Bangera MG, Bumgarner RE, Parsek MR, Teitzel GM, Lory S, and Greenberg EP. Gene expression in Pseudomonas aeruginosa biofilms. Nature. 2001 Oct 25;413(6858):860-4. DOI:10.1038/35101627 |
20. Xu KD, Franklin MJ, Park CH, McFeters GA, and Stewart PS. Gene expression and protein levels of the stationary phase sigma factor, RpoS, in continuously-fed Pseudomonas aeruginosa biofilms. FEMS Microbiol Lett. 2001 May 15;199(1):67-71. DOI:10.1111/j.1574-6968.2001.tb10652.x |

MRSA Specific

21. Manago K, Nishi J, Wakimoto N, Miyanohara H, Sarantuya J, Tokuda K, Iwashita M, Yamamoto K, Yoshinaga M, Maruyama I, and Kawano Y. Biofilm formation by and accessory gene regulator typing of methicillin-resistant Staphylococcus aureus strains recovered from patients with nosocomial infections. Infect Control Hosp Epidemiol. 2006 Feb;27(2):188-90. DOI:10.1086/500620 |
22. Vuong C, Saenz HL, Götz F, and Otto M. Impact of the agr quorum-sensing system on adherence to polystyrene in Staphylococcus aureus. J Infect Dis. 2000 Dec;182(6):1688-93. DOI:10.1086/317606 |
23. Grinholc M, Wegrzyn G, and Kurlenda J. Evaluation of biofilm production and prevalence of the icaD gene in methicillin-resistant and methicillin-susceptible Staphylococcus aureus strains isolated from patients with nosocomial infections and carriers. FEMS Immunol Med Microbiol. 2007 Aug;50(3):375-9. DOI:10.1111/j.1574-695X.2007.00262.x |
24. Cramton SE, Gerke C, Schnell NF, Nichols WW, and Götz F. The intercellular adhesion (ica) locus is present in Staphylococcus aureus and is required for biofilm formation. Infect Immun. 1999 Oct;67(10):5427-33. DOI:10.1128/IAI.67.10.5427-5433.1999 |
25. Martín-López JV, Pérez-Roth E, Claverie-Martín F, Díez Gil O, Batista N, Morales M, and Méndez-Alvarez S. Detection of Staphylococcus aureus Clinical Isolates Harboring the ica Gene Cluster Needed for Biofilm Establishment. J Clin Microbiol. 2002 Apr;40(4):1569-70. DOI:10.1128/JCM.40.4.1569-1570.2002 |
26. McKenney D, Hübner J, Muller E, Wang Y, Goldmann DA, and Pier GB. The ica locus of Staphylococcus epidermidis encodes production of the capsular polysaccharide/adhesin. Infect Immun. 1998 Oct;66(10):4711-20. DOI:10.1128/IAI.66.10.4711-4720.1998 |
27. Ziebuhr W, Heilmann C, Götz F, Meyer P, Wilms K, Straube E, and Hacker J. Detection of the intercellular adhesion gene cluster (ica) and phase variation in Staphylococcus epidermidis blood culture strains and mucosal isolates. Infect Immun. 1997 Mar;65(3):890-6. DOI:10.1128/IAI.65.3.890-896.1997 |
28. O'Gara JP. ica and beyond: biofilm mechanisms and regulation in Staphylococcus epidermidis and Staphylococcus aureus. FEMS Microbiol Lett. 2007 May;270(2):179-88. DOI:10.1111/j.1574-6968.2007.00688.x |

29. Country Doctor

30. Shitrit P, Gottesman BS, Katzir M, Kilman A, Ben-Nissan Y, and Chowers M. Active surveillance for methicillin-resistant Staphylococcus aureus (MRSA) decreases the incidence of MRSA bacteremia. Infect Control Hosp Epidemiol. 2006 Oct;27(10):1004-8. DOI:10.1086/507914 |

31. [1]

Biofilms in the Medical Environment

• keywords: biofilm, catheter, infection, urinary
• [1] biofilm on catheters]

Urinary Catheter Specific

• Guideline for Prevention of Catheter-associated Urinary Tract Infections
• NHS program on CAUTI

32. Stickler DJ, Morris NS, McLean RJ, and Fuqua C. Biofilms on indwelling urethral catheters produce quorum-sensing signal molecules in situ and in vitro. Appl Environ Microbiol. 1998 Sep;64(9):3486-90. DOI:10.1128/AEM.64.9.3486-3490.1998 |
33. Danchaivijitr S, Dhiraputra C, Cherdrungsi R, Jintanothaitavorn D, and Srihapol N. Catheter-associated urinary tract infection. J Med Assoc Thai. 2005 Dec;88 Suppl 10:S26-30.
34. Morris NS, Stickler DJ, and McLean RJ. The development of bacterial biofilms on indwelling urethral catheters. World J Urol. 1999 Dec;17(6):345-50. DOI:10.1007/s003450050159 |
35. Trautner BW, Hull RA, Thornby JI, and Darouiche RO. Coating urinary catheters with an avirulent strain of Escherichia coli as a means to establish asymptomatic colonization. Infect Control Hosp Epidemiol. 2007 Jan;28(1):92-4. DOI:10.1086/510872 |
36. Drinka PJ. Complications of chronic indwelling urinary catheters. J Am Med Dir Assoc. 2006 Jul;7(6):388-92. DOI:10.1016/j.jamda.2006.01.020 |
37. Ha US and Cho YH. Catheter-associated urinary tract infections: new aspects of novel urinary catheters. Int J Antimicrob Agents. 2006 Dec;28(6):485-90. DOI:10.1016/j.ijantimicag.2006.08.020 |
38. Warren JW. Catheter-associated urinary tract infections. Infect Dis Clin North Am. 1987 Dec;1(4):823-54.
39. Trautner BW and Darouiche RO. Role of biofilm in catheter-associated urinary tract infection. Am J Infect Control. 2004 May;32(3):177-83. DOI:10.1016/j.ajic.2003.08.005 |
40. Stickler DJ, Jones SM, Adusei GO, and Waters MG. A sensor to detect the early stages in the development of crystalline Proteus mirabilis biofilm on indwelling bladder catheters. J Clin Microbiol. 2006 Apr;44(4):1540-2. DOI:10.1128/JCM.44.4.1540-1542.2006 |
41. Nicolle LE. Catheter-related urinary tract infection. Drugs Aging. 2005;22(8):627-39. DOI:10.2165/00002512-200522080-00001 |
42. Godfrey H and Fraczyk L. Preventing and managing catheter-associated urinary tract infections. Br J Community Nurs. 2005 May;10(5):205-6, 208-12. DOI:10.12968/bjcn.2005.10.5.18048 |
43. Toughill E. Indwelling urinary catheters: common mechanical and pathogenic problems. Am J Nurs. 2005 May;105(5):35-7. DOI:10.1097/00000446-200505000-00025 |
44. Trautner BW, Hull RA, and Darouiche RO. Prevention of catheter-associated urinary tract infection. Curr Opin Infect Dis. 2005 Feb;18(1):37-41. DOI:10.1097/00001432-200502000-00007 |
45. Saint S and Chenoweth CE. Biofilms and catheter-associated urinary tract infections. Infect Dis Clin North Am. 2003 Jun;17(2):411-32. DOI:10.1016/s0891-5520(03)00011-4 |

General

46. Lindsay D and von Holy A. Bacterial biofilms within the clinical setting: what healthcare professionals should know. J Hosp Infect. 2006 Dec;64(4):313-25. DOI:10.1016/j.jhin.2006.06.028 |
47. Warren JW. Catheter-associated urinary tract infections. Infect Dis Clin North Am. 1987 Dec;1(4):823-54.
48. Percival SL and Kite P. Intravascular catheters and biofilm control. J Vasc Access. 2007 Apr-Jun;8(2):69-80.
49. Donlan RM. Biofilms: microbial life on surfaces. Emerg Infect Dis. 2002 Sep;8(9):881-90. DOI:10.3201/eid0809.020063 |
50. Donlan RM. Biofilm formation: a clinically relevant microbiological process. Clin Infect Dis. 2001 Oct 15;33(8):1387-92. DOI:10.1086/322972 |
51. Tenke P, Kovacs B, Jäckel M, and Nagy E. The role of biofilm infection in urology. World J Urol. 2006 Feb;24(1):13-20. DOI:10.1007/s00345-005-0050-2 |
52. Tenke P, Riedl CR, Jones GL, Williams GJ, Stickler D, and Nagy E. Bacterial biofilm formation on urologic devices and heparin coating as preventive strategy. Int J Antimicrob Agents. 2004 Mar;23 Suppl 1:S67-74. DOI:10.1016/j.ijantimicag.2003.12.007 |
53. Maki DG and Tambyah PA. Engineering out the risk for infection with urinary catheters. Emerg Infect Dis. 2001 Mar-Apr;7(2):342-7. DOI:10.3201/eid0702.010240 |
54. Trautner BW, Hull RA, and Darouiche RO. Prevention of catheter-associated urinary tract infection. Curr Opin Infect Dis. 2005 Feb;18(1):37-41. DOI:10.1097/00001432-200502000-00007 |

Biofilm detection using LuxR/pluxI system

http://aem.asm.org/cgi/reprint/67/2/575

Growth of E.coli biofilms in controlled environments

http://inls.ucsd.edu/~volfson/biofilm/

Developmental pathway for biofilm formation in curli-producing Escherichia coli strains: role of flagella, curli and colanic acid. Combaret et al.

http://www.springerlink.com/content/jh442x351242n044/fulltext.pdf

AHL concentration in biofilms

http://www.blackwell-synergy.com/doi/abs/10.1046/j.1462-2920.2000.00136.x

Resources

Imperial College contacts:

• Prof Andrew J Livingston
• Prof David C Stuckey
• Dr Dieudonne-Guy Ohandja

Web pages:

• Biofilms Online
• Biofilm Hypertextbook
  • With a very rich references section.
• Biofilms and Medical Devices]