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

Biofilm Detection: References

• Introduction
• Specifications
• Design
• Modelling
• Implementation
• Testing/Validation
• Notes
• References

Biofilm References

• 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 |

[Biofilm Mechanics]

• Modelling biofilms

11. 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 |
12. 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 |
13. 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 |
14. 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 |

• Cell signalling

14. 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 |
15. 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 |
16. 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

17. 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 |
18. 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

19. 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 |
20. 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 |
21. 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 |
22. 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 |
23. 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 |
24. 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 |
25. 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 |
26. 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 |

27. Country Doctor

28. 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 |

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