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

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Infector Detector: 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 | PubMed ID:8157581 | HubMed [Microniche]
  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 | PubMed ID:11741870 | HubMed [Dispersal]
  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 | PubMed ID:17592147 | HubMed [Phage]

All Medline abstracts: PubMed | HubMed

Heterogeneity of phenotypes

  1. 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. PubMed ID:9758837 | HubMed [Spatial]
  2. 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. PubMed ID:2383005 | HubMed [Layered]
  3. 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. PubMed ID:10473423 | HubMed [Distribution]

All Medline abstracts: PubMed | HubMed

Experimental techniques

  1. 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. PubMed ID:8633864 | HubMed [Hybridisation]

Diffusion and flow in biofilms

  1. 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 | PubMed ID:10099336 | HubMed [Review]
  2. Stoodley P, Debeer D, and Lewandowski Z. Liquid flow in biofilm systems. Appl Environ Microbiol. 1994 Aug;60(8):2711-6. PubMed ID:16349345 | HubMed [Flow]
  3. 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 | PubMed ID:11788949 | HubMed [Calculation]
  4. 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 | PubMed ID:11397086 | HubMed [AHL]

All Medline abstracts: PubMed | HubMed

[Biofilm Mechanics]

Modelling biofilms

  1. 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 | PubMed ID:10099266 | HubMed [Hybrid]
  2. Kreft JU, Picioreanu C, Wimpenny JW, and van Loosdrecht MC. Individual-based modelling of biofilms. Microbiology. 2001 Nov;147(Pt 11):2897-912. DOI:10.1099/00221287-147-11-2897 | PubMed ID:11700341 | HubMed [Individual]
  3. Hermanowicz SW. A simple 2D biofilm model yields a variety of morphological features. Math Biosci. 2001 Jan;169(1):1-14. PubMed ID:11137525 | HubMed [2D]
  4. 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 | PubMed ID:11146885 | HubMed [Quorum]
  5. 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 | PubMed ID:11397086 | HubMed [Diffusion]

All Medline abstracts: PubMed | HubMed

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

Cell signalling

  1. Redfield RJ. Is quorum sensing a side effect of diffusion sensing?. Trends Microbiol. 2002 Aug;10(8):365-70. PubMed ID:12160634 | HubMed [Quorum]
  2. 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 | PubMed ID:9535661 | HubMed [Development]
  3. 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 | PubMed ID:10629189 | HubMed [Crc]

All Medline abstracts: PubMed | HubMed

Gene expression

  1. 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 | PubMed ID:11677611 | HubMed [GeneExp]
  2. 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 | PubMed ID:11356569 | HubMed [RpoS]

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MRSA Specific

  1. 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 | PubMed ID:16465637 | HubMed [agr]
  2. 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 | PubMed ID:11069241 | HubMed [MRSA-agr]
  3. 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 | PubMed ID:17537178 | HubMed [ica]
  4. 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. PubMed ID:10496925 | HubMed [ica2]
  5. 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 | PubMed ID:11923401 | HubMed [detection]
  6. 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. PubMed ID:9746568 | HubMed [icalocus]
  7. 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. PubMed ID:9038293 | HubMed [icadetection]
  8. 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 | PubMed ID:17419768 | HubMed [icareg]
  9. [CountryDoctor]
  10. 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 | PubMed ID:17006805 | HubMed [Surv]
  11. [amoeba]

All Medline abstracts: PubMed | HubMed

Biofilms in the Medical Environment

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

Urinary Catheter Specific

  1. 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. PubMed ID:9726901 | HubMed [urinary-catheter1]
  2. 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. PubMed ID:16850636 | HubMed [urinary-catheter2]
  3. 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. PubMed ID:10654364 | HubMed [urinary-catheter3]
  4. 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 | PubMed ID:17230395 | HubMed [urinary-catheter4]
  5. 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 | PubMed ID:16843240 | HubMed [urinary-catheter5]
  6. 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 | PubMed ID:17045784 | HubMed [urinary-catheter6]
  7. Warren JW. Catheter-associated urinary tract infections. Infect Dis Clin North Am. 1987 Dec;1(4):823-54. PubMed ID:3333661 | HubMed [urinary-catheter7]
  8. 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 | PubMed ID:15153930 | HubMed [urinary-catheter8]
  9. 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 | PubMed ID:16597888 | HubMed [urinary-catheter9]
  10. Nicolle LE. Catheter-related urinary tract infection. Drugs Aging. 2005;22(8):627-39. DOI:10.2165/00002512-200522080-00001 | PubMed ID:16060714 | HubMed [urinary-catheter10]
  11. 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. PubMed ID:15923986 | HubMed [urinary-catheter11]
  12. 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 | PubMed ID:15867530 | HubMed [urinary-catheter12]
  13. Trautner BW, Hull RA, and Darouiche RO. Prevention of catheter-associated urinary tract infection. Curr Opin Infect Dis. 2005 Feb;18(1):37-41. PubMed ID:15647698 | HubMed [urinary-catheter13]
  14. Saint S and Chenoweth CE. Biofilms and catheter-associated urinary tract infections. Infect Dis Clin North Am. 2003 Jun;17(2):411-32. PubMed ID:12848477 | HubMed [urinary-catheter14]

All Medline abstracts: PubMed | HubMed


  1. 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 | PubMed ID:17046102 | HubMed [biofilm1]
  2. Warren JW. Catheter-associated urinary tract infections. Infect Dis Clin North Am. 1987 Dec;1(4):823-54. PubMed ID:3333661 | HubMed [biofilm2]
  3. Percival SL and Kite P. Intravascular catheters and biofilm control. J Vasc Access. 2007 Apr-Jun;8(2):69-80. PubMed ID:17534791 | HubMed [biofilm3]
  4. Donlan RM. Biofilms: microbial life on surfaces. Emerg Infect Dis. 2002 Sep;8(9):881-90. DOI:10.3201/eid0809.020063 | PubMed ID:12194761 | HubMed [biofilm4]
  5. Donlan RM. Biofilm formation: a clinically relevant microbiological process. Clin Infect Dis. 2001 Oct 15;33(8):1387-92. DOI:10.1086/322972 | PubMed ID:11565080 | HubMed [biofilm5]
  6. 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 | PubMed ID:16402262 | HubMed [biofilm6]
  7. 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 | PubMed ID:15037330 | HubMed [biofilm7]
  8. 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 | PubMed ID:11294737 | HubMed [biofilm8]
  9. Trautner BW, Hull RA, and Darouiche RO. Prevention of catheter-associated urinary tract infection. Curr Opin Infect Dis. 2005 Feb;18(1):37-41. PubMed ID:15647698 | HubMed [biofilm9]

All Medline abstracts: PubMed | HubMed

Biofilm detection using LuxR/pluxI system


Growth of E.coli biofilms in controlled environments


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


AHL concentration in biofilms



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