Detection and Evaluation of Biofilms

This chapter describes a variety of ways for detecting and evaluating biofilms. The biological methods include staining, gene analysis, and proteomics. An instrumental analysis section is available too. It introduces many microscopes and discusses their uses for observing and analyzing biofilms.

[1]  H. Kanematsu,et al.  Evaluation of Various Metallic Coatings on Steel to Mitigate Biofilm Formation , 2009, International journal of molecular sciences.

[2]  S. Bhargava,et al.  At the solid/liquid interface: FTIR/ATR--the tool of choice. , 2001, Advances in colloid and interface science.

[3]  Brian C. Smith.  Fundamentals of Fourier Transform Infrared Spectroscopy , 1995 .

[4]  S. Asher,et al.  Development of a New Optical Wavelength Rejection Filter: Demonstration of its Utility in Raman Spectroscopy , 1984 .

[5]  H. Flemming,et al.  The biofilm matrix , 2010, Nature Reviews Microbiology.

[6]  Roberto Kolter,et al.  Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis , 1998, Molecular microbiology.

[7]  D. Stokes.  Characterisation of soft condensed matter and delicate materials using environmental scanning electron microscopy (ESEM) , 2001 .

[8]  C. Solano,et al.  Genetic analysis of Salmonella enteritidis biofilm formation: critical role of cellulose , 2002, Molecular microbiology.

[9]  A. Shoreit,et al.  Application of Fungal Biofilm Supported on Activated Carbon for Adsorption of Two Azodyes: Adsorption Kinetics and Isotherms , 2015 .

[10]  H. Flemming.  EPS—Then and Now , 2016, Microorganisms.

[11]  J. C. Junqueira,et al.  Comparison of the effect of rose bengal- and eosin Y-mediated photodynamic inactivation on planktonic cells and biofilms of Candida albicans , 2014, Lasers in Medical Science.

[12]  Jonathan D. Suter,et al.  Are those bugs reflective? non-destructive biofilm imaging with white light interferometry , 2016, Optical Engineering + Applications.

[13]  G. Peters,et al.  Adherence and growth of coagulase-negative staphylococci on surfaces of intravenous catheters. , 1982, The Journal of infectious diseases.

[14]  Asad U. Khan,et al.  Obliteration of bacterial growth and biofilm through ROS generation by facilely synthesized green silver nanoparticles , 2017, PloS one.

[15]  Jennifer D. Schuttlefield,et al.  ATR FTIR Spectroscopy in the Undergraduate Chemistry Laboratory. Part I: Fundamentals and Examples. , 2008 .

[16]  Effect of Silver or Copper Nanoparticles-Dispersed Silane Coatings on Biofilm Formation in Cooling Water Systems , 2016, Materials.

[17]  Joshua Xu,et al.  Differential gene expression in Staphylococcus aureus exposed to Orange II and Sudan III azo dyes , 2015, Journal of Industrial Microbiology & Biotechnology.

[18]  N. Lin,et al.  Effect of dental monomers and initiators on Streptococcus mutans oral biofilms. , 2018, Dental materials : official publication of the Academy of Dental Materials.

[19]  S. Davis,et al.  A Wound‐Isolated Pseudomonas aeruginosa Grows a Biofilm In Vitro Within 10 Hours and Is Visualized by Light Microscopy , 2003, Dermatologic surgery : official publication for American Society for Dermatologic Surgery [et al.].

[20]  S. Mandal.  A novel hydroxyproline rich glycopeptide from pericarp of Datura stramonium: proficiently eradicate the biofilm of antifungals resistant Candida albicans. , 2012, Biopolymers.

[21]  H. Busscher,et al.  Biomaterials Associated Infection: Immunological Aspects and Antimicrobial Strategies , 2013 .

[22]  N. Kamjunke,et al.  Use of confocal laser scanning microscopy for biofilm investigation on paints under field conditions , 2012 .

[23]  Shree K. Nayar,et al.  Microscopic shape from focus using active illumination , 1994, Proceedings of 12th International Conference on Pattern Recognition.

[24]  H. Beyenal,et al.  In situ effective diffusion coefficient profiles in live biofilms using pulsed‐field gradient nuclear magnetic resonance , 2010, Biotechnology and bioengineering.

[25]  P. Angell,et al.  Technical note: Staining procedures for characterising biofilms in corrosion investigations , 1988 .

[26]  P. Bishop,et al.  Aerobic biodegradation of azo dyes in biofilms , 1994 .

[27]  P. Watnick,et al.  Genetic approaches to study of biofilms. , 1999, Methods in enzymology.

[28]  R. Wyckoff,et al.  Applications of Metallic Shadow‐Casting to Microscopy , 1946 .

[29]  P. Larkin,et al.  General Outline and Strategies for IR and Raman Spectral Interpretation , 2011 .

[30]  P. Penczek,et al.  A Primer to Single-Particle Cryo-Electron Microscopy , 2015, Cell.

[31]  Sheriase Q Sanders,et al.  Temperature and nutrient effects on Campylobacter jejuni attachment on multispecies biofilms on stainless steel. , 2008, Journal of food protection.

[32]  R. Kolter,et al.  Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili , 1998, Molecular microbiology.

[33]  R. Kolter,et al.  Genetic analyses of bacterial biofilm formation. , 1999, Current opinion in microbiology.

[34]  R. Ellison,et al.  Damage of the outer membrane of enteric gram-negative bacteria by lactoferrin and transferrin , 1988, Infection and immunity.

[35]  D. Rice,et al.  Biofilm detection with hematoxylin-eosin staining. , 2010, Archives of otolaryngology--head & neck surgery.

[36]  T. Beveridge,et al.  High-Resolution Visualization of Pseudomonas aeruginosa PAO1 Biofilms by Freeze-Substitution Transmission Electron Microscopy , 2005, Journal of bacteriology.

[37]  R. Aebersold,et al.  Mass spectrometry-based proteomics , 2003, Nature.

[38]  S. Chatterjee,et al.  Atomic force microscopy in biofilm study. , 2014, Microscopy.

[39]  S. Hanash.  Disease proteomics : Proteomics , 2003 .

[40]  P. Bishop,et al.  Characterization of aerobic azo dye-degrading bacteria and their activity in biofilms , 1997 .

[41]  T. Wdowiak,et al.  Laser–Raman imagery of Earth's earliest fossils , 2002, Nature.

[42]  S. Davis,et al.  LISFESYLES OF BACTERIA IN WOUNDS: PRESENCE OF BIOFILMS? , 2001 .

[43]  Bradley J. Nelson,et al.  Visually guided microassembly using optical microscopes and active vision techniques , 1997, Proceedings of International Conference on Robotics and Automation.

[44]  Curtis Larimer,et al.  Monitoring bacterial biofilms with a microfluidic flow chip designed for imaging with white-light interferometry. , 2017, Biomicrofluidics.

[45]  Yogesh,et al.  Polysulfone-azo composite membrane: New preparative approach, importance in bactericidal and biofilm inhibition activities , 2010 .

[46]  M. Shen,et al.  Plasma-deposited membranes for controlled release of antibiotic to prevent bacterial adhesion and biofilm formation. , 2000, Journal of biomedical materials research.

[47]  A. Danchin,et al.  Genome‐based analysis of virulence genes in a non‐biofilm‐forming Staphylococcus epidermidis strain (ATCC 12228) , 2003, Molecular microbiology.

[48]  M. Mann,et al.  Proteomics to study genes and genomes , 2000, Nature.

[49]  J. Schrenzel,et al.  Repeated exposures to blue light-activated eosin Y enhance inactivation of E. faecalis biofilms, in vitro. , 2015, Photodiagnosis and photodynamic therapy.

[50]  D. Pritchard,et al.  Blow fly Lucilia sericata nuclease digests DNA associated with wound slough/eschar and with Pseudomonas aeruginosa biofilm , 2012, Medical and veterinary entomology.

[51]  C. Preston.  Applications of NMR to soil organic matter analysis : History and prospects , 1996 .

[52]  D. Welch,et al.  A brief history of high-power semiconductor lasers , 2000, IEEE Journal of Selected Topics in Quantum Electronics.

[53]  Yin Yin Lau,et al.  Cloning and characterization of short‐chain N‐acyl homoserine lactone‐producing Enterobacter asburiae strain L1 from lettuce leaves , 2018, MicrobiologyOpen.

[54]  M. Hackett,et al.  Rapid isolation method for lipopolysaccharide and lipid A from gram-negative bacteria. , 2000, The Analyst.

[55]  Santiago Villaverde,et al.  Combined anaerobic-aerobic treatment of azo dyes--a short review of bioreactor studies. , 2005, Water research.

[56]  R. Ramakrishnan,et al.  Labeling fluorescence in situ hybridization probes for genomic targets. , 2002, Methods in molecular biology.

[57]  M. Levoy,et al.  Light field microscopy , 2006, SIGGRAPH 2006.

[58]  Shree K. Nayar,et al.  Transactions on Pattern Analysis and Machine Intelligence Flexible Depth of Field Photography 1 Depth of Field , 2022 .

[59]  David W Williams,et al.  Introduction to biofilms , 2011 .

[60]  J. Finne,et al.  Polyacrylamide gel electrophoresis of the capsular polysaccharides of Escherichia coli K1 and other bacteria , 1988, Journal of bacteriology.

[61]  Zbigniew Lewandowski,et al.  Effects of biofilm structures on oxygen distribution and mass transport , 1994, Biotechnology and bioengineering.

[62]  Blaise R. Boles,et al.  Identification of Genes Involved in Polysaccharide-Independent Staphylococcus aureus Biofilm Formation , 2010, PloS one.

[63]  P. Stewart,et al.  Quantitative observations of heterogeneities in Pseudomonas aeruginosa biofilms , 1993, Applied and environmental microbiology.

[64]  K. S. Krishnan.  Influence of Temperature on the Raman Effect. , 1928, Nature.

[65]  Kevin R Minard,et al.  NMR methods for in situ biofilm metabolism studies. , 2005, Journal of microbiological methods.

[66]  M. Chengalroyen,et al.  The microbial degradation of azo dyes: minireview , 2013, World journal of microbiology & biotechnology.

[67]  K. S. Krishnan,et al.  A New Type of Secondary Radiation , 1928, Nature.

[68]  P. Stewart,et al.  A genetic basis for Pseudomonas aeruginosa biofilm antibiotic resistance , 2003, Nature.

[69]  Georgeta Crivat,et al.  Imaging proteins inside cells with fluorescent tags. , 2012, Trends in biotechnology.

[70]  R. S. Krishnan,et al.  Raman effect: History of the discovery , 1981 .

[71]  Roberto Kolter,et al.  Biofilms: the matrix revisited. , 2005, Trends in microbiology.

[72]  A. Mooradian,et al.  First order Raman effect in III–V compounds , 1966 .

[73]  Robert L. Kleinberg,et al.  An introduction to the history of NMR well logging , 2001 .

[74]  P. Larkin.  Infrared and Raman Spectroscopy: Principles and Spectral Interpretation , 2011 .

[75]  Kenneth H Downing,et al.  Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon , 2009, The ISME Journal.

[76]  Sureshbabu Ram Kumar Pandian,et al.  Silver nanoparticles impede the biofilm formation by Pseudomonas aeruginosa and Staphylococcus epidermidis. , 2010, Colloids and surfaces. B, Biointerfaces.

[77]  Toshihiro Tanaka,et al.  Composite coating to control biofilm formation and effect of alternate electro-magnetic field , 2015 .

[78]  Paul Stoodley,et al.  Evolving concepts in biofilm infections , 2009, Cellular microbiology.

[79]  Daniel Cressey,et al.  Cryo-electron microscopy wins chemistry Nobel , 2017, Nature.

[80]  Z. Lewandowski,et al.  Fundamentals of Biofilm Research, Second Edition , 2013 .

[81]  Bing Li,et al.  Crystal Violet and XTT Assays on Staphylococcus aureus Biofilm Quantification , 2016, Current Microbiology.

[82]  H. Kanematsu,et al.  Microbiome Analysis of Biofilms of Silver Nanoparticle-Dispersed Silane-Based Coated Carbon Steel Using a Next-Generation Sequencing Technique , 2018, Antibiotics.

[83]  H. Awad,et al.  Electrochemical degradation of Acid Blue and Basic Brown dyes on Pb/PbO2 electrode in the presence of different conductive electrolyte and effect of various operating factors. , 2005, Chemosphere.

[84]  D. Allison,et al.  Extracellular products as mediators of the formation and detachment of Pseudomonas fluorescens biofilms. , 1998, FEMS microbiology letters.

[85]  H. Kanematsu,et al.  Application of bacterial 16S rRNA gene analysis to a comparison of the degree of biofilm formation on the surface of metal coated glasses , 2015 .

[86]  D. Mehta,et al.  Microbial Biofilm and Quorum Sensing Inhibition: Endowment of Medicinal Plants to Combat Multidrug-Resistant Bacteria. , 2018, Current drug targets.

[87]  Lizeng Gao,et al.  Ferromagnetic nanoparticles with peroxidase-like activity enhance the cleavage of biological macromolecules for biofilm elimination. , 2014, Nanoscale.

[88]  K. Chittur,et al.  FTIR/ATR for protein adsorption to biomaterial surfaces. , 1998, Biomaterials.

[89]  C. Edmiston,et al.  Bacterial biofilms: strategies for preparing glycocalyx for electron microscopy. , 1999, Methods in enzymology.

[90]  B. C. Hoskins,et al.  Selective imaging of biofilms in porous media by NMR relaxation. , 1999, Journal of magnetic resonance.

[91]  Olivier Thomas,et al.  Aromatic amines from azo dye reduction: status review with emphasis on direct UV spectrophotometric detection in textile industry wastewaters , 2004 .

[92]  R. Cole.  Electrospray and MALDI Mass Spectrometry: Fundamentals, Instrumentation, Practicalities, and Biological Applications , 2010 .

[93]  P. Watnick,et al.  Biofilm, City of Microbes , 2000 .

[94]  J. Flood,et al.  Prevalence of microbial biofilms on selected fresh produce and household surfaces. , 2004, International journal of food microbiology.

[95]  L. Kiemeney,et al.  Obesity, metabolic factors and risk of different histological types of lung cancer: A Mendelian randomization study , 2017, PloS one.

[96]  Yo Kobayashi,et al.  Nickel, molybdenum, and tungsten nanoparticle-dispersed alkylalkoxysilane polymer for biomaterial coating: evaluation of effects on bacterial biofilm formation and biosafety , 2017 .

[97]  A. Uitterlinden,et al.  Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA , 1993, Applied and environmental microbiology.

[98]  Tom Berman,et al.  Don't fall foul of biofilm through high TEP levels , 2005 .

[99]  Afreenish Hassan,et al.  Evaluation of different detection methods of biofilm formation in the clinical isolates. , 2011, The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases.

[100]  Rosário Oliveira,et al.  Confocal laser scanning microscopy analysis of S. epidermidis biofilms exposed to farnesol, vancomycin and rifampicin , 2012, BMC Research Notes.

[101]  Paige J. Novak,et al.  Biofilm Cohesiveness Measurement Using a Novel Atomic Force Microscopy Methodology , 2007, Applied and Environmental Microbiology.

[102]  J. Pawley,et al.  Handbook of Biological Confocal Microscopy , 1990, Springer US.

[103]  C. Dass.  Fundamentals of Contemporary Mass Spectrometry , 2007 .

[104]  M. F. Malik,et al.  Biosynthesis of silver nanoparticles from leaf extract of Litchi chinensis and its dynamic biological impact on microbial cells and human cancer cell lines. , 2018, Cellular and molecular biology.

[105]  S. Altobelli,et al.  NMR and Microelectrode Studies of Hydrodynamics and Kinetics in Biofilms , 1993 .