This research was supported by the Main Research Program (E0210702-03) of the Korea Food Research Institute (KFRI), funded by the Ministry of Science and ICT.

1. Preparation of bacterial inoculum
<ol>
	<li>Remove the glycerol stock vial stored at -80 &#176;C.</li>
	<li>Remove the bacterial strain (2-10 &#181;L) from the vial using a sterile pipette tip. 
	NOTE: Acinetobacter strains, A. bouvetii (13-1-1), A. junii (13-1-2), A. pittii (13-2-5), A. baumannii (13-2-9), A. radioresistens (20-1), and A. ursingii (24-1) are used in this protocol.</li>
	<li>Inoculate a commercially available blood agar plate (tryptic soy agar supplemented with 5% sheep blood, see Table of Materials) with the bacteria. 
	NOTE: Other media, such as nutrient agar or MacConkey agar, can also be used.</li>
	<li>Streak the agar surface using a sterile loop with intermittent flaming to thin it out.</li>
	<li>Place the agar plate upside down in an incubator and incubate at 30 &#176;C overnight for 20-24 h.</li>
	<li>Pick a single colony of the bacterial culture with a sterile needle and inoculate 5 mL sterile brain heart infusion broth (BHI, see Table of Materials) with the culture.</li>
	<li>Incubate the inoculated broth in a shaking incubator at 30 &#176;C overnight for 20-24 h at around 150 rpm.</li>
	<li>Transfer 1 mL of the overnight culture to a sterile microcentrifuge tube and centrifuge the overnight culture at 6,000 &#215; g for 10 min at room temperature (RT).</li>
	<li>Remove the supernatant with a pipette.</li>
	<li>Using a vortex, resuspend the pellet in 1 mL sterile phosphate-buffered saline (PBS).</li>
	<li>Centrifuge at 6,000 &#215; g for 10 min at RT and remove the supernatant.</li>
	<li>Resuspend the pellet in sterile ten-fold diluted BHI using vortex to an optical density of around 0.1 at 600 nm. 
	NOTE: The optical density of around 0.1 is equivalent to approximately 107 CFU/mL.</li>
</ol>
2. Biofilm quantification using crystal violet
<ol>
	<li>Add 200 &#181;L inoculum to each well of a sterile polystyrene 96-well plate (see Table of Materials) and add 200 &#181;L deionized water to each of the outermost wells to prevent the inner wells from drying out15.</li>
	<li>Add 200 &#181;L ten-fold diluted BHI to each well of the same plate as a negative control.</li>
	<li>Incubate the plate at 25 &#176;C for 24 h.</li>
	<li>Remove the supernatant with a pipette. 
	NOTE: Multichannel pipette is often more convenient for multiple samples.</li>
	<li>Carefully add 300 &#181;L PBS to each well and remove the supernatant with a pipette. 
	&#8203;NOTE: Multichannel pipette is often more convenient for multiple samples.</li>
	<li>Repeat step 2.5 two more times.</li>
	<li>Add 200 &#181;L crystal violet solution (1%) (see Table of Materials) to each well and incubate at RT for 30 min.</li>
	<li>Repeat steps 2.4-2.6.</li>
	<li>Add 200 &#181;L of absolute ethanol to each well and incubate for 15 min at RT. Mix thoroughly by pipetting up and down several times.</li>
	<li>Transfer 100 &#181;L elution from each well to a new 96-well plate.</li>
	<li>Measure the absorbance at 595 nm using a microplate reader (see Table of Materials).</li>
	<li>When the absorbance exceeds 2.0, make a proper dilution of the sample to the absorbance below 2.0 in absolute ethanol and measure it as in step 2.11. Then, calculate the absorbance of the sample (final value) by multiplying the observed value by the dilution factor.</li>
	<li>Calculate the true absorbance of the samples by subtracting the average value of the negative control from the value of each well of the test samples on the same well plate.</li>
</ol>
3. Biofilm viability count
<ol>
	<li>Add 1 mL inoculum (step 1) to each well of a sterile polystyrene 12-well plate15. Incubate the plate at 25 &#176;C for 24 h. Remove the supernatant with a pipette.</li>
	<li>Carefully add 1.5 mL sterile PBS to each well and remove the supernatant with a pipette. Add 1 mL sterile PBS to each well.</li>
	<li>Scrape off the bottom and wall surfaces of the well using fitted cell scrapers.</li>
	<li>Transfer the harvested cell suspension to a sterile plastic tube (10-1) containing 9 mL saline (0.85% NaCl) and 10-20 glass beads (see Table of Materials). 
	NOTE: To collect any residual biofilm debris left on the bottom surface of the well, it can be resuspended and transferred by pipette using saline from the 10-1 tube.</li>
	<li>Vortex the 10-1 tube for 60 s at a maximum speed.</li>
	<li>Make a 10-fold serial dilution by transferring 1 mL to the next sterile tube (10-2) containing 9 mL saline (0.85 % NaCl) up to 10-7.</li>
	<li>Spread 100 &#181;L from each dilution on Acinetobacter agar (see Table of Materials) and incubate the agar plates at 30 &#176;C for 24-42 h.</li>
	<li>Count the number of the typical red colonies on each plate manually in the range between 10 and 250.</li>
	<li>Calculate the number of viable cells in the biofilm of each well by using the equation below: 
	Viable cells = Number of colonies&#160;&#215; Dilution factors&#160;&#215; 10</li>
</ol>
4. Biofilm visualization using confocal laser scanning microscopy (CLSM)
<ol>
	<li>Add 200 &#181;L inoculum to each well of a sterile 96-well plate intended for microscopic analysis.</li>
	<li>Incubate the plate at 25 &#176;C for 24 h.</li>
	<li>Remove the supernatant with a pipette.</li>
	<li>Carefully add 300 &#181;L filter-sterilized deionized water to each well and remove the supernatant with a pipette.</li>
	<li>Repeat step 4.4.</li>
	<li>Prepare the mixture of SYTO 9 and propidium iodide (see Table of Materials) diluted in filter-sterilized deionized water to a final concentration of 10 &#181;M and 60 &#181;M, respectively.</li>
	<li>Add the mixture to each well at 200 &#181;L and incubate the plate for 20-30 min at RT in the dark.</li>
	<li>Repeat steps 4.3-4.4</li>
	<li>Visualize the bottom-surface attached biofilms using CLSM with the excitation wavelength of 488 nm and 561 nm and the emission wavelength range of 499-535 nm and 568-712 nm, respectively.</li>
</ol>

Assessment of Acinetobacter Biofilm Formation and Characterization of Biofilms

<ol>
	<li>Wong, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clinical+and+pathophysiological+overview+of+Acinetobacter+infections:+a+century+of+challenges.">Clinical and pathophysiological overview of Acinetobacter infections: a century of challenges.</a> Clinical Microbiology Reviews. 30 (1), 409-447 (2017).</li><li>Carvalheira, A., Silva, J., Teixeira, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acinetobacter+spp.+in+food+and+drinking+water+-+A+review.">Acinetobacter spp. in food and drinking water - A review.</a> Food Microbiology. 95, 103675 (2021).</li><li>Towner, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acinetobacter:+an+old+friend,+but+a+new+enemy.">Acinetobacter: an old friend, but a new enemy.</a> Journal of Hospital Infection. 73 (4), 355-363 (2009).</li><li>Weber, D. J., Rutala, W. A., Miller, M. B., Huslage, K., Sickbert-Bennett, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+hospital+surfaces+in+the+transmission+of+emerging+health+care-associated+pathogens:+Norovirus,+Clostridium+difficile,+and+Acinetobacter+species.">Role of hospital surfaces in the transmission of emerging health care-associated pathogens: Norovirus, Clostridium difficile, and Acinetobacter species.</a> American Journal of Infection Control. 38 (5), S25-S33 (2010).</li><li>Flemming, H. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+biofilm+matrix:+multitasking+in+a+shared+space.">The biofilm matrix: multitasking in a shared space.</a> Nature Reviews Microbiology. 21 (2), 70-86 (2023).</li><li>Flemming, H. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilms:+an+emergent+form+of+bacterial+life.">Biofilms: an emergent form of bacterial life.</a> Nature Reviews Microbiology. 14 (9), 563-575 (2016).</li><li>Yin, W., Wang, Y., Liu, L., He, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilms:+the+microbial+&amp;#34;protective+clothing&amp;#34;+in+extreme+environments.">Biofilms: the microbial &amp;#34;protective clothing&amp;#34; in extreme environments.</a> International Journal of Molecular Sciences. 20 (14), 3423 (2019).</li><li>Gedefie, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acinetobacter+baumannii+biofilm+formation+and+its+role+in+disease+pathogenesis:+a+review.">Acinetobacter baumannii biofilm formation and its role in disease pathogenesis: a review.</a> Infection and drug resistance. 14, 3711-3719 (2021).</li><li>Whiteway, C., Breine, A., Philippe, C., Van der Henst, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acinetobacter+baumannii.">Acinetobacter baumannii.</a> Trends in Microbiology. 30 (2), 199-200 (2022).</li><li>Longo, F., Vuotto, C., Donelli, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilm+formation+in+Acinetobacter+baumannii.">Biofilm formation in Acinetobacter baumannii.</a> New Microbiologica. 37 (2), 119-127 (2014).</li><li>Azeredo, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Critical+review+on+biofilm+methods.">Critical review on biofilm methods.</a> Critical Reviews in Microbiology. 43 (3), 313-351 (2017).</li><li>Jia, J., Xue, X., Guan, Y., Fan, X., Wang, Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilm+characteristics+and+transcriptomic+profiling+of+Acinetobacter+johnsonii+defines+signatures+for+planktonic+and+biofilm+cells.">Biofilm characteristics and transcriptomic profiling of Acinetobacter johnsonii defines signatures for planktonic and biofilm cells.</a> Environmental Research. 213, 113714 (2022).</li><li>Yang, C., Su, P., Moi, S., Chuang, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilm+formation+in+Acinetobacter+baumannii:+genotype-phenotype+correlation.">Biofilm formation in Acinetobacter baumannii: genotype-phenotype correlation.</a> Molecules. 24 (10), 1849 (2019).</li><li>Alamri, A. M., Alsultan, A. A., Ansari, M. A., Alnimr, A. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilm-formation+in+clonally+unrelated+multidrug-resistant+Acinetobacter+baumannii+isolates.">Biofilm-formation in clonally unrelated multidrug-resistant Acinetobacter baumannii isolates.</a> Pathogens. 9 (8), 630 (2020).</li><li>Lim, E. S., Nam, S. J., Koo, O. K., Kim, J. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protective+role+of+Acinetobacter+and+Bacillus+for+Escherichia+coli+O157:H7+in+biofilms+against+sodium+hypochlorite+and+extracellular+matrix-degrading+enzymes.">Protective role of Acinetobacter and Bacillus for Escherichia coli O157:H7 in biofilms against sodium hypochlorite and extracellular matrix-degrading enzymes.</a> Food Microbiology. 109, 104125 (2023).</li><li>Stepanovi&#263;, S., &#262;irkovi&#263;, I., Ranin, L., Svabi&#263;-Vlahovi&#263;, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Biofilm+formation+by+Salmonella+spp.+and+Listeria+monocytogenes+on+plastic+surface.">Biofilm formation by Salmonella spp. and Listeria monocytogenes on plastic surface.</a> Letters in Applied Microbiology. 38 (5), 428-432 (2004).</li><li>Boone, R. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+virulence+phenotypes+and+antibiotic+resistance+in+clinical+strains+of+Acinetobacter+baumannii+isolated+in+Nashville,+Tennessee.">Analysis of virulence phenotypes and antibiotic resistance in clinical strains of Acinetobacter baumannii isolated in Nashville, Tennessee.</a> BMC Microbiology. 21 (1), 21 (2021).</li><li>Otter, J. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surface-attached+cells,+biofilms+and+biocide+susceptibility:+implications+for+hospital+cleaning+and+disinfection.">Surface-attached cells, biofilms and biocide susceptibility: implications for hospital cleaning and disinfection.</a> Journal of Hospital Infection. 89 (1), 16-27 (2015).</li><li>Ravishankar, S., Juneja, V. K., Yousef, A. E., Juneja, V. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Adaptation+or+resistance+responses+of+microorganisms+to+stresses+in+the+food+processing+environment.">Adaptation or resistance responses of microorganisms to stresses in the food processing environment.</a> Microbial Stress Adaptation and Food Safety. , (2003).</li><li>Dewanti, R., Wong, A. C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Influence+of+culture+conditions+on+biofilm+formation+by+Escherichia+coli+O157:H7.">Influence of culture conditions on biofilm formation by Escherichia coli O157:H7.</a> International Journal of Food Microbiology. 26 (2), 147-164 (1995).</li><li>McConnell, M. J., Actis, L., Pach&#243;n, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acinetobacter+baumannii:+human+infections,+factors+contributing+to+pathogenesis+and+animal+models.">Acinetobacter baumannii: human infections, factors contributing to pathogenesis and animal models.</a> FEMS Microbiology Reviews. 37 (2), 130-155 (2013).</li><li>McQueary, C. N., Actis, L. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acinetobacter+baumannii+biofilms:+variations+among+strains+and+correlations+with+other+cell+properties.">Acinetobacter baumannii biofilms: variations among strains and correlations with other cell properties.</a> The Journal of Microbiology. 49 (2), 243-250 (2011).</li></ol>

The authors have nothing to disclose.

Using the protocol described, the biofilm formation of Acinetobacter isolates with varying degrees was measured, visualized, and the viable cells in the biofilms were estimated (Figure 1, Figure 2, and Figure 3).
In this protocol, two different temperatures were used, 30 &#176;C for the growth and 25 &#176;C for the biofilm formation of Acinetobacter. 30 &#176;C was used because many stu...

Acinetobacter is known to cause nosocomial infections, and its human infection, especially in healthcare facilities, is increasingly reported1. It is widespread in hospitals, healthcare facilities, and food-associated environments2,3,4. It can survive for a long period in environments including hospital surfaces such as bed rails, bedside tables, the surface of ventilators, and sinks4. Such persistence on environmental surfaces may be one of the significant factors contributing to the nosocomial infections of Acinetobacter4.
Biofilm is a form of microbial life and is a microbial matrix composed of live microbial cells and extracellular polymeric substances (EPS) from the cells5. The microbial cells are embedded in the matrix and are often highly resistant to environmental stresses such as heat, salts, dryness, antibiotics, disinfectants, and shear forces6,7.
Acinetobacter can form biofilms on surfaces, suggesting that it may contribute to extended survival on environmental surfaces, including hospital surfaces, and enhanced resistance to antibiotic treatment8,9. In addition, the biofilm formation of Acinetobacter could be highly associated with human clinical outcomes8. Therefore, the biofilm formability of Acinetobacter strains could be one of the indicators in predicting environmental survival and human infections8,10.
The surface-attached biofilms can be quantified and visualized to assess biofilm formability. To quantify surface-attached biofilms, the biofilms are normally stained by biofilm-staining dyes such as crystal violet, and the dyes are eluted in solution and measured for optical density11. Visualization of biofilms is another good approach to assess biofilm formability11. Confocal Laser Scanning Microscopy (CLSM) visualization method employing specificity using fluorescent dyes could be more useful to characterize biofilm morphology compared to other techniques such as SEM12,13.
The viable cells in biofilms can be counted to estimate the number of viable cells in biofilms11. The viable cells embedded in biofilms are detached, diluted, spread on agar plates, incubated, and enumerated. Because the higher number of cells is likely to meet the infectious dose, it can provide more detailed information on biofilms, such as infection potentials associated with the number of cells13,14.
This article presents step-by-step protocols to (1) quantify surface-attached biofilms, (2) count viable cells in the biofilms, and (3) visualize the biofilms using CLSM of Acinetobacter. The presented protocols describe the methods to assess the biofilm formability of Acinetobacter isolates and characterize their biofilms.

<table><tbody><tr><td>96-well cell culture plate</td><td>SPL</td><td>30096</td><td>Polystyrene 96-well plate</td></tr><tr><td>BHI (Brain Heart Infusion) broth</td><td>Merck KGaA</td><td>1.10493.0500</td><td></td></tr><tr><td>Blood Agar Base Plate</td><td>KisanBio</td><td>MB-B1005-P50</td><td>Growth media for Acinetobacter</td></tr><tr><td>CHROMagar Acinetobacter</td><td>CHROMagar</td><td>AC092</td><td>Selective plate for Acinetobacter</td></tr><tr><td>Crystal violet solution</td><td>Sigma-Aldrich</td><td>V5265</td><td></td></tr><tr><td>Filmtracer LIVE/DEAD biofilm viability kit</td><td>Invitrogen</td><td>L10316</td><td>SYTO9 and propidium iodide</td></tr><tr><td>Microplate reader</td><td>Tecan</td><td>Infinite M200 PRO NanoQuant</td><td>Biofilm measurement</td></tr><tr><td>RBC Glass Plating Beads</td><td>RBC</td><td>RG001</td><td>Glass beads</td></tr><tr><td>&amp;mu;-Plate 96 Well Black</td><td>ibidi</td><td>89621</td><td>Microplate intended for CLSM</td></tr></tbody></table>

quantification, viability assessment, and visualization strategies for acinetobacter biofilms

Acinetobacter causes nosocomial infections and its biofilm formation can contribute to the survival on dry surfaces such as hospital environments. Thus, biofilm quantification and visualization are important methods to assess the potential of Acinetobacter strains to cause nosocomial infections. The biofilms forming on the surface of the microplate can be quantified in terms of volume and cell numbers. Biofilm volumes can be quantified by staining using crystal violet, washing, destaining using ethanol, then measuring the solubilized dye using a microplate reader. To quantify the number of cells embedded in the biofilms, the biofilms are scrapped off using cell scrapers, harvested in the saline, vigorously agitated in the presence of glass beads, and spread on Acinetobacter agar. Then, the plates are incubated at 30 &#176;C for 24-42 h. After incubation, the red colonies are enumerated to estimate the number of cells in biofilms. This viable count method can also be useful for counting Acinetobacter cells in mixed-species biofilms. Acinetobacter biofilms can be visualized using fluorescent dyes. A commercially available microplate designed for microscopic analysis is employed to form biofilms. Then, the bottom-surface attached biofilms are stained with SYTO9 and propidium iodide dyes, washed, then visualized with confocal laser scanning microscopy.

Following the protocol, the biofilms of Acinetobacter isolates, originally isolated from kitchen surfaces, were formed on a polystyrene 96-well plate, stained with crystal violet, and the dyes were solubilized in ethanol and measured for biofilm mass (Figure 1). The number of biofilms greatly varied depending on the strains ranging from OD 0.04 to 1.69 (Figure 1). Based on the criteria established by Stepanovi&#263; et al.16, all...

Watch this Scientific Journal Video about A Comprehensive Protocol for Acinetobacter Biofilm Quantification, Assessment, and Visualization at JoVE.com

Author Spotlight: A Comprehensive Protocol for Acinetobacter Biofilm Quantification, Assessment, and Visualization 

This protocol describes the preparation of the inoculum, the biofilm quantification on microtiter plates using crystal violet dye, the viable count in biofilms, and the visualization of biofilms of Acinetobacter.

Quantification, Viability Assessment, and Visualization Strategies for Acinetobacter Biofilms

Acinetobacter causes nosocomial infections and its biofilm formation can contribute to the survival on dry surfaces such as hospital environments. Thus, ...

quantification-viability-assessment-visualization-strategies-for

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2.9K Views.  Korea Food Research Institute. This protocol describes the preparation of the inoculum, the biofilm quantification on microtiter plates using crystal violet dye, the viable count in biofilms, and the visualization of biofilms of Acinetobacter.

Video: Author Spotlight: A Comprehensive Protocol for Acinetobacter Biofilm Quantification, Assessment, and Visualization 

Concurrent Quantification of Cellular and Extracellular Components of Biofilms

Confocal laser scanning microscopy (CLSM) is a powerful tool for investigation of biofilms. Very few investigations have successfully quantified concurrent distribution of more than two components within biofilms because: 1)&#160;selection of fluorescent dyes having minimal spectral overlap is complicated, and 2)&#160;quantification of multiple fluorochromes poses a multifactorial problem. Objectives: Report a methodology to quantify and compare concurrent 3-dimensional distributions of three cellular/extracellular components of biofilms grown on relevant substrates. Methods: The method consists of distinct, interconnected steps involving biofilm growth, staining, CLSM imaging, biofilm structural analysis and visualization, and statistical analysis of structural parameters. Biofilms of Streptococcus mutans (strain UA159) were grown for 48 hr on sterile specimens of Point 4 and TPH3 resin composites. Specimens were subsequently immersed for 60 sec in either Biot&#232;ne PBF (BIO) or Listerine Total Care (LTO) mouthwashes, or water (control group; n=5/group). Biofilms were stained with fluorochromes for extracellular polymeric substances, proteins and nucleic acids before imaging with CLSM. Biofilm structural parameters calculated using ISA3D image analysis software were biovolume and mean biofilm thickness. Mixed models statistical analyses compared structural parameters between mouthwash and control groups (SAS software; &#945;=0.05). Volocity software permitted visualization of 3D distributions of overlaid biofilm components (fluorochromes). Results: Mouthwash BIO produced biofilm structures that differed significantly from the control (p&#60;0.05) on both resin composites, whereas LTO did not produce differences (p&#62;0.05) on either product. Conclusions: This methodology efficiently and successfully quantified and compared concurrent 3D distributions of three major components within S. mutans biofilms on relevant substrates, thus overcoming two challenges to simultaneous assessment of biofilm components. This method can also be used to determine the efficacy of antibacterial/antifouling agents against multiple biofilm components, as shown using mouthwashes. Furthermore, this method has broad application because it facilitates comparison of 3D structures/architecture of biofilms in a variety of disciplines.

A protocol for the concurrent quantification and comparison of three cellular and extracellular components within biofilms is presented. The methodology involves the use of confocal laser scanning microscopy, biofilm structural analysis and visualization software, and statistical analysis software.

Confocal laser scanning microscopy (CLSM) is a powerful tool for investigation of biofilms. Very few investigations have successfully quantified ...

Immunology and Infection

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

There are few high-throughput in vitro systems which facilitate the development of multi-species biofilms that contain numerous species commonly detected within in vivo oral biofilms. Furthermore, a system that uses natural human saliva as the nutrient source, instead of artificial media, is particularly desirable in order to support the expression of cellular and biofilm-specific properties that mimic the in vivo communities. We describe a method for the development of multi-species oral biofilms that are comparable, with respect to species composition, to supragingival dental plaque, under conditions similar to the human oral cavity. Specifically, this methods article will describe how a commercially available microfluidic system can be adapted to facilitate the development of multi-species oral biofilms derived from and grown within pooled saliva. Furthermore, a description of how the system can be used in conjunction with a confocal laser scanning microscope to generate 3-D biofilm reconstructions for architectural and viability analyses will be presented. Given the broad diversity of microorganisms that grow within biofilms in the microfluidic system (including Streptococcus, Neisseria, Veillonella, Gemella, and Porphyromonas), a protocol will also be presented describing how to harvest the biofilm cells for further subculture&#160;or DNA extraction and analysis. The limits of both the microfluidic biofilm system and the current state-of-the-art data analyses will be addressed. Ultimately, it is envisioned that this article will provide a baseline technique that will improve the study of oral biofilms and aid in the development of additional technologies that can be integrated with the microfluidic platform.

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

The goal of this methods paper is to describe the use of a microfluidic system for the development of multi-species biofilms that contain species typically identified in human supragingival dental plaque.&#160;Methods to describe biofilm architecture, biofilm viability, and an approach to harvest biofilm for culture-dependent or culture-independent analyses are highlighted.

There are few high-throughput in vitro systems which facilitate the development of multi-species biofilms that contain numerous species commonly detected ...

Bioengineering

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

This work assesses different methodologies to study the impact of small molecule biofilm inhibitors, such as D-amino acids, on the development and resilience of Bacillus subtilis biofilms. First, methods are presented that select for small molecule inhibitors with biofilm-specific targets in order to separate the effect of the small molecule inhibitors on planktonic growth from their effect on biofilm formation. Next, we focus on how inoculation conditions affect the sensitivity of multicellular, floating B. subtilis cultures to small molecule inhibitors. The results suggest that discrepancies in the reported effects of such inhibitors such as D-amino acids are due to inconsistent pre-culture conditions. Furthermore, a recently developed protocol is described for evaluating the contribution of small molecule treatments towards biofilm resistance to antibacterial substances. Lastly, scanning electron microscopy (SEM) techniques are presented to analyze the three-dimensional spatial arrangement of cells and their surrounding extracellular matrix in a B. subtilis biofilm. SEM facilitates insight into the three-dimensional biofilm architecture and the matrix texture. A combination of the methods described here can greatly assist the study of biofilm development in the presence and absence of biofilm inhibitors, and shed light on the mechanism of action of these inhibitors.

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

This study presents the development of reproducible methodologies to study biofilm inhibitors and their effects on Bacillus subtilis multicellularity.

This work assesses different methodologies to study the impact of small molecule biofilm inhibitors, such as D-amino acids, on the development and ...

A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy

Bacterial biofilms frequently form on fungal surfaces and can be involved in numerous bacterial-fungal interaction processes, such as metabolic cooperation, competition, or predation. The study of biofilms is important in many biological fields, including environmental science, food production, and medicine. However, few studies have focused on such bacterial biofilms, partially due to the difficulty of investigating them. Most of the methods for qualitative and quantitative biofilm analyses described in the literature are only suitable for biofilms forming on abiotic surfaces or on homogeneous and thin biotic surfaces, such as a monolayer of epithelial cells.
While laser scanning confocal microscopy (LSCM) is often used to analyze in situ and in vivo biofilms, this technology becomes very challenging when applied to bacterial biofilms on fungal hyphae, due to the thickness and the three dimensions of the hyphal networks. To overcome this shortcoming, we developed a protocol combining microscopy with a method to limit the accumulation of hyphal layers in fungal colonies. Using this method, we were able to investigate the development of bacterial biofilms on fungal hyphae at multiple scales using both LSCM and scanning electron microscopy (SEM). This report describes the protocol, including microorganism cultures, bacterial biofilm formation conditions, biofilm staining, and LSCM and SEM visualizations.

This protocol describes a new method to grow and qualitatively analyze bacterial biofilms on fungal hyphae by confocal and electron microscopy.

Bacterial biofilms frequently form on fungal surfaces and can be involved in numerous bacterial-fungal interaction processes, such as metabolic ...

Visualizing the Effects of Sputum on Biofilm Development Using a Chambered Coverglass Model

Biofilms consist of groups of bacteria encased in a self-secreted matrix. They play an important role in industrial contamination as well as in the development and persistence of many health related infections. One of the most well described and studied biofilms in human disease occurs in chronic pulmonary infection of cystic fibrosis patients. When studying biofilms in the context of the host, many factors can impact biofilm formation and development. In order to identify how host factors may affect biofilm formation and development, we used a static chambered coverglass method to grow biofilms in the presence of host-derived factors in the form of sputum supernatants. Bacteria are seeded into chambers and exposed to sputum filtrates. Following 48 hr of growth, biofilms are stained with a commercial biofilm viability kit prior to confocal microscopy and analysis. Following image acquisition, biofilm properties can be assessed using different software platforms. This method allows us to visualize key properties of biofilm growth in presence of different substances including antibiotics.

This protocol describes the visualization of biofilm development following exposure to host-factors using a slide chamber model. This model allows for direct visualization of biofilm development as well as analysis of biofilm parameters using computer software programs.

Biofilms consist of groups of bacteria encased in a self-secreted matrix. They play an important role in industrial contamination as well as in the ...

A Platform of Anti-biofilm Assays Suited to the Exploration of Natural Compound Libraries

Biofilms are regarded as one of the most challenging topics of modern biomedicine, and they are potentially responsible for over 80% of antibiotic-tolerant infections. Biofilms have displayed an exceptionally high tolerance for chemotherapy, which is thought to be multifactorial. For instance, the matrix provides a physical barrier that decreases the penetration of antibiotics into the biofilm. Also, cells within the biofilms are phenotypically diverse. Likely, biofilm resilience arises from a combination of these and other, yet unknown, mechanisms. All of the currently existing antibiotics have been developed against single-cells (planktonic) bacteria. Therefore, so far, a very limited repertoire of molecules exists that can selectively act on mature biofilms. This situation has driven a progressive paradigm shift in drug discovery, in which searching for anti-biofilms has been urged to occupy a more prominent place. An additional challenge is that there are a very limited number of standardized methods for biofilm research, especially those that can be used for large-throughput screening of chemical libraries. Here, an experimental anti-biofilm platform for chemical screening is presented. It uses three assays to measure biofilm viability (with resazurin staining), total biomass (with crystal violet staining), and biofilm matrix (using a wheat germ agglutinin, WGA-fluorescence-based staining of the poly-N-acetyl-glucosamine, PNAG, fraction). All the assays were developed using Staphylococcus aureus as the model bacteria. Examples of how the platform can be used for primary screening as well as for functional characterization of identified anti-biofilm hits are presented. This experimental sequence further allows for the classification of the hits based upon the measured end-points. It also provides information on their mode of action, especially on long-term versus short-term chemotherapeutic effects. Thus, it is very advantageous for the quick identification of high-quality hit compounds that can serve as starting points for various biomedical applications.

Biofilm infections show high tolerance towards chemotherapy. No single assay captures the complexity of biofilms. Instead, complementary assays are needed. We present a screening platform (developed for S. aureus) that combines assays for viability, biomass, and biofilm matrix. It allows anti-biofilm drug discovery, including the assessment of long-term chemotherapeutic effects.

Biofilms are regarded as one of the most challenging topics of modern biomedicine, and they are potentially responsible for over 80% of ...

Live Cell Analysis of Shear Stress on Pseudomonas aeruginosa Using an Automated Higher-Throughput Microfluidic System

A higher-throughput microfluidic in vitro bioreactor coupled with fluorescence microscopy has been used to study bacterial biofilm growth and morphology, including Pseudomonas aeruginosa (P. aeruginosa). Here, we will describe how the system can be used to study the growth kinetics and the morphological properties such as the surface roughness and textural entropy of P. aeruginosa strain PA01 that expresses an enhanced green fluorescent protein (PA01-EGFP). A detailed protocol will describe how to grow and seed PA01-EGFP cultures, how to set up the microscope and autorun, and conduct the image analysis to determine growth rate and morphological properties using a variety of shear forces that are controlled by the microfluidic device. This article will provide a detailed description of a technique to improve the study of PA01-EGFP biofilms which eventually can be applied towards other strains of bacteria, fungi, or algae biofilms using the microfluidic platform.

Live Cell Analysis of Shear Stress on Pseudomonas aeruginosa Using an Automated Higher-Throughput Microfluidic System

Here, we describe the use of a higher-throughput microfluidic bioreactor coupled with a fluorescent microscope for the analysis of shear stress effects on Pseudomonas aeruginosa biofilms expressing green fluorescent proteins, including instrument set up, the determination of biofilm coverage, growth rate, and morphological properties.

A higher-throughput microfluidic in vitro bioreactor coupled with fluorescence microscopy has been used to study bacterial biofilm growth and morphology, ...

Quantitative Examination of Antibiotic Susceptibility of Neisseria gonorrhoeae Aggregates Using ATP-utilization Commercial Assays and Live/Dead Staining

The emergence of antibiotic resistant Neisseria gonorrhoeae (GC) is a worldwide health threat and highlights the need to identify individuals who fail treatment. This Gram-negative bacterium causes gonorrhea exclusively in humans. During infection, it is able to form aggregates and/or biofilms. The minimum inhibitory concentration (MIC) test is used for to determine susceptibility to antibiotics and to define appropriate treatment. However, the mechanism of the eradication in vivo and its relationship to laboratory results are not known. A method that examines how GC aggregation affects antibiotic susceptibility and shows the relationship between aggregate size and antibiotic susceptibility was developed. When GC aggregate, they are more resistant to antibiotic killing, with bacteria in the center surviving ceftriaxone treatment better than those in the periphery. The data indicate that N. gonorrhoeae aggregation can reduce its susceptibility to ceftriaxone, which is not reflected using the standard agar plate-based MIC methods. The method used in this study will allow researchers to test bacterial susceptibility under clinically relevant conditions.

Quantitative Examination of Antibiotic Susceptibility of Neisseria gonorrhoeae Aggregates Using ATP-utilization Commercial Assays and Live/Dead Staining

A simple ATP-measuring assay and live/dead staining method were used to quantify and visualize Neisseria gonorrhoeae survival after treatment with ceftriaxone. This protocol can be extended to examine the antimicrobial effects of any antibiotic and can be used to define the minimal inhibitory concentration of antibiotics in bacterial biofilms.

The emergence of antibiotic resistant Neisseria gonorrhoeae (GC) is a worldwide health threat and highlights the need to identify individuals who fail ...

Quantifying the Effects of Antimicrobials on In vitro Biofilm Architecture using COMSTAT Software

Biofilms are aggregates of microorganisms that rely on a self-produced matrix of extracellular polymeric substance for protection and structural integrity. The nosocomial pathogen, Pseudomonas aeruginosa, is known to adopt a biofilm mode of growth, causing chronic pulmonary infection in patients with cystic fibrosis (CF). The computer program, COMSTAT, is a useful tool for quantifying antimicrobial-induced changes in P. aeruginosa biofilm architecture by extracting data from three-dimensional confocal images. However, standardized operation of the software is less commonly addressed, which is important for optimal reporting of biofilm behavior and cross-center comparison. Thus, the aim of this protocol is to provide a simple and reproducible framework for quantifying in vitro biofilm structures under varying antimicrobial conditions via COMSTAT. The technique is modeled using a CF P. aeruginosa isolate, grown in the form of biofilm replicates, and exposed to tobramycin and the anti-Psl monoclonal antibody, Psl0096. The step-by-step approach aims to reduce user ambiguity and minimize the chance of overlooking crucial image-processing steps. Specifically, the protocol emphasizes the elimination of subjective variations associated with the manual operation of COMSTAT, including image segmentation and the selection of appropriate quantitative analysis functions. Although this method requires users to spend additional time processing confocal images prior to running COMSTAT, it helps minimize misrepresented biofilm heterogenicity in automated outputs.

Quantifying the Effects of Antimicrobials on In vitro Biofilm Architecture using COMSTAT Software

Antimicrobial-induced changes to Pseudomonas aeruginosa biofilm architecture differ among clinical isolates cultured from patients with cystic fibrosis and chronic pulmonary infection. Following confocal microscopy, COMSTAT software can be utilized to quantify variations in biofilm architecture (e.g., surface area, thickness, biomass) for individual isolates to assess the efficacy of anti-infective agents.

Biofilms are aggregates of microorganisms that rely on a self-produced matrix of extracellular polymeric substance for protection and structural ...

Tools for the Real-Time Assessment of a Pseudomonas aeruginosa Infection Model

Pseudomonas aeruginosa (Pa) is one of the most common opportunistic pathogens associated with cystic fibrosis (CF). Once Pa colonization is established, a large proportion of the infecting bacteria form biofilms within airway sputum. Pa biofilms isolated from CF sputum have been shown to grow in small, dense aggregates of ~10-1,000 cells that are spatially organized and exhibit clinically relevant phenotypes such as antimicrobial tolerance. One of the biggest challenges to studying how Pa aggregates respond to the changing sputum environment is the lack of nutritionally relevant and robust systems that promote aggregate formation. Using a synthetic CF sputum medium (SCFM2), the life history of Pa aggregates can be observed using confocal laser scanning microscopy (CLSM) and image analysis at the resolution of a single cell. This in vitro system allows the observation of thousands of aggregates of varying size in real time, three dimensions, and at the micron scale. At the individual and population levels, having the ability to group aggregates by phenotype and position facilitates the observation of aggregates at different developmental stages and their response to changes in the microenvironment, such as antibiotic treatment, to be differentiated with precision.

Tools for the Real-Time Assessment of a Pseudomonas aeruginosa Infection Model

Synthetic cystic fibrosis sputum medium (SCFM2) can be utilized in combination with both confocal laser scanning microscopy and fluorescence-activated cell sorting to observe bacterial aggregates at high resolution. This paper details methods to assess aggregate populations during antimicrobial treatment as a platform for future studies.

Pseudomonas aeruginosa (Pa) is one of the most common opportunistic pathogens associated with cystic fibrosis (CF). Once Pa colonization is established, a ...

Quantification, Viability Assessment, and Visualization Strategies for Acinetobacter Biofilms

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Chapters in this video

Concurrent Quantification of Cellular and Extracellular Components of Biofilms

Use of a High-throughput In Vitro Microfluidic System to Develop Oral Multi-species Biofilms

Methodologies for Studying B. subtilis Biofilms as a Model for Characterizing Small Molecule Biofilm Inhibitors

A New Method for Qualitative Multi-scale Analysis of Bacterial Biofilms on Filamentous Fungal Colonies Using Confocal and Electron Microscopy

Visualizing the Effects of Sputum on Biofilm Development Using a Chambered Coverglass Model

A Platform of Anti-biofilm Assays Suited to the Exploration of Natural Compound Libraries

Live Cell Analysis of Shear Stress on Pseudomonas aeruginosa Using an Automated Higher-Throughput Microfluidic System

Quantitative Examination of Antibiotic Susceptibility of Neisseria gonorrhoeae Aggregates Using ATP-utilization Commercial Assays and Live/Dead Staining

Quantifying the Effects of Antimicrobials on In vitro Biofilm Architecture using COMSTAT Software

Tools for the Real-Time Assessment of a Pseudomonas aeruginosa Infection Model