Confusion over live/dead stainings for the detection of vital microorganisms in oral biofilms--which stain is suitable?

Precise, Sensitive Detection of Viable Foodborne Pathogenic Bacteria with a 6-Order Dynamic Range via Digital Rolling Circle Amplification

The presence of viable pathogenic bacteria in food can lead to serious foodborne diseases, thus posing a risk to human health. Here, we develop a digital rolling circle amplification (dRCA) assay that enables the precise and sensitive quantification of viable foodborne pathogenic bacteria. Directly targeting pathogenic RNAs via a ligation-based padlock probe allows for precisely discriminating viable bacteria from dead one. The one-target-one-amplicon characteristic of dRCA enables high sensitivity and a broad quantitative detection range, conferring a detection limit of 10 CFU/mL and a dynamic range of 6 orders. dRCA can detect rare viable bacteria, even at a proportion as low as 0.1%, which is 50 times more sensitive than the live/dead staining method. The high sensitivity for detecting viable bacteria accommodates dRCA for assessing sterilization efficiency. Based on the assay, we found that, for pasteurization, slightly elevating the temperature to 68 °C can reduce the heating time to 10 min, which may minimize nutrient degradation caused by high-temperature exposure. The assay can serve as a precise tool for estimating the contamination by viable pathogenic bacteria and assessing sterilization, which facilitates food safety control.

Efficacy of the GentleWave System in the removal of biofilm from the mesial roots of mandibular molars before and after minimal instrumentation: An ex vivo study

AIM

To compare the efficacy of Enterococcus faecalis biofilm removal using the GentleWave System (GWS) (Sonendo Inc, CA) on non-instrumented versus minimally instrumented root canal systems.

METHODOLOGY

Thirty-four mandibular molars were autoclaved and allocated to four groups: Negative control (n = 5); positive control (n = 5); Group 1: non-instrumentation + GWS (NI + GWS) (n = 12); and Group 2: minimal instrumentation + GWS (MI + GWS) (n = 12). Of 34 samples, 24 samples with Vertucci type 2 configuration within the mesial root of each sample were allocated to Groups 1 and 2 and then matched based on the working length and root canal configuration. After inoculation of samples with E. faecalis for 3 weeks, the GWS was used on Group 1 without any instrumentation and Group 2 after instrumentation of mesial canals until size 20/06v. CFU and SEM analysis were used.

RESULTS

Log10 (CFU/mL) from the positive control, and Group 1 and 2 were 7.41 ± 0.53, 3.41 ± 1.54, and 3.21 ± 1.54, respectively. Both groups showed a statistically significant difference in the reduction of viable E. faecalis cells compared to the positive control (Group 1 [p = .0001] and Group 2 [p < .0001]), whilst showing no significant difference between the two tested groups (p < .05).

CONCLUSION

The use of GWS on the non-instrumented root canal system could be an effective disinfection protocol in removing the biofilm without dentin debris formation.

The effect of the enzymes trypsin and DNase I on the antimicrobial efficiency of root canal irrigation solutions

The purpose of this study was to evaluate the antibacterial efficacy of using 2.5% NaOCl, 2% chlorhexidine (CHX), Irritrol, and chitosan-coated silver nanoparticles (AgCNPs) alone or in combination with deoxyribonuclease I (DNase I) and trypsin pre-enzyme applications in dentin samples contaminated with Enterococcus faecalis (E. faecalis) by CLSM. 144 dentin blocks with confirmed E. faecalis biofilm formation were divided randomly according to the irrigation protocol (n = 12): NaOCl, CHX, Irritrol, AgCNPs, trypsin before NaOCl, CHX, Irritrol, AgCNPs, and DNase I before NaOCl, CHX, Irritrol, AgCNPs. Dentin blocks were stained with the Live/Dead BacLight Bacterial Viability Kit and viewed with CLSM after irrigation applications. The percentage of dead and viable bacteria was calculated using ImageJ software on CLSM images. At a significance level of p < 0.05, the obtained data were analyzed using one-way Anova and post-hoc Tukey tests. In comparison with NaOCl, CHX had a higher percentage of dead bacteria, both when no pre-enzyme was applied and when DNase I was applied as a pre-enzyme (p < 0.05). There was no difference in the percentage of dead bacteria between the irrigation solutions when trypsin was applied as a pre-enzyme (p > 0.05). AgCNPs showed a higher percentage of dead bacteria when trypsin was applied as a pre-enzyme compared to other irrigation solutions (p < 0.05), while the pre-enzyme application did not affect the percentage of dead bacteria in NaOCl, CHX, and Irritrol (p > 0.05). No irrigation protocol tested was able to eliminate the E. faecalis biofilm. While the application of trypsin as a pre-enzyme improved the antimicrobial effect of AgCNPs, it did not make any difference over other irrigation solutions.

Deep learning unlocks label-free viability assessment of cancer spheroids in microfluidics

Despite recent advances in cancer treatment, refining therapeutic agents remains a critical task for oncologists. Precise evaluation of drug effectiveness necessitates the use of 3D cell culture instead of traditional 2D monolayers. Microfluidic platforms have enabled high-throughput drug screening with 3D models, but current viability assays for 3D cancer spheroids have limitations in reliability and cytotoxicity. This study introduces a deep learning model for non-destructive, label-free viability estimation based on phase-contrast images, providing a cost-effective, high-throughput solution for continuous spheroid monitoring in microfluidics. Microfluidic technology facilitated the creation of a high-throughput cancer spheroid platform with approximately 12 000 spheroids per chip for drug screening. Validation involved tests with eight conventional chemotherapeutic drugs, revealing a strong correlation between viability assessed via LIVE/DEAD staining and phase-contrast morphology. Extending the model's application to novel compounds and cell lines not in the training dataset yielded promising results, implying the potential for a universal viability estimation model. Experiments with an alternative microscopy setup supported the model's transferability across different laboratories. Using this method, we also tracked the dynamic changes in spheroid viability during the course of drug administration. In summary, this research integrates a robust platform with high-throughput microfluidic cancer spheroid assays and deep learning-based viability estimation, with broad applicability to various cell lines, compounds, and research settings.

Influence of different presentation forms of chlorhexidine on contaminated root canals during agitation

This in vitro study aimed to verify the influence of chlorhexidine (CHX) (gel and solution) in association with different activation protocols on disinfection of root canals contaminated with Enterococcus faecalis. In total, 120 lower premolar roots were selected, contaminated and divided into 12 groups according to irrigation technique and substance. Samples were collected before and after each irrigation technique and analysed for colony-forming units (CFU). Three dentin discs were obtained for quantification of viable intratubular cells by using confocal laser scanning microscopy (CLSM). CFU results showed that sonic and ultrasonic were more effective than conventional irrigation. Ultrasonic activation was more effective than sonic for CHX gel (p < 0.05). CLSM showed that either activation was better than conventional in all groups and root canal thirds (p < 0.05). It was concluded that ultrasonic/sonic activation was more effective than conventional techniques and CHX enhanced intratubular dentin decontamination across all irrigation methods.

The antibacterial activity of a photoactivatable diarylacetylene against Gram-positive bacteria

The emergence of antibiotic resistance is a growing threat to human health, and therefore, alternatives to existing compounds are urgently needed. In this context, a novel fluorescent photoactivatable diarylacetylene has been identified and characterised for its antibacterial activity, which preferentially eliminates Gram-positive over Gram-negative bacteria. Experiments confirmed that the Gram-negative lipopolysaccharide-rich outer surface is responsible for tolerance, as strains with reduced outer membrane integrity showed increased susceptibility. Additionally, bacteria deficient in oxidative damage repair pathways also displayed enhanced sensitivity, confirming that reactive oxygen species production is the mechanism of antibacterial activity. This new diarylacetylene shows promise as an antibacterial agent against Gram-positive bacteria that can be activated in situ, potentially for the treatment of skin infections.

Evaluating models and assessment techniques for understanding oral biofilm complexity

Oral biofilms are three-dimensional (3D) complex entities initiating dental diseases and have been evaluated extensively in the scientific literature using several biofilm models and assessment techniques. The list of biofilm models and assessment techniques may overwhelm a novice biofilm researcher. This narrative review aims to summarize the existing literature on biofilm models and assessment techniques, providing additional information on selecting an appropriate model and corresponding assessment techniques, which may be useful as a guide to the beginner biofilm investigator and as a refresher to experienced researchers. The review addresses previously established 2D models, outlining their advantages and limitations based on the growth environment, availability of nutrients, and the number of bacterial species, while also exploring novel 3D biofilm models. The growth of biofilms on clinically relevant 3D models, particularly melt electrowritten fibrous scaffolds, is discussed with a specific focus that has not been previously reported. Relevant studies on validated oral microcosm models that have recently gaining prominence are summarized. The review analyses the advantages and limitations of biofilm assessment methods, including colony forming unit culture, crystal violet, 2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide inner salt assays, confocal microscopy, fluorescence in situ hybridization, scanning electron microscopy, quantitative polymerase chain reaction, and next-generation sequencing. The use of more complex models with advanced assessment methodologies, subject to the availability of equipment/facilities, may help in developing clinically relevant biofilms and answering appropriate research questions.

Evaluation of the polyphenolic profile of native Ecuadorian stingless bee honeys (Tribe: Meliponini) and their antibiofilm activity on susceptible and multidrug-resistant pathogens: An exploratory analysis

Biofilms are associated with infections that are resistant to conventional therapies, contributing to the antimicrobial resistance crisis. The need for alternative approaches against biofilms is well-known. Although natural products like stingless bee honeys (tribe: Meliponini) constitute an alternative treatment, much is still unknown. Our main goal was to evaluate the antibiofilm activity of stingless bee honey samples against multidrug-resistant (MDR) pathogens through biomass assays, fluorescence (cell count and viability), and scanning electron (structural composition) microscopy. We analyzed thirty-five honey samples at 15% (v/v) produced by ten different stingless bee species (Cephalotrigona sp., Melipona sp., M. cramptoni, M. fuscopilosa, M. grandis, M. indecisa, M. mimetica, M. nigrifacies, Scaptotrigona problanca, and Tetragonisca angustula) from five provinces of Ecuador (Tungurahua, Pastaza, El Oro, Los Ríos, and Loja) against 24-h biofilms of Staphylococcus aureus, Klebsiella pneumoniae, Candida albicans, and Candida tropicalis. The present honey set belonged to our previous study, where the samples were collected in 2018-2019 and their physicochemical parameters, chemical composition, mineral elements, and minimal inhibitory concentration (MIC) were screened. However, the polyphenolic profile and their antibiofilm activity on susceptible and multidrug-resistant pathogens were still unknown. According to polyphenolic profile of the honey samples, significant differences were observed according to their geographical origin in terms of the qualitative profiles. The five best honey samples (OR24.1, LR34, LO40, LO48, and LO53) belonging to S. problanca, Melipona sp., and M. indecisa were selected for further analysis due to their high biomass reduction values, identification of the stingless bee specimens, and previously reported physicochemical parameters. This subset of honey samples showed a range of 63-80% biofilm inhibition through biomass assays. Fluorescence microscopy (FM) analysis evidenced statistical log reduction in the cell count of honey-treated samples in all pathogens (P <0.05), except for S. aureus ATCC 25923. Concerning cell viability, C. tropicalis, K. pneumoniae ATCC 33495, and K. pneumoniae KPC significantly decreased (P <0.01) by 21.67, 25.69, and 45.62%, respectively. Finally, scanning electron microscopy (SEM) analysis demonstrated structural biofilm disruption through cell morphological parameters (such as area, size, and form). In relation to their polyphenolic profile, medioresinol was only found in the honey of Loja, while scopoletin, kaempferol, and quercetin were only identified in honey of Los Rios, and dihydrocaffeic and dihydroxyphenylacetic acids were only detected in honey of El Oro. All the five honey samples showed dihydrocoumaroylhexose, luteolin, and kaempferol rutinoside. To the authors' best knowledge, this is the first study to analyze stingless bees honey-treated biofilms of susceptible and/or MDR strains of S. aureus, K. pneumoniae, and Candida species.

Effectiveness of conservative instrumentation in root canal disinfection

OBJECTIVES

The impact of conservative instrumentation on the disinfection of root canals with different curvatures has not yet been determined. This ex vivo study aimed to evaluate and compare the effect of conservative instrumentation with TruNatomy (TN) and Rotate and a conventional rotary system, ProTaper Gold (PTG), on root canal disinfection during chemomechanical preparation of straight and curved canals.

MATERIALS AND METHODS

Ninety mandibular molars with straight (n = 45) and curved (n = 45) mesiobuccal root canals were contaminated with polymicrobial clinical samples. Teeth were divided into three subgroups (n = 14) according to the file systems and the curvature. Canals were instrumented with TN, Rotate, and PTG, respectively. Sodium hypochlorite and EDTA were used as irrigants. Intracanal samples were taken before (S1) and after (S2) instrumentation. Six uninfected teeth were used as negative controls. The bacterial reduction between S1 and S2 was measured by ATP assay, flow cytometry, and culture methods. Kruskal-Wallis and ANOVA tests were followed by the Duncan post hoc test (p < 0.05).

RESULTS

Bacterial reduction percentages were similar for the three file systems in straight canals (p > 0.05). However, PTG showed a lower reduction percentage of intact membrane cells in flow cytometry than TN and Rotate (p = 0.036). For the curved canals, no significant differences were obtained (p > 0.05).

CONCLUSION

Conservative instrumentation of straight and curved canals using TN and Rotate files resulted in similar bacterial reduction compared to PTG.

CLINICAL RELEVANCE

The disinfection efficacy of conservative instrumentation is similar to conventional instrumentation in straight and curved root canals.

Using staining as reference for spectral imaging: Its application for the development of an analytical method to predict the presence of bacterial biofilms

At present, although spectral imaging is known to have a great potential to provide a massive amount of valuable information, the lack of reference methods remains as one of the bottlenecks to access the full capacity of this technique. This work aims to present a staining-based reference method with digital image treatment for spectral imaging, in order to propose a fast, efficient, contactless and non-invasive analytical method to predict the presence of biofilms. Spectral images of Pseudomonasaeruginosa biofilms formed on high density polyethylene coupons were acquired in visible and near infrared (vis-NIR) range between 400 and 1000 nm. Crystal violet staining served as a biofilm indicator, allowing the bacterial cells and the extracellular matrix to be marked on the coupon. Treated digital images of the stained biofilms were used as a reference. The size and pixels of the hyperspectral and digital images were scaled and matched to each other. Intensity color thresholds were used to differentiate the pixels associate to areas containing biofilms from those ones placed in biofilm-free areas. The model facultative Gram-negative bacterium, P. aeruginosa, which can form highly irregularly shaped and heterogeneous biofilm structures, was used to enhance the strength of the method, due to its inherent difficulties. The results showed that the areas with high and low intensities were modeled with good performance, but the moderate intensity areas (with potentially weak or nascent biofilms) were quite challenging. Image processing and artificial neural networks (ANN) methods were performed to overcome the issues resulted from biofilm heterogeneity, as well as to train the spectral data for biofilm predictions.

Efficient remediation of meropenem using Bacillus tropicus EMB20 β-lactamase immobilized on magnetic nanoparticles

Reducing antibiotic pollution in the environment in essential to preserve the effectiveness of the available antibiotics. In the present study, β-lactamase from Bacillus tropicus EMB20 was immobilized onto magnetic nanoparticles (Fe₃O₄) through covalent coupling method. The nanoconjugate was structurally characterized using SEM, FTIR, UV-spectrometry, and XRD diffraction analyses. The prepared enzyme nanoconjugate was thereafter used for remediation of meropenem (Mer) and showed complete removal of 10 mgL^-1 Mer within 3 h of treatment. Moreover, the immobilized enzyme was successfully recovered and reused for up to 5 cycles with 57% removal efficiency. The immobilized preparation was also observed to be effective in the removal of higher Mer concentrations of 25 and 50 mgL^-1 with 79% and 75% removal efficiency, respectively. The major hydrolyzed product of Mer was found to be opened-lactam ring structure with m/z 402.16. The hydrolyzed product(s) were observed to be non-toxic as revealed through microbial MTT, confocal microscopy, and growth studies. Under the mixed conditions of 50 mgL^-1 ampicillin (Amp), 10 mgL^-1 amoxicillin (Amox) and, Mer, the nanoconjugate showed simultaneous complete removal of Amp and Mer, while 49% Amox removal was detected after 3 h of treatment. Moreover, the nanoconjugates also showed concomitant complete removal of antibiotic mixture with in 2 h from aquaculture wastewater. Overall, the study comes out with an efficient approach for remediation of β-lactam antibiotics from contaminated systems.

Fernandez de Henestrosa A, Furmanczyk M, Trullàs C, Jourdan E, López-López J, Jorba M. Substantivity of mouth-rinse formulations containing cetylpyridinium chloride and O-cymen-5-ol: a randomized-crossover trial

BACKGROUND

The efficacy of mouth-rinses strongly depends upon their substantivity. The use of natural and non-toxic products that avoid secondary effects is gaining interest in preventive dentistry. The purpose of this study was to evaluate the substantivity of two formulations of mouth-washing solutions based on cetylpyridinium (CPC) and O-cymen-5-ol.

METHODS

This was a randomized, double-blind, crossover trial conducted at the Faculty of Medicine and Health Sciences of the University of Barcelona. Bacterial re-colonization was followed by live/dead (SYTO^TM9 + propidium iodide) bacterial staining and measured by confocal laser scanning microscopy and fluorometry. Unstimulated saliva samples were collected from 16 healthy individuals at baseline saliva and then, at 15 min, 30 min and 1, 2, 3, and 4 h after the following mouth-rinses: (i) a single, 1-min mouth-rinse with 15 ml of placebo (negative control); (ii) a single, 1-min mouth-rinse with 15 ml of CPC (0.05%) ; (iii) a single, 1-min mouth-rinse with 15 ml of O-cymen-5-ol (0.09%); (iv) a single, 1-min mouth-rinse with 15 ml of CPC (0.05%) + O-cymen-5-ol (0.09%).

RESULTS

Proportion of dead bacteria was significantly higher for all mouthrinses during the first 15 min compared to baseline (CPC = 48.0 ± 13.9; 95% CI 40.98-56.99; p < 0.001, O-cymen-5-ol = 79.8 ± 21.0; 95% CI 67.71-91.90; p < 0.05, CPC + O-cymen-5-ol = 49.4 ± 14; 95% CI 40.98-56.99; p < 0.001 by fluorometry and 54.8 ± 23.0; 95% CI 41.50-68.06; p < 0.001, 76.3 ± 17.1; 95% CI 66.36-86.14; p < 0.001, 47.4 ± 11.9; 95% CI 40.49-54.30; p < 0.001 by confocal laser scanning microscopy, respectively). Nevertheless, after 4 h, CPC + O-cymen-5-ol was the only one that obtained significant values as measured by the two quantification methods used (80.3 ± 22.8; 95% CI 67.15-93.50; p < 0.05 and 81.4 ± 13.8; 95% CI 73.45-89.43; p < 0.05). The combined use of CPC + O-cymen-5-ol increased the substantivity of the mouthrinse with respect to mouthrinses prepared with either of the two active products alone.

CONCLUSION

The synergistic interaction of CPC and O-cymen-5-ol prolongs their substantivity. The resulting formulation may be as effective as other antimicrobials, such as triclosan or chlorhexidine, but without their undesirable secondary effects. Thus, mouthrinsing products based on Combinations of CPC and O-cymen-5-ol may replace in the near future Triclosan and Chlorhexidine-based mouthrinses.

An intrinsically disordered antimicrobial peptide dendrimer from stereorandomized virtual screening

Membrane-disruptive amphiphilic antimicrobial peptides behave as intrinsically disordered proteins by being unordered in water and becoming α-helical in contact with biological membranes. We recently discovered that synthesizing the α-helical antimicrobial peptide dendrimer L-T25 ((KL)₈(KKL)₄(KLL)₂ KKLL) using racemic amino acids to form stereorandomized sr-T25, an analytically pure mixture of all possible diastereoisomers of L-T25, preserved antibacterial activity but abolished hemolysis and cytotoxicity, pointing to an intrinsically disordered antibacterial conformation and an α-helical cytotoxic conformation. In this study, to identify non-toxic intrinsically disordered homochiral antimicrobial peptide dendrimers (AMPDs), we surveyed sixty-three sr-analogs of sr-T25 selected by virtual screening. One of the analogs, sr-X18 ((KL)₈(KLK)₄(KLL)₂ KLLL), lost antibacterial activity as L-enantiomer and became hemolytic due to α-helical folding. By contrast, the L- and D-enantiomers of sr-X22 ((KL)₈(KL)₄(KKLL)₂ KLKK) were equally antibacterial, non-hemolytic, and non-toxic, implying an intrinsically disordered bioactive conformation. Screening stereorandomized libraries may be generally useful to identify or optimize intrinsically disordered bioactive peptides.

The Assessment of Activity of Antiseptic Agents against Biofilm of Staphylococcus aureus Measured with the Use of Processed Microscopic Images

Staphylococcal biofilms are major causative factors of non-healing wound infections. Their treatment algorithms recommend the use of locally applied antiseptic agents to counteract the spread of infection. The efficacy of antiseptics against biofilm is assessed in vitro by a set of standard quantitative and semi-quantitative methods. The development of software for image processing additionally allowed for the obtainment of quantitative data from microscopic images of biofilm dyed with propidium iodine and SYTO-9 reagents, differentiating dead cells from live ones. In this work, the method of assessment of the impact of antiseptic agents on staphylococcal biofilm in vitro, based on biofilms’ processed images, was proposed and scrutinized with regard to clinically relevant antiseptics, polyhexanide, povidone–iodine and hypochlorite. The standard quantitative culturing method was applied to validate the obtained data from processed images. The results indicated significantly higher activity of polyhexanide and povidone–iodine than hypochlorite against staphylococcal biofilm. Taking into account the fact that in vitro results of the efficacy of antiseptic agents against staphylococcal biofilm are frequently applied to back up their use in hospitals and ambulatory units, our work should be considered an important tool; providing reliable, quantitative data in this regard.

Single-cell stable isotope probing in microbial ecology

Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.

Characterization of spatiotemporal electroactive anodic biofilm activity distribution using 1D simulations

Activity distribution limitation in electroactive biofilm remains an unclear phenomenon. Some observations using confocal microscopy have shown notable difference between activity close to the anode and activity at the liquid interface. A numerical model is developed in this work to describe biofilm growth and local biomass segregation in electroactive biofilm. Under our model hypothesis, metabolic activity distribution in the biofilm results from the competition between two limiting factors: acetate diffusion and electronic conduction in the biofilm. Influence of inactive biomass fraction (i.e. non-growing biomass fraction) properties (such as conductivity and density) is simulated to show variation in local biomass distribution. Introducing a dependence of effective diffusion to local density leads to a drastic biomass fraction segregation. Increasing density of inactive fraction reduces significantly acetate diffusion in biofilm, enhances biomass activity on the outer layer (liquid/biofilm interface) and maintains inner core largely inactive. High inactive fraction conductivity enhances biomass activity in the outer layer and enhances current production. Hence, investment in extracellular polymer substance (EPS), anchoring redox components, is benefit for biofilm electroactivity. However, under our model hypothesis it means that conductivity should be two order lower than biofilm conductivity reported in order to observe inner core active biomass segregation.

Biofilm on Toothbrushes of Children with Cystic Fibrosis: A Potential Source of Lung Re-Infection after Antibiotic Treatment?

Frequent recurrent lung infections result in irreversible lung damage in children with cystic fibrosis (CF). This study aimed to determine if toothbrushes contain biofilms of pathogens, and act as potential reservoirs for lung re-infection following antibiotic treatment of acute exacerbations. Toothbrushes were collected from children with CF of lung infection before, during and after antibiotic treatment. Toothbrushes were rinsed with sterile saline and cultured. Bacterial isolates from toothbrushes were identified by 16s rRNA gene sequencing and compared with isolates from a sputum sample of the same patient. Scanning electron microscopy (SEM) was used to visually confirm the presence of bacterial biofilms and confocal laser scanning microscopy (CLSM) combined with Live/Dead stain to confirm bacterial viability. Large numbers of bacteria and biofilms were present on all toothbrushes. SEM confirmed the presence of biofilms and CLSM confirmed bacterial viability on all toothbrushes. Pathogens identified on toothbrushes from children before and during antibiotics treatment were in concordance with the species found in sputum samples. Pseudomonas aeruginosa and Staphylococcus aureus was able to be cultured from children’s toothbrushes despite antibiotic treatment. Toothbrushes were shown to be contaminated with viable pathogens and biofilms before and during antibiotic treatment and could be a potential source of lung re-infections.

A critical analysis of research methods and experimental models to study irrigants and irrigation systems

Irrigation plays an essential role in root canal treatment. The purpose of this narrative review was to critically appraise the experimental methods and models used to study irrigants and irrigation systems and to provide directions for future research. Studies on the antimicrobial effect of irrigants should use mature multispecies biofilms grown on dentine or inside root canals and should combine at least two complementary evaluation methods. Dissolution of pulp tissue remnants should be examined in the presence of dentine and, preferably, inside human root canals. Micro-omputed tomography is currently the method of choice for the assessment of accumulated dentine debris and their removal. A combination of experiments in transparent root canals and numerical modeling is needed to address irrigant penetration. Finally, models to evaluate irrigant extrusion through the apical foramen should simulate the periapical tissues and provide quantitative data on the amount of extruded irrigant. Mimicking the in vivo conditions as close as possible and standardization of the specimens and experimental protocols are universal requirements irrespective of the surrogate endpoint studied. Obsolete and unrealistic models must be abandoned in favour of more appropriate and valid ones that have more direct application and translation to clinical Endodontics.

In vitro model systems for exploring oral biofilms: From single-species populations to complex multi-species communities

Numerous in vitro biofilm model systems are available to study oral biofilms. Over the past several decades, increased understanding of oral biology and advances in technology have facilitated more accurate simulation of intraoral conditions and have allowed for the increased generalizability of in vitro oral biofilm studies. The integration of contemporary systems with confocal microscopy and 16S rRNA community profiling has enhanced the capabilities of in vitro biofilm model systems to quantify biofilm architecture and analyse microbial community composition. In this review, we describe several model systems relevant to modern in vitro oral biofilm studies: the constant depth film fermenter, Sorbarod perfusion system, drip-flow reactor, modified Robbins device, flowcells and microfluidic systems. We highlight how combining these systems with confocal microscopy and community composition analysis tools aids exploration of oral biofilm development under different conditions and in response to antimicrobial/anti-biofilm agents. The review closes with a discussion of future directions for the field of in vitro oral biofilm imaging and analysis.

A critical analysis of research methods and experimental models to study intracanal medicaments

In order to ensure predictable decontamination of the root canal system, chemo-mechanical preparation of the root canal space is sometimes supplemented with the use of intracanal medication. As microbial control of the root canal space is fundamental to the resolution of apical periodontitis, root canal disinfection strategies haven been researched intensively. The use of intracanal medication as a supplementary step to the chemo-mechanical preparation of the root canal space is one of them. Because of the costs and limitations of clinical research it is relevant and common practice to first evaluate alternative or new root canal disinfection modalities in laboratory studies. This involves the simulation of a root canal infection in a laboratory model, on which different disinfection strategies can be tested. When modelling the infected root canal, different levels of infection can be discriminated: suspended bacteria, microbial biofilms and infected dentine. This review describes the experimental models associated with these infection levels and critically appraises their value and methodological details. Suggestions for relevant research methods and experimental models are given, as well as some good practices for laboratory-based microbiological studies.

Crystal Violet Staining Alone Is Not Adequate to Assess Synergism or Antagonism in Multi-Species Biofilms of Bacteria Associated With Bacterial Vaginosis

Bacterial Vaginosis (BV) involves the presence of a multi-species biofilm adhered to vaginal epithelial cells, but its in-depth study has been limited due to the complexity of the bacterial community, which makes the design of in vitro models challenging. Perhaps the most common experimental technique to quantify biofilms is the crystal violet (CV) staining method. Despite its widespread utilization, the CV method is not without flaws. While biofilm CV quantification within the same strain in different conditions is normally accepted, assessing multi-species biofilms formation by CV staining might provide significant bias. For BV research, determining possible synergism or antagonism between species is a fundamental step for assessing the roles of individual species in BV development. Herein, we provide our perspective on how CV fails to properly quantify an in vitro triple-species biofilm composed of Gardnerella vaginalis, Fannyhessea (Atopobium) vaginae, and Prevotella bivia, three common BV-associated bacteria thought to play key roles in incident BV pathogenesis. We compared the CV method with total colony forming units (CFU) and fluorescence microscopy cell count methods. Not surprisingly, when comparing single-species biofilms, the relationship between biofilm biomass, total number of cells, and total cultivable cells was very different between each tested method, and also varied with the time of incubation. Thus, despite its wide utilization for single-species biofilm quantification, the CV method should not be considered for accurate quantification of multi-species biofilms in BV pathogenesis research.

Analytical challenges and perspectives of assessing viability of Giardia muris cysts and Cryptosporidium parvum oocysts by live/dead simultaneous staining

Giardia and Cryptosporidium are pathogenic protozoa often present in the environment in their infective form(cysts and oocysts). These parasites are very resistant to disinfection, which makes them important target organisms in environmental quality monitoring and sanitation. Viability assessment provides an interpretation of cell inactivation, and it can be evaluated by membrane integrity as well as enzyme activity, using different staining methods. These are straightforward and adequate to laboratories that lack infrastructure for molecular-based technologies or animal infectivity tests. This study investigated simultaneous staining by a commercial live/dead kit, in order to assess viability of Cryptosporidium parvum oocysts and Giardia muris cysts, comparing it to propidium iodide (PI) incorporation, a common stain applied in viability estimation. Results suggested that, although the central hypothesis of one-panel visualization (α = 0.05) was met, simultaneous staining impaired (oo)cyst detection by immunofluorescence assay (IFA), which was found to be essential to enumeration, as the live/dead test led to poor (oo)cyst labelling or a 10-fold lower recovery when carried out concomitantly to IFA. As for the viability assessment itself, although red dye uptake occurred as expected by dead or weakened organisms, neither live G. muris cysts or C. parvum oocysts present any green fluorescence by esterase metabolism. This may have been caused by low enzyme activity in the infective form and/or wall thickness of these parasites. The results do not exclude the possibility of simultaneous fluorescence staining for protozoa, but it is a starting point for a broader analysis, that may consider, for instance, different incubation conditions.

How Do We Determine the Efficacy of an Antibacterial Surface? A Review of Standardised Antibacterial Material Testing Methods

Materials that confer antimicrobial activity, be that by innate property, leaching of biocides or design features (e.g., non-adhesive materials) continue to gain popularity to combat the increasing and varied threats from microorganisms, e.g., replacing inert surfaces in hospitals with copper. To understand how efficacious these materials are at controlling microorganisms, data is usually collected via a standardised test method. However, standardised test methods vary, and often the characteristics and methodological choices can make it difficult to infer that any perceived antimicrobial activity demonstrated in the laboratory can be confidently assumed to an end-use setting. This review provides a critical analysis of standardised methodology used in academia and industry, and demonstrates how many key methodological choices (e.g., temperature, humidity/moisture, airflow, surface topography) may impact efficacy assessment, highlighting the need to carefully consider intended antimicrobial end-use of any product.

Role of Penicillin-Binding Proteins in the Viability, Morphology, Stress Tolerance, and Pathogenicity of Clavibacter michiganensis

Previous research has shown that penicillin-binding proteins (PBPs), enzymes involved in peptidoglycan (PG) assembly, could play an important role during the induction of the viable but nonculturable (VBNC) state, which allows non-spore-forming bacteria to survive adverse environmental conditions. The current study found that Clavibacter michiganensis has seven PBPs. Mutant analysis indicated that deletion of either of the class B PBPs was lethal and that the class A PBPs had an important role in PG synthesis, with the ΔpbpC mutant having an altered cellular morphology that resulted in longer cells that were swollen at one end and had thinner cell walls. The ΔpbpC mutant was also found to produce mucoid colonies in solid culture and a lower final cell titer in liquid medium, as well as having high sensitivity to osmotic stress and lysozyme treatment and surprisingly high pathogenicity. The double mutant, ΔdacB/ΔpbpE, also had a slightly altered phenotype, resulting in longer cells. Further analysis revealed that both mutants had high sensitivity to copper, which resulted in quicker induction into the VBNC state. However, only the ΔpbpC mutant had significantly reduced survivorship in the VBNC state. The study also confirmed that the VBNC state significantly improved the survivorship of wild-type C. michiganensis cells in response to environmental stresses and systemically demonstrated the protective role of the VBNC state in C. michiganensis, which is an important finding regarding its epidemiology and has serious implications for disease management.

Antibacterial effect of silver nanoparticles mixed with calcium hydroxide or chlorhexidine on multispecies biofilms

The purpose is to evaluate the antibacterial effects of the silver nanoparticles (AgNPs) (Nanografi, METU Teknokent, Ankara, Turkey) mixed with calcium hydroxide (Ca(OH)₂) (Ultracal XS, Ultradent, St Louis, US) or chlorhexidine gel (CHX) (Gluco-Chex, Cerkamed, Stalowa Wola, Poland) against a multispecies biofilm, by confocal laser scanning microscopy (CLSM) and culture-based analysis. Dentine blocks were inoculated with Enterococcus faecalis, Streptococcus mutans, Lactobacillus acidophilus and Actinomyces naeslundii for 1 week. Infected dentine blocks were randomly divided into groups according to medication; saline solution (SS), Ca(OH)₂, Ca(OH)₂ + AgNP, 2%CHX gel and 2%CHX gel + AgNP and time of application: 1 and 7 days (all groups, n = 5). Bacterial samples were collected before and after medication to quantify the bacterial load. Biofilm elimination was quantitatively analyzed by Live/Dead BacLight Bacterial Viability staining and CLSM. The addition of AgNPs to Ca(OH)₂ increased the effectiveness of medicament in terms of bacterial reduction in both application times (1 and 7 days) (p < 0.05: ANOVA, Tukey's test) according to culture-based analysis. The CLSM images revealed that mixture of AgNP with CHX killed significantly more bacteria when compared with all other medicaments at 1- and 7-day application times (p < 0.05 and p > 0.05, respectively: Kruskal-Wallis, Dunn post hoc tests). The efficacy of Ca(OH)₂ mixed with AgNPs was superior to Ca(OH)₂ used alone in both application times (p < 0.05) according to CLSM analysis. The present study put forth the potential use of AgNPs mixed with Ca(OH)₂ or CHX on multispecies (Enterococcus faecalis, Streptococcus mutans, Lactobacillus acidophilus and Actinomyces naeslundii) biofilm in 1 and 7day application periods.

Resilience of the oral microbiome

The human mouth harbors a complex microbiota, the composition of which is potentially influenced by a wide range of factors, including the intake of food and drink, the availability of endogenous nutrients, the host immune system, drug treatments, and systemic diseases. Despite these possible influences, the oral microbiota is remarkably resilient, particularly in comparison with the microbiota of the large intestine. Diet, with the exception of excessive and/or frequent consumption of fermentable carbohydrate or supplementation with nitrate, has minimal impact on the composition of the oral bacterial community. The common oral diseases dental caries and the periodontal diseases is associated with modification of the oral microbiota primarily as a result of the ecological changes induced by excessive acid production and inflammation, respectively. Systemically-administered antimicrobials have only a small effect on the composition of the oral bacterial community, and while locally delivered antimicrobials can have some clinical benefits, the biofilm lifestyle of oral bacteria lends them substantial resistance to the agents used. Saliva plays an important role in oral microbial ecology, by supplying nutrients and providing protection against colonization by nonoral organisms. Dry mouth is one condition that has a major effect on the microbiota, resulting in increased colonization by opportunistic pathogens. Some systemic diseases do affect the oral microbiome, notably diabetes, in which raised levels of glucose in saliva and tissue impact on bacterial nutrition.

Cryptosporidium spp. and Giardia spp. (oo)cysts as target-organisms in sanitation and environmental monitoring: A review in microscopy-based viability assays

Cysts and (oo)cysts are the infective forms of parasitic protozoa, as Giardia and Cryptosporidium, which are widespread and associated to worldwide waterborne diseases outbreaks. These microorganisms pose a challenge to public health, as they are resistant to conventional disinfection methods, which make them important parameters when evaluating inactivation efficiency. However, when (oo)cysts are targets, it is challenging to infer inactivation efficacy, as it may require infectivity tests that are not often an option for laboratory routine analysis. In this scene, (oo)cyst viability based on induced excystation, membrane integrity and enzyme activity evaluated by dye inclusion and/or exclusion, as well as fluorescence reduction consist on microscopy-based techniques that may be options to estimate inactivation in the environmental context. This scoping review presents applications, advantages and limitations of these methodologies for viability assessment, in order to shed light on the (oo)cyst viability topic and provide insight strategies for choosing protocols in the environmental and sanitation field, in laboratory applications and novel research.

Combatting fungal biofilm formation by diffusive release of fluconazole from heptylamine plasma polymer coating

A drug-eluting coating applied onto biomedical devices and implants is an appropriate way to ensure that an inhibitory concentration of antimicrobial drugs is present at the device surface, thus preventing surface colonization and subsequent biofilm formation. In this study, a thin polymer coating was applied to materials, and it acted as a drug-delivery reservoir capable of surface delivery of the antifungal drug fluconazole to amounts up to 21 μg/cm². The release kinetics into aqueous solution were quantified by UV spectroscopy and conformed to the Ritger-Peppas and Korsmeyer-Peppas model. Complementary microbiological assays were used to determine effectiveness against Candida albicans attachment and biofilm formation, and against the control heptylamine plasma polymer coating without drug loading, on which substantial fungal growth occurred. Fluconazole release led to marked antifungal activity in all assays, with log 1.6 reduction in CFUs/cm². Cell viability assays and microscopy revealed that fungal cells attached to the fluconazole-loaded coating remained rounded and did not form hyphae and biofilm. Thus, in vitro screening results for fluconazole-releasing surface coatings showed efficacy in the prevention of the formation of Candida albicans biofilm.

Synergistic Effect of Propidium Iodide and Small Molecule Antibiotics with the Antimicrobial Peptide Dendrimer G3KL against Gram-Negative Bacteria

There is an urgent need to develop new antibiotics against multidrug-resistant bacteria. Many antimicrobial peptides (AMPs) are active against such bacteria and often act by destabilizing membranes, a mechanism that can also be used to permeabilize bacteria to other antibiotics, resulting in synergistic effects. We recently showed that G3KL, an AMP with a multibranched dendritic topology of the peptide chain, permeabilizes the inner and outer membranes of Gram-negative bacteria including multidrug-resistant strains, leading to efficient bacterial killing. Here, we show that permeabilization of the outer and inner membranes of Pseudomonas aeruginosa by G3KL, initially detected using the DNA-binding fluorogenic dye propidium iodide (PI), also leads to a synergistic effect between G3KL and PI in this bacterium. We also identify a synergistic effect between G3KL and six different antibiotics against the Gram-negative Klebsiella pneumoniae, against which G3KL is inactive.

Multiple assessment methodologies in determining the antibiofilm actions of sodium hypochlorite mixed with clodronate or etidronate in endodontic irrigation

This study aimed to use multiple methodologies, including a novel usage of scanning electron microscopy (SEM), to evaluate the antimicrobial actions of sodium hypochlorite (NaOCl) admixed with clodronate or etidronate in root canal irrigation. The study also examined the usefulness of colony counting as a biofilm assessment methodology. Seven day Enterococcus faecalis biofilms were grown on hydroxyapatite discs. The discs were disinfected with 0.26 M clodronate-5% NaOCl, 0.26 M etidronate-5% NaOCl, 5% NaOCl, or treated with phosphate buffered saline (PBS). Assessments were performed using colony counting, SEM and the XTT reduction assay. The XTT assessment used the same groups but with 2.5% NaOCl. For colony counting, bacteria were removed from the discs by vortex mixing, followed by plating. The discs were subsequently fixed for SEM imagining and evaluators scored the SEM micrographs for remaining bacteria. Antibiofilm actions were assessed with the Kruskal-Wallis and Dunn's multiple comparison tests. SEM micrographs and the XTT assay revealed no differences between the NaOCl controls and the clodronate or etidronate mixtures with NaOCl (P > 0.05). It was concluded that the chelator mixtures with NaOCl had antibiofilm actions comparable to NaOCl. Furthermore, vortex mixing incompletely removed biofilm from HA discs in the PBS controls and hence colony counting using E. faecalis biofilms on hydroxyapatite discs could not be used for intergroup comparisons involving PBS. Additionally, colony counting could not be used for comparisons between the NaOCl treatment groups because the removal of bacteria from the substrate by vortex mixing was affected by the irrigant type.

Bioorthogonal Non-canonical Amino Acid Tagging Combined With Flow Cytometry for Determination of Activity in Aquatic Microorganisms

In this study, we have combined bioorthogonal non-canonical amino acid tagging (BONCAT) and flow cytometry (FCM) analysis, and we demonstrate the applicability of the method for marine prokaryotes. Enumeration of active marine bacteria was performed by combining the DNA stain SYBR Green with detection of protein production with BONCAT. After optimization of incubation condition and substrate concentration on monoculture of Escherichia coli, we applied and modified the method to natural marine samples. We found that between 10 and 30% of prokaryotes in natural communities were active. The method is replicable, fast, and allow high sample throughput when using FCM. We conclude that the combination of BONCAT and FCM is an alternative to current methods for quantifying active populations in aquatic environments.

Interaction between the Oral Microbiome and Dental Composite Biomaterials: Where We Are and Where We Should Go

Dental composites are routinely placed as part of tooth restoration procedures. The integrity of the restoration is constantly challenged by the metabolic activities of the oral microbiome. This activity directly contributes to a less-than-desirable half-life for the dental composite formulations currently in use. Therefore, many new antimicrobial dental composites are being developed to counteract the microbial challenge. To ensure that these materials will resist microbiome-derived degradation, the model systems used for testing antimicrobial activities should be relevant to the in vivo environment. Here, we summarize the key steps in oral microbial colonization that should be considered in clinically relevant model systems. Oral microbial colonization is a clearly defined developmental process that starts with the formation of the acquired salivary pellicle on the tooth surface, a conditioned film that provides the critical attachment sites for the initial colonizers. Further development includes the integration of additional species and the formation of a diverse, polymicrobial mature biofilm. Biofilm development is discussed in the context of dental composites, and recent research is highlighted regarding the effect of antimicrobial composites on the composition of the oral microbiome. Future challenges are addressed, including the potential of antimicrobial resistance development and how this could be counteracted by detailed studies of microbiome composition and gene expression on dental composites. Ultimately, progress in this area will require interdisciplinary approaches to effectively mitigate the inevitable challenges that arise as new experimental bioactive composites are evaluated for potential clinical efficacy. Success in this area could have the added benefit of inspiring other fields in medically relevant materials research, since microbial colonization of medical implants and devices is a ubiquitous problem in the field.

Calcium hypochlorite on mouse embryonic fibroblast cells (NIH3T3) in vitro cytotoxicity and genotoxicity: MTT and comet assay

Antimicrobial irrigation solutions are widely used under clinical settings. Their effect on dental tissue is a subject of recent research, which aims for a safer irrigant for clinical use. In this regard, here our goal was to evaluate the cytotoxicity and the genotoxicity of calcium hypochlorite (Ca(OCl)₂) solution, along with NaOCl, on Mouse embryonic fibroblast cells (NIH3T3). First, Cells were treated either with NaOCl or Ca(OCl)₂ in a time- and dose-dependent manner for cytotoxicity by 3-(4,5-dimethylthiazolyl-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, then cell viability was calculated according to cell proliferation plots. Secondly, genotoxicity was assessed by Comet assay. Data were statistically analyzed by Tukey's test (P < .05). NaOCl and Ca(OCl)₂ had similar effects on cellular viability at 3 and 6 h treatments. Cell viability of Ca(OCl)₂ at concentrations of 0.0125%, 0.025%, 0.05%, or 0.125% was significantly lower than that of NaOCl at 24 h treatment (P < .05).Comparing Ca(OCl)₂ and NaOCl treatments at all time points and concentrations, the damaged cell number of Ca(OCl)₂ was almost fourfold higher than that of NaOCl. In conclusion, both, NaOCl and Ca(OCl)₂ solutions were cytotoxic and genotoxic to NIH3T3, however, Ca(OCl)₂ had a significantly higher damaged cell percentage than NaOCl at all time points and concentrations investigated.

Rapid determination of carbapenem resistance by low-cost colorimetric methods: Propidium Iodide and alamar blue staining

Carbapenems are a class of β-lactam antibiotics with a broad antimicrobial activity spectrum. Owing to their sturdy structures resistant to most β-lactamases, they have been regarded as one of the last-resort antibiotics for combating multidrugresistant bacterial infections. However, the emergence of carbapenem resistance increases predominantly in nosocomial pathogens. To prevent spread of carbapenem resistance in early stages, it is imperative to develop rapid diagnostic tests that will substantially reduce the time and cost in determining carbapenem resistance. Thus, we devised a staining-based diagnostic method applicable to three different Gram-negative pathogens of Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae, all with the high potential to develop carbapenem resistance. Regardless of the resistance mechanisms presented by bacterial species and strains, double staining with propidium iodide (PI) and alamar blue (AB) identified resistant bacteria with an average sensitivity of 95.35%, 7 h after imipenem treatments in 343 clinical isolates. Among the three species tested, A. baumannii showed the highest diagnostic sensitivity of 98.46%. The PI and ABmediated staining method could be a promising diagnostic method with high-throughput efficacy and low cost.

Next-generation physiology approaches to study microbiome function at single cell level

The function of cells in their native habitat often cannot be reliably predicted from genomic data or from physiology studies of isolates. Traditional experimental approaches to study the function of taxonomically and metabolically diverse microbiomes are limited by their destructive nature, low spatial resolution or low throughput. Recently developed technologies can offer new insights into cellular function in natural and human-made systems and how microorganisms interact with and shape the environments that they inhabit. In this Review, we provide an overview of these next-generation physiology approaches and discuss how the non-destructive analysis of cellular phenotypes, in combination with the separation of the target cells for downstream analyses, provide powerful new, complementary ways to study microbiome function. We anticipate that the widespread application of next-generation physiology approaches will transform the field of microbial ecology and dramatically improve our understanding of how microorganisms function in their native environment.

It takes two for chronic wounds to heal: dispersing bacterial biofilm and modulating inflammation with dual action plasma coatings

Chronic wounds are affecting increasingly larger portions of the general population and their treatment has essentially remained unchanged for the past century. This lack of progress is due to the complex problem that chronic wounds are simultaneously infected and inflamed. Both aspects need to be addressed together to achieve a better healing outcome. Hence, we hereby demonstrate that the stable nitroxide radical (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO) can be plasma polymerized into smooth coatings (TEMPOpp), as seen via atomic force microscopy, X-ray photoelectron spectroscopy and ellipsometry. Upon contact with water, these coatings leach nitroxides into aqueous supernatant, as measured via EPR. We then exploited the known cell-signalling qualities of TEMPO to change the cellular behaviour of bacteria and human cells that come into contact with the surfaces. Specifically, the TEMPOpp coatings not only suppressed biofilm formation of the opportunistic bacterium Staphylococcus epidermidis but also dispersed already formed biofilm in a dose-dependent manner; a crucial aspect in treating chronic wounds that contain bacterial biofilm. Thus the coatings' microbiological efficacy correlated with their thickness and the thickest coating was the most efficient. Furthermore, this dose-dependent effect was mirrored in significant cytokine reduction of activated THP-1 macrophages for the four cytokines TNF-α, IL-1β, IL-6 and IP-10. At the same time, the THP-1 cells retained their ability to adhere and colonize the surfaces, as verified via SEM imaging. Thus, summarily, we have exploited the unique qualities of plasma polymerized TEMPO coatings in targeting both infection and inflammation simultaneously; demonstrating a novel alternative to how chronic wounds could be treated in the future.

We plasma polymerized the stable nitroxide radical TEMPO into thin coatings and exploited the coatings' unique qualities in targeting both infection and inflammation simultaneously; demonstrating a novel alternative as to how chronic wounds could be treated in the future.

Widespread cryptic viral infections in lotic biofilms

Viruses have important impacts on aquatic microbial ecology and have been studied at length in the global ocean. However, the roles of bacteriophages in lotic ecosystems, particularly in benthic biofilms, have been largely under-studied. The main goals of this work were to determine whether viruses are consistent members of natural benthic biofilm communities of freshwater streams; whether temperate phages are present and active in such biofilms; and whether community profiling approaches like RAPD-PCR can be adapted to characterize biofilm virus communities. Results from both field and laboratory experiments suggest that viruses are consistent members of lotic biofilm communities. Interestingly, prophage induction was statistically significant but only a small percentage of the total bacterial population appeared to harbor prophage or engaged in induction. Finally, while the use of RAPD-PCR for the community level profiling of biofilm viral communities suggests temporal change in response to biofilm maturity, further refinements are required for broad-scale quantitative application.

Erythrosin B: a versatile colorimetric and fluorescent vital dye for bacteria

Rapidly assaying cell viability for diverse bacteria species is not always straightforward. In eukaryotes, cell viability is often determined using colorimetric dyes; however, such dyes have not been identified for bacteria. We screened different dyes and found that erythrosin B (EB), a visibly red dye with fluorescent properties, functions as a vital dye for many Gram-positive and -negative bacteria. EB worked at a similar concentration for all bacteria studied and incubations were as short as 5 min. Given EB's spectral properties, diverse experimental approaches are possible to rapidly visualize and/or quantitate dead bacterial cells in a population. As the first broadly applicable colorimetric viability dye for bacteria, EB provides a cost-effective alternative for researchers in academia and industry.

Sublethal antibiotics collapse gut bacterial populations by enhancing aggregation and expulsion

Antibiotics induce large and highly variable changes in the intestinal microbiome even at sublethal concentrations, through mechanisms that remain elusive. Using gnotobiotic zebrafish, which allow high-resolution examination of microbial dynamics, we found that sublethal doses of the common antibiotic ciprofloxacin cause severe drops in bacterial abundance. Contrary to conventional views of antimicrobial tolerance, disruption was more pronounced for slow-growing, aggregated bacteria than for fast-growing, planktonic species. Live imaging revealed that antibiotic treatment promoted bacterial aggregation and increased susceptibility to intestinal expulsion. Intestinal mechanics therefore amplify the effects of antibiotics on resident bacteria. Microbial dynamics are captured by a biophysical model that connects antibiotic-induced collapses to gelation phase transitions in soft materials, providing a framework for predicting the impact of antibiotics on the intestinal microbiome.

Methods Used for the Eradication of Staphylococcal Biofilms

Staphylococcus aureus is considered one of the leading pathogens responsible for community and healthcare-associated infections. Among them, infections caused by methicillin-resistant strains (MRSA) are connected with ineffective or prolonged treatment. The therapy of staphylococcal infections faces many difficulties, not only because of the bacteria's resistance to antibiotics and the multiplicity of virulence factors it produces, but also due to its ability to form a biofilm. The present review focuses on several approaches used for the assessment of staphylococcal biofilm eradication. The methods described here are successfully applied in research on the prevention of biofilm-associated infections, as well as in their management. They include not only the evaluation of the antimicrobial activity of novel compounds, but also the methods for biomaterial functionalization. Moreover, the advantages and limitations of different dyes and techniques used for biofilm characterization are discussed. Therefore, this review may be helpful for those scientists who work on the development of new antistaphylococcal compounds.

Testing Anti-Biofilm Polymeric Surfaces: Where to Start?

Present day awareness of biofilm colonization on polymeric surfaces has prompted the scientific community to develop an ever-increasing number of new materials with anti-biofilm features. However, compared to the large amount of work put into discovering potent biofilm inhibitors, only a small number of papers deal with their validation, a critical step in the translation of research into practical applications. This is due to the lack of standardized testing methods and/or of well-controlled in vivo studies that show biofilm prevention on polymeric surfaces; furthermore, there has been little correlation with the reduced incidence of material deterioration. Here an overview of the most common methods for studying biofilms and for testing the anti-biofilm properties of new surfaces is provided.

Antibacterial Additives in Epoxy Resin-Based Root Canal Sealers: A Focused Review

Dental materials used in root canal treatment have undergone substantial improvements over the past decade. However, one area that still remains to be addressed is the ability of root canal fillings to effectively entomb, kill bacteria, and prevent the formation of a biofilm, all of which will prevent reinfection of the root canal system. Thus far, no published review has analysed the literature on antimicrobial additives to root canal sealers and their influence on physicochemical properties. The aim of this paper was to systematically review the current literature on antimicrobial additives in root canal sealers, their anti-fouling effects, and influence on physicochemical properties. A systematic search was performed in two databases (PubMed and Scopus) to identify studies that investigated the effect of antimicrobial additives in epoxy resin-based root canal sealers. The nature of additives, their antimicrobial effects, methods of antimicrobial testing are critically discussed. The effects on sealer properties have also been reviewed. A total of 31 research papers were reviewed in this work. A variety of antimicrobial agents have been evaluated as additives to epoxy resin-based sealers, including quaternary ammonium compounds, chlorhexidine, calcium hydroxide, iodoform, natural extracts, antibiotics, antifungal drugs, and antimicrobial agent-functionalised nanoparticles. Antimicrobial additives generally improved the antimicrobial effect of epoxy resin-based sealers mainly without deteriorating the physicochemical properties, which mostly remained in accordance with ISO and ANSI/ADA specifications.

Efficiency of chlorine and UV in the inactivation of Cryptosporidium and Giardia in wastewater

Wastewater from different sources is contaminated by protozoan parasites including Cryptosporidium and Giardia. Many protozoan parasites are becoming resistant to chemical treatment. The challenge of finding alternatives is presented to researchers by exploring other methods of eliminating protozoan parasites from wastewater. The aim of this study was to assess the speciation and the viability of Cryptosporidium and Giardia in environmental samples with the specific objective of evaluating if effluent chlorination and UV affect the viability. Different doses of chlorine with different exposure times were experimented with both distilled water and waste water spiked with (oo)cysts derived from environmental samples. UV irradiation at different doses was also experimented using the same spiked samples. Two methods of quantification and detection, namely, microscopy and flow cytometry, were used in the experiment. Two vital dyes, Syto-9+PI and DAPI+PI, were the used for staining the collected wastewater samples. It was found that the (oo)cysts responded to chlorination and UV treatments with Giardia responding better than Cryptosporidium. Giardia responded very well to UV irradiations with almost 0 percent remaining viable after a low dose of UV. Cryptosporidium was found to be resistant to chlorination even at high doses but responded well to high UV doses. DAPI+PI dye gave a lower mean percentage viability values than Syto-9+PI. Flow cytometry gave higher mean percentage than microscopy from the results. It is concluded that UV is a promising alternative to Chlorine in removing Cryptosporidium and Giardia from waste water. Appropriate treatment method for wastewater is necessary to minimize water resources pollution when wastewater is released into water systems.

Fast and simple tool for the quantification of biofilm-embedded cells sub-populations from fluorescent microscopic images

Fluorescent staining is a common tool for both quantitative and qualitative assessment of pro- and eukaryotic cells sub-population fractions by using microscopy and flow cytometry. However, direct cell counting by flow cytometry is often limited, for example when working with cells rigidly adhered either to each other or to external surfaces like bacterial biofilms or adherent cell lines and tissue samples. An alternative approach is provided by using fluorescent microscopy and confocal laser scanning microscopy (CLSM), which enables the evaluation of fractions of cells subpopulations in a given sample. For the quantitative assessment of cell fractions in microphotographs, we suggest a simple two-step algorithm that combines single cells selection and the statistical analysis. To facilitate the first step, we suggest a simple procedure that supports finding the balance between the detection threshold and the typical size of single cells based on objective cell size distribution analysis. Based on a series of experimental measurements performed on bacterial and eukaryotic cells under various conditions, we show explicitly that the suggested approach effectively accounts for the fractions of different cell sub-populations (like the live/dead staining in our samples) in all studied cases that are in good agreement with manual cell counting on microphotographs and flow cytometry data. This algorithm is implemented as a simple software tool that includes an intuitive and user-friendly graphical interface for the initial adjustment of algorithm parameters to the microphotographs analysis as well as for the sequential analysis of homogeneous series of similar microscopic images without further user intervention. The software tool entitled BioFilmAnalyzer is freely available online at https://bitbucket.org/rogex/biofilmanalyzer/downloads/.

First evaluation of alkylpyrazine application as a novel method to decrease microbial contaminations in processed meat products

Every year about 20% of the globally produced meat gets lost due to microbial spoilage. Nevertheless, the demand for processed meat is constantly rising and producers are searching for novel strategies to reduce microbial contaminations in their products. In the present study, we evaluated the applicability of alkylpyrazines as antimicrobial agents. These fragrant molecules naturally occur in different vegetables, fruits, roasted nut and meat. Several pyrazine derivatives are readily added to processed products for flavoring purposes in the food industry. To evaluate their potential for application, two derivatives were tested for their antimicrobial activity against meat-associated bacterial contaminants and chicken meat as a whole. Isolates assigned to Carnobacteriaceae, Enterobacteriaceae, Listeriaceae, and Moraxellaceae were substantially inhibited in the pilot tests. Moreover, treatments of pyrazine-susceptible isolates resulted in 4-log reductions in bacterial cell counts. The effect was more pronounced when the model contaminants were exposed to higher concentrations of 5-isobutyl-2,3-dimethylpyrazine. In a first small-scale application with processed chicken meat, it was demonstrated that the antimicrobial effects of 2-isobutyl-3-methylpyrazine can be improved by additionally lowering the water activity on the meat surface when maltodextrin is used as a carrier substance. At low pyrazine dosages, the number of viable bacteria was decreased up to 95% in comparison to the corresponding controls. A complementary imaging method that was developed to assess the efficacy on the product, reinforced the applicability of this two-component system.

In vitro methods for the evaluation of antimicrobial surface designs

Bacterial adhesion and subsequent biofilm formation on biomedical implants and devices are a major cause of their failure. As systemic antibiotic treatment is often ineffective, there is an urgent need for antimicrobial biomaterials and coatings. The term "antimicrobial" can encompass different mechanisms of action (here termed "antimicrobial surface designs"), such as antimicrobial-releasing, contact-killing or non-adhesivity. Biomaterials equipped with antimicrobial surface designs based on different mechanisms of action require different in vitro evaluation methods. Available industrial standard evaluation tests do not address the specific mechanisms of different antimicrobial surface designs and have therefore been modified over the past years, adding to the myriad of methods available in the literature to evaluate antimicrobial surface designs. The aim of this review is to categorize fourteen presently available methods including industrial standard tests for the in vitro evaluation of antimicrobial surface designs according to their suitability with respect to their antimicrobial mechanism of action. There is no single method or industrial test that allows to distinguish antimicrobial designs according to all three mechanisms identified here. However, critical consideration of each method clearly relates the different methods to a specific mechanism of antimicrobial action. It is anticipated that use of the provided table with the fourteen methods will avoid the use of wrong methods for evaluating new antimicrobial designs and therewith facilitate translation of novel antimicrobial biomaterials and coatings to clinical use. The need for more and better updated industrial standard tests is emphasized.

STATEMENT OF SIGNIFICANCE

European COST-action TD1305, IPROMEDAI aims to provide better understanding of mechanisms of antimicrobial surface designs of biomaterial implants and devices. Current industrial evaluation standard tests do not sufficiently account for different, advanced antimicrobial surface designs, yet are urgently needed to obtain convincing in vitro data for approval of animal experiments and clinical trials. This review aims to provide an innovative and clear guide to choose appropriate evaluation methods for three distinctly different mechanisms of antimicrobial design: (1) antimicrobial-releasing, (2) contact-killing and (3) non-adhesivity. Use of antimicrobial evaluation methods and definition of industrial standard tests, tailored toward the antimicrobial mechanism of the design, as identified here, fulfill a missing link in the translation of novel antimicrobial surface designs to clinical use.