Eradication of Enterococcus faecalis Biofilms on Human Dentin

Investigating the effect of Er,Cr:YSGG laser agitation of sodium hypochlorite on the removal of mature biofilm in the complex root canal systems using atomic force microscopy

Background

Endodontic infections caused by remaining biofilm following disinfection with chemical fluids encourage secondary bacterial infection; hence, employing laser pulses to activate the fluids is advised to improve microbial biofilm clearance. This study investigated the performance of Er,Cr:YSGG laser in photon-induced photoacoustic streaming (PIPS) agitation of 5.25% sodium hypochlorite (NaOCl) to enhance the removal of mature Enterococcus faecalis (E. faecalis) biofilms in complex root canal systems.

Methods

The mesial roots of the lower first and second molars were separated and inoculated with E. faecalis bacteria for 30 days. The roots were irrigated with 5.25% NaOCl, some of them were agitated with passive ultrasonic irrigation (PUI), and the other roots were agitated by Er,Cr:YSGG laser using PIPS at 60 µs/pulse, 5 Hz, and 0.25, 0.5, 0.75, 1, and 1.25 W. An atomic force microscope (AFM) was used as a new method to obtain the results in the isthmus area; the results that have been obtained from each group were compared with each other. ANOVA was utilized to compare the means of the test groups.

Results

Based on the AFM and SEM analyses, laser agitation and passive ultrasonic activation groups have shown higher antimicrobial efficacy than the conventional syringe irrigation group (P<0.05).

Conclusion

Based on the findings of this investigation, the agitation of 5.25% NaOCl solution by Er,Cr:YSGG laser in PIPS at (60 µs/pulse, 5 Hz, 1.25 W) offers better mature bacterial biofilm removal in the mesial root of lower human molars than the same irrigant with syringe irrigation and passive ultrasonic activation technique.

Promising applications of D-amino acids in periprosthetic joint infection

Due to the rise in our aging population, a disproportionate demand for total joint arthroplasty (TJA) in the elderly is forecast. Periprosthetic joint infection (PJI) represents one of the most challenging complications that can occur following TJA, and as the number of primary and revision TJAs continues to rise, an increasing PJI burden is projected. Despite advances in operating room sterility, antiseptic protocols, and surgical techniques, approaches to prevent and treat PJI remain difficult, primarily due to the formation of microbial biofilms. This difficulty motivates researchers to continue searching for an effective antimicrobial strategy. The dextrorotatory-isoforms of amino acids (D-AAs) are essential components of peptidoglycan within the bacterial cell wall, providing strength and structural integrity in a diverse range of species. Among many tasks, D-AAs regulate cell morphology, spore germination, and bacterial survival, evasion, subversion, and adhesion in the host immune system. When administered exogenously, accumulating data have demonstrated that D-AAs play a pivotal role against bacterial adhesion to abiotic surfaces and subsequent biofilm formation; furthermore, D-AAs have substantial efficacy in promoting biofilm disassembly. This presents D-AAs as promising and novel targets for future therapeutic approaches. Despite their emerging antibacterial efficacy, their role in disrupting PJI biofilm formation, the disassembly of established TJA biofilm, and the host bone tissue response remains largely unexplored. This review aims to examine the role of D-AAs in the context of TJAs. Data to date suggest that D-AA bioengineering may serve as a promising future strategy in the prevention and treatment of PJI.

Role of Enterococcus faecalis in refractory apical periodontitis: from pathogenicity to host cell response

BACKGROUND

Refractory apical periodontitis (RAP) is an oral infectious disease characterised by persistent inflammation, progressive alveolar bone destruction, and delayed bone healing. RAP has received increasing attention, because it cannot be cured after repeated root canal therapies. The aetiology of RAP is related to the complex interplay between the pathogen and its host. However, the exact pathogenesis of RAP remains unclarified and includes several factors, such as microorganism immunogenicity, host immunity and inflammation, and tissue destruction and repair. Enterococcus faecalis is the dominant pathogen involved in RAP, and has evolved multiple strategies to ensure survival, which cause persistent intraradicular and extraradicular infections.

OBJECTIVE

To review the crucial role of E. faecalis in the pathogenesis of RAP, and open new avenues for prevention and treatment of RAP.

METHODS

The PubMed and Web of Science databases were searched for pertinent publications, employing the search terms "Enterococcus faecalis", "refractory apical periodontitis", "persistent periapical periodontitis", "pathogenicity", "virulence", "biofilm formation", "dentine tubule", "immune cell", "macrophage", and "osteoblast".

RESULTS AND CONCLUSION

Besides its high pathogenicity due to various virulence mechanisms, E. faecalis modulates the macrophage and osteoblast responses, including regulated cell death, cell polarisation, cell differentiation, and inflammatory response. An in-depth understanding of the multifaceted host cell responses modulated by E. faecalis will help to design potential future therapeutic strategies and overcome the challenges of sustained infection and delayed tissue healing in RAP.

The Potential of Phenothiazines against Endodontic Pathogens: A Focus on Enterococcus-Candida Dual-Species Biofilm

Persistent apical periodontitis occurs when the endodontic treatment fails to eradicate the intraradicular infection, and is mainly caused by Gram-positive bacteria and yeasts, such as Enterococcus faecalis and Candida albicans, respectively. Phenothiazines have been described as potential antimicrobials against bacteria and fungi. This study aimed to investigate the antimicrobial potential of promethazine (PMZ) and chlorpromazine (CPZ) against E. faecalis and C. albicans dual-species biofilms. The susceptibility of planktonic cells to phenothiazines, chlorhexidine (CHX) and sodium hypochlorite (NaOCl) was initially analyzed by broth microdilution. Interaction between phenothiazines and CHX was examined by chequerboard assay. The effect of NaOCl, PMZ, CPZ, CHX, PMZ + CHX, and CPZ + CHX on biofilms was investigated by susceptibility assays, biochemical and morphological analyses. Results were evaluated through one-way ANOVA and Tukey’s multiple comparison post-test. PMZ, alone or in combination with irrigants, was the most efficient phenothiazine, capable of reducing cell counts, biomass, biovolume, carbohydrate and protein contents of dual-species biofilms. Neither PMZ nor CPZ increased the antimicrobial activity of CHX. Further investigations of the properties of phenothiazines should be performed to encourage their use in endodontic clinical practice.

Benefits and Challenges of the Use of Two Novel vB_Efa29212_2e and vB_Efa29212_3e Bacteriophages in Biocontrol of the Root Canal Enterococcus faecalis Infections

Bacteriophage therapy has emerged as a strategy supplementing traditional disinfection protocols to fight biofilms. The aim of the study was to isolate the phages against E. faecalis and to characterize its biological features, morphology, and lytic activity in a formed biofilm model.

METHODS

E. faecalis ATCC 29212 strain was used for the trial. Two novel vB_Efa29212_2e and vB_Efa29212_3e virulent phages were isolated from urban wastewater and characterized. The E. faecalis biofilm was established in 15 bovine teeth for 21 days. Transmission (TEM) and scanning electron (SEM) microscopes with the colony-forming unit (CFU) counting were used for assessment.

RESULTS

Isolated phages differed in morphology. Taxonomy for vB_Efa29212_2e (Siphoviridae, Efquatovirus) and for vB_Efa29212_3e (Herelleviridae, Kochikohdavirus) was confirmed. Both phages were stable at a temperature range of 4-50 °C and showed a different tolerance to chemicals: 15% EDTA, 1-3% sodium hypochlorite, and chlorhexidine. SEM analysis showed distortion of bacteria cells after phage inoculation, which proved the lytic activity against E. faecalis. A 54.6% reduction in the E. faecalis biofilm confirmed bacteriophage efficacy against isolates in the ex vivo model.

CONCLUSIONS

Results strongly support the concept that phage therapy has a real therapeutic potential for the prevention and treatment of E. faecalis-associated infections.

Antibiofilm Activity of LL-37 Peptide and D-Amino Acids Associated with Antibiotics Used in Regenerative Endodontics on an Ex Vivo Multispecies Biofilm Model

The antimicrobial peptide LL-37 and D-amino acids (D-AAs) have been proposed as antibiofilm agents. Therefore, this study aimed to test the antimicrobial effect of antibiofilm agents associated with antibiotics used in regenerative endodontic procedures (the triple antibiotic paste—TAP: ciprofloxacin + metronidazole + minocycline). An endodontic-like biofilm model grown on bovine dentin discs was used in this study. After 21-day growth, the biofilms were treated with 1 mg/mL TAP, 10 μM LL-37, an association of LL-37 + TAP, 40 mM D-AAs solution, an association of D-AAs + TAP, and phosphate-buffered saline (negative control). Colony forming unit (CFU) data were analyzed by two-way ANOVA and Tukey’s multiple comparison test (p < 0.05). LL-37 + TAP showed the best antibacterial activity (7-log10 CFU/mL ± 0.5), reaching a 1 log reduction of cells in relation to the negative control (8-log10 CFU/mL ± 0.7) (p < 0.05). In turn, no significant reduction in bacterial cells was observed with TAP, LL-37, D-AAs, and D-AAs + TAP compared to the negative control. In conclusion, the combination of antibiotics and LL-37 peptide showed mild antibacterial activity, while the combination of antibiotics and D-AAs showed no activity against complex biofilms.

Antimicrobial Peptides Active in In Vitro Models of Endodontic Bacterial Infections Modulate Inflammation in Human Cardiac Fibroblasts

Endodontic and periodontal disease are conditions of infectious origin that can lead to tooth loss or develop into systemic hyperinflammation, which may be associated with a wide variety of diseases, including cardiovascular. Endodontic and periodontal treatment often relies on antibiotics. Since new antimicrobial resistances are a major threat, the use of standard antibiotics is not recommended when the infection is only local. Antimicrobial peptides were recently demonstrated to be valid alternatives for dental treatments. The antimicrobial peptide M33D is a tetrabranched peptide active against Gram-negative and Gram-positive bacteria. It has a long life, unusual for peptides, because its branched form provides resistance to proteases. Here the efficacy of M33D and of its analog M33i/l as antibiotics for local use in dentistry was evaluated. M33D and M33i/l were active against reference strains and multidrug-resistant clinical isolates of Gram-negative and Gram-positive species. Their minimum inhibitory concentration against different strains of dental interest was between 0.4 and 6.0 μM. Both peptides acted rapidly on bacteria, impairing membrane function. They also disrupted biofilm effectively. Disinfection of the root canal is crucial for endodontic treatments. M33D and M33i/l reduced E. faecalis colonies to one-twentieth in a dentin slices model reproducing root canal irrigation. They both captured and neutralized lipopolysaccharide (LPS), a bacterial toxin responsible for inflammation. The release of IL-1β and TNFα by LPS-stimulated murine macrophages was reduced by both peptides. Human cardiac fibroblasts respond to different insults with the release of proinflammatory cytokines, and consequently, they are considered directly involved in atherogenic cardiovascular processes, including those triggered by infections. The presence of M33D and M33i/l at MIC concentration reduced IL6 release from LPS- stimulated human cardiac fibroblasts, hence proving to be promising in preventing bacteria-induced atherogenesis. The two peptides showed low toxicity to mammalian cells, with an EC50 one order of magnitude higher than the average MIC and low hemolytic activity. The development of antimicrobial peptides for dental irrigations and medication is a very promising new field of research that will provide tools to fight dental infections and their severe consequences, while at the same time protecting standard antibiotics from new outbreaks of antimicrobial resistance.

New insights into the inhibitory roles and mechanisms of D-amino acids in bacterial biofilms in medicine, industry, and agriculture

Biofilms are complex aggregates of microbes that are tightly protected by an extracellular matrix (ECM) and may attach to a surface or adhere together. A higher persistence of bacteria on biofilms makes them resistant not only to harsh conditions but also to various antibiotics which led to the emergence of problems in different applications. Recently, it has been discovered that many bacteria produce and release various D-amino acids (D-AAs) to inhibit biofilm formation, which made a great deal of interest in research into the control of bacterial biofilms in diverse fields, such as human health, industrial settings, and medical devices. D-AAs have various mechanisms to inhibit bacterial biofilms such as: (i) interfering with protein synthesis (ii) Inhibition of extracellular polymeric materials (EPS) productions (protein, eDNA, and polysaccharide) (iii) Inhibition of quorum sensing (autoinducers), and (iv) interfere with peptidoglycan synthesis, these various modes of action, enables these small molecules to inhibit both Gram-negative and Gram-positive bacterial biofilms. Since most biofilms are multi-species, D-AAs in combination with other antimicrobial agents are good choices to combat a variety of bacterial biofilms without displaying toxicity on human cells. This review article addressed the role of D-AAs in controlling several bacterial biofilms and described the possible or definite mechanisms involved in this process.

Targeting Persistent Biofilm Infections: Reconsidering the Topography of the Infection Site during Model Selection

The physiology of an organism in the environment reflects its interactions with the diverse physical, chemical, and biological properties of the surface. These principles come into consideration during model selection to study biofilm–host interactions. Biofilms are communities formed by beneficial and pathogenic bacteria, where cells are held together by a structured extracellular matrix. When biofilms are associated with a host, chemical gradients and their origins become highly relevant. Conventional biofilm laboratory models such as multiwall biofilm models and agar plate models poorly mimic these gradients. In contrast, ex vivo models possess the partial capacity to mimic the conditions of tissue-associated biofilm and a biofilm associated with a mineralized surface enriched in inorganic components, such as the human dentin. This review will highlight the progress achieved using these settings for two models of persistent infections: the infection of the lung tissue by Pseudomonas aeruginosa and the infection of the root canal by Enterococcus faecalis. For both models, we conclude that the limitations of the conventional in vitro systems necessitate a complimentary experimentation with clinically relevant ex vivo models during therapeutics development.

Preclinical Testing of Boron-Doped Diamond Electrodes for Root Canal Disinfection—A Series of Preliminary Studies

While numerous approaches have meanwhile been described, sufficient disinfection of root canals is still challenging, mostly due to limited access and the porous structure of dentin. Instead of using different rinsing solutions and activated irrigation, the electrolysis of saline using boron-doped diamond (BDD) electrodes thereby producing reactive oxygen species may be an alternative approach. In a first step, experiments using extracted human teeth incubated with multispecies bacterial biofilm were conducted. The charge quantities required for electrochemical disinfection of root canals were determined, which were subsequently applied in an animal trial using an intraoral canine model. It could be shown that also under realistic clinical conditions, predictable disinfection of root canals could be achieved using BDD electrodes. The parameters required are in the range of 5.5 to 7.0 V and 9 to 38 mA, applied for 2.5 to 6.0 min with approximately 5 to 8 mL of saline. The direct generation of disinfective agents inside the root canal seems to be advantageous especially in situations with compromised access and limited canal sizes. The biologic effect with respect to the host reaction on BDD-mediated disinfection is yet to be examined.

Enterococcus faecalis and Candida albicans dual-species biofilm: establishment of an in vitro protocol and characterization

Enterococcus faecalis is the most important agent of persistent apical periodontitis, and recently, Candida albicans has also been implicated in periapical infections. This study aimed to optimize an in vitro E. faecalis and C. albicans dual-species biofilm protocol for endodontic research. Different physicochemical conditions for biofilm formation were tested. Susceptibility assays to antimicrobials, biochemical composition and an ultra-morphological structure analyses were performed. Reproducible dual-species biofilms were established in BHI medium at 35 °C, for 48 h and in a microaerophilic atmosphere. An increase in biomass and chitin content was detected after vancomycin treatment. Structural analysis revealed that the dual-species biofilm was formed by both microorganisms adhered to the substrate. The proposed protocol could be useful for the study of interkingdom relationships and help to find new strategies against periapical infections.

The Products of Probiotic Bacteria Effectively Treat Persistent Enterococcus faecalis Biofilms

Objectives: Enterococcus faecalis is a Gram-positive commensal bacterium that possesses various survival and virulence factors, including the ability to compete with other microorganisms, invade dentinal tubules, and resist nutritional deprivation. E. faecalis is associated with persistent endodontic infections where biofilms formed by this bacterium in the root canal frequently resist dental therapies. Aseptic techniques, such as the inclusion of sodium hypochlorite, are the most commonly used methods to treat E. faecalis infections within the root canal system. In this work, we assess the effectiveness of probiotic strains to prevent the regrowth of E. faecalis biofilm cells treated by sodium hypochlorite irrigation. Methods: First, methods are presented that evaluate the effects of short-term exposure to sodium-hypochlorite on established E. faecalis. Next, we evaluate the effects of the secreted products of probiotic strains on biofilm cells and planktonic cells. Results: Sodium hypochlorite, the treatment conventionally used to decontaminate infected root canal systems, was extremely toxic to planktonic bacteria but did not fully eradicate biofilm cells. Furthermore, low concentrations of sodium hypochlorite induced eDNA dependent biofilms. Strikingly, conditioned medium from the probiotic bacteria Lactobacillus plantarum and Lactobacillus casei was sufficient to fully prevent the regrowth of treated biofilms while showing reduced potency towards planktonic cells. Conclusion: Sodium hypochlorite irrigations may contribute to the persistence of biofilm cells if used at concentrations lower than 3%. Probiotic strains and their products represent a new reservoir of biofilm therapies for E. faecalis infections formed in the root canal system.

Acetylornithine aminotransferase TM1785 performs multiple functions in the hyperthermophile Thermotoga maritima

The hyperthermophilic bacterium Thermotoga maritima peptidoglycan contains unusual d-lysine alongside typical d-alanine and d-glutamate. We previously identified lysine racemase and threonine dehydratase, but knowledge of d-amino acid metabolism remains limited. Herein, we identified and characterized T. maritima acetylornithine aminotransferase TM1785. The enzyme was most active towards acetyl-l-ornithine, but also utilized l-glutamate, l-ornithine and acetyl-l-lysine as amino donors, and 2-oxoglutarate was the preferred amino acceptor. TM1785 also displayed racemase activity towards four amino acids and lyase activity towards l-cysteine, but no dehydratase activity towards l-serine, l-threonine or corresponding d-amino acids. Catalytic efficiency (k_cat /K_m ) was highest for aminotransferase activity and lowest for racemase activity. TM1785 is a novel acetylornithine aminotransferase associated with l-arginine biosynthesis that possesses two additional distinct activities.

The antibacterial efficacy of photon-initiated photoacoustic streaming in root canals with different diameters or tapers

BACKGROUND

In recent years, the concept of minimally invasive endodontics has been proposed, which could be described as preventing or treating diseases by preserving more dental tissue and creating minimal damage. In the process of root canal preparation, it was recommended to use instruments with a smaller taper to preserve more tooth tissue and improve the preservation rate of the affected teeth. Photon-induced photoacoustic streaming (PIPS) was a new type of laser-activated irrigation technology, which was now widely used in endodontic treatment. The purpose of this article was to evaluate the bactericidal effect of PIPS with NaOCl in root canals with different widths or tapers.

METHODS

Twenty-three maxillary first molars with three independent root canals were included in this study. The mesiobuccal (MB), distobuccal (DB), and palatal (P) root canals were prepared at sizes of #10/.02, #25/.02, and #25/.06, respectively. After being incubated with a bacterial suspension for 4 weeks, the specimen were irrigated with 2% NaOCl activated by conventional needle irrigation (CNI) (n = 10) or PIPS (n = 10). Three specimen were not treated (control group). Before and after irrigation, the presence of bacteria was assessed with an adenosine 5'-triphosphate (ATP) assay kit and biofilms were assessed using confocal laser scanning microscopy and scanning electron microscopy.

RESULTS

In specimen prepared using PIPS irrigation, the ATP was reduced by more than 98%. When the root canal taper was 0.02, the size #25 root canals had a higher percentage of dead bacteria than the size #10 root canals in all regions (P < 0.05) in the PIPS group. When the root canal width was #25, the 0.02 taper group had a higher percentage of dead bacteria than the 0.06 taper group in the apical region (P < 0.05), except coronal and middle regions (P > 0.05). PIPS irrigation results in a greater percentage of dead bacteria and reduction of ATP in size #10/.02 root canals than CNI in size #25/.06 root canals in three regions (P < 0.05).

CONCLUSION

Increasing the width from #10 to #25 improves the bactericidal effect of PIPS in the root canal. Increasing the taper of the root canal from 0.02 to 0.06 at size #25 did not affect the bactericidal effects of PIPS. PIPS resulted in more dead bacteria in specimen with smaller tapers and root canal widths than CNI. PIPS can be used to clean the smear layer in the coronal region and open the dentin tubules.

CLINICAL SIGNIFICANCE

Activation of irrigants with PIPS brought about significant bacterial reduction smaller tapers and width root canals compared to CNI, which was beneficial to prevent excessive loss of tooth tissue and conserve the structural integrity of teeth.

Identification and biochemical characterization of threonine dehydratase from the hyperthermophile Thermotoga maritima

The peptidoglycan of the hyperthermophile Thermotoga maritima contains an unusual component, D-lysine (D-Lys), in addition to the typical D-alanine (D-Ala) and D-glutamate (D-Glu). In a previous study, we identified a Lys racemase that is presumably associated with D-Lys biosynthesis. However, our understanding of D-amino acid metabolism in T. maritima and other bacteria remains limited, although D-amino acids in the peptidoglycan are crucial for preserving bacterial cell structure and resistance to environmental threats. Herein, we characterized enzymatic and structural properties of TM0356 that shares a high amino acid sequence identity with serine (Ser) racemase. The results revealed that TM0356 forms a tetramer with each subunit containing a pyridoxal 5'-phosphate as a cofactor. The enzyme did not exhibit racemase activity toward various amino acids including Ser, and dehydratase activity was highest toward L-threonine (L-Thr). It also acted on L-Ser and L-allo-Thr, but not on the corresponding D-amino acids. The catalytic mechanism did not follow typical Michaelis-Menten kinetics; it displayed a sigmoidal dependence on substrate concentration, with highest catalytic efficiency (k_cat/K_0.5) toward L-Thr. Interestingly, dehydratase activity was insensitive to allosteric regulators L-valine and L-isoleucine (L-Ile) at low concentrations, while these L-amino acids are inhibitors at high concentrations. Thus, TM0356 is a biosynthetic Thr dehydratase responsible for the conversion of L-Thr to α-ketobutyrate and ammonia, which is presumably involved in the first step of the biosynthesis of L-Ile.

Disruption of Enterococcus Faecalis biofilms using individual and plasma polymer encapsulated D-amino acids

OBJECTIVE

Our aim was to assess the anti-biofilm ability of previously unverified individual D-amino acids (DAAs), to produce plasma polymer encapsulated DAAs (PPEDAAs), to measure the shell thickness and subsequent release of DAAs, and to assess the effects of PPEDAAs on Enterococcus faecalis biofilms.

MATERIALS AND METHODS

Microtitre tray assays were used to evaluate the effect of individual DAAs (D-leucine, D-methionine, D-tryptophan, and D-tyrosine) on E. faecalis biofilms of different maturity. A mixture and individual DAAs were encapsulated with a plasma polymer for 10, 20, 40, and 60 min. The shell thickness of PPEDAAs was analyzed by ultra-high-resolution scanning electron microscopy. The release of DAAs from the PPEDAAs encapsulated for 60 min was measured over 7 days using high-performance liquid chromatography. Static biofilms were used to assess the effect of PPEDAAs on E. faecalis biofilms.

RESULTS

Individual DAAs reduced biofilm formation to various degrees, according to the DAA and the experimental times. The shell thicknesses of the PPEDAAs ranged between 31 and 76 nm and increased with encapsulation time. Diffusion of DAAs from the PPEDAAs occurred over 60 min for encapsulated D-leucine, D-methionine, and D-tyrosine and up to 7 days for D-tryptophan. PPEDAAs disrupted biofilms at every experimental time.

CONCLUSIONS

PPEDAAs of various shell thickness can be produced with the proposed methodology, DAAs are subsequently released, and the anti-biofilm activity remains unaltered.

CLINICAL RELEVANCE

Individual DAAs and PPEDAAs have anti-biofilm ability and can be considered as part of a biological strategy in endodontics.

Antibacterial Effect of High-Purity Nisin Alone and in Combination with D-Amino Acids or Chlorhexidine in an Endodontic-Like Biofilm Model

New strategies to eradicate endodontic biofilms are needed. Therefore, we evaluated the effect of high-purity nisin alone and in combination with D-amino acids (D-AAs) or chlorhexidine (CHX) against an “endodontic-like” biofilm model. Biofilms were grown on hydroxyapatite discs for 64 h and treated with nisin, eight D-AAs mixture, nisin + eight D-AAs, 2% CHX, and nisin + 2% CHX. After the 5 min and 24 h treatments, biofilm cells were harvested and total colony-forming units were counted. Differences between groups were tested by two-way ANOVA followed by Tukey’s multiple comparisons test (p < 0.05). Nisin and D-AAs, alone or in combination, were not effective in reducing bacteria after short or long exposure times. After 5 min, treatment with 2% CHX and nisin + 2% CHX resulted in 2 and 2.4-log cell reduction, respectively, compared with the no treatment control (p < 0.001). After 24 h, 2% CHX and nisin + 2% CHX drastically reduced bacterial counts. In conclusion, high-purity nisin alone or in combination with D-AAs did not show antibacterial activity against multispecies biofilms. Moreover, combined treatment using nisin and CHX showed similar antibiofilm activity compared with the use of CHX alone.

The Invasion of Bacterial Biofilms into the Dentinal Tubules of Extracted Teeth Retrofilled with Fluorescently Labeled Retrograde Filling Materials

In this study, we evaluated the invasion of bacteria into the dentinal tubules of retrofilled extracted human teeth, and the influence of different fluorescently labeled retrograde filling materials on the bacterial invasion and viability, by means of confocal laser scanning microscopy (CLSM). The root apices of extracted teeth were cut, prepared, and filled retrogradely using either intermediate restorative material (IRM), mineral trioxide aggregate (MTA), or Biodentine. The roots were filled with Enterococcus faecalis bacteria from their coronal part for 21 days. Then, 3-mm-long apical segments were cut to get root axial slices, and the bacteria were fluorescently stained and evaluated by CLSM. Bacterial penetration into the dentinal tubules favored the bucco-lingual directions. The filling materials penetrated up to 957 µm into the tubuli, and the bacteria, up to 1480 µm (means: 130 and 167 μm, respectively). Biodentine fillings penetrated less and the associated bacteria penetrated deeper into the tubuli compared to MTA or IRM (p = 0.004). Deeper filling penetration was associated with shallower penetration of both dead and live, or live alone, bacteria (p = 0.015). In conclusion, the current study enables better understanding of the microbiological–pathological course after endodontic surgical procedures. It was found that even with retrograde fillings, bacteria invade deep into the dental tubules, where deeper filling penetration prevents deeper penetration of the bacteria and adversely affects the viability of the bacteria.

Visualization and characterization of Enterococcus faecalis biofilm structure in bovine dentin using 2D and 3D microscopic techniques

Bacterial biofilms are related to various dental and periodontal infectious diseases, and the characterization of this biological structure with micro-computed tomography (micro-CT) may offer valuable information for clinical and research applications. In this study, we aimed to develop a model to visualize three-dimensionally the biofilm structure on dentin using micro-CT. Dentin blocks were prepared and incubated in tryptic soy broth with Enterococcus faecalis (ATCC 29212). The control group did not receive any staining procedure, while groups 1 and 2 were stained with 100% and 50% barium sulfate, respectively. Transmission electron microscopy (TEM) and confocal laser scanning microscopy (CLSM) were used to detect biofilm formation, barium sulfate penetration, and microbial cell density in the biofilm. Micro-computed tomography (micro-CT) (SkyScan 1172, Bruker Co., Belgium) was used to visualize biofilm formation on the dentin blocks. Biofilm thicknesses were measured from 10 different locations on the specimen surfaces, using CTAn v.1.14.4 software. Obtained data were statistically analyzed using Kruskal-Wallis and Dunn's tests. TEM photomicrographs showed that barium sulfate could penetrate the biofilm structure. CLSM analysis showed that viable and total cell densities were similar between the control and barium sulfate-treated groups (P > 0.05), indicating barium sulfate had no significant influence on cell density. In barium sulfate-treated blocks, biofilm could be discriminated from the dentin, and its thickness could be measured with micro-CT. This study showed that bacterial biofilm on dentin could be characterized by micro-CT after barium sulfate staining without causing any significant side effect on viable and total cell densities.

Near-infrared NIR irradiation and sodium hypochlorite: An efficacious association to counteract the Enterococcus faecalis biofilm in endodontic infections

New strategies are necessary for the prevention of endodontic infections caused by Enterococcus faecalis, a common resistant pathogen and biofilm producer. Aim of the present study was to compare the effects of Near-Infrared (NIR) Light-Emitting Diode (LED) irradiation and different concentrations of sodium hypochlorite (NaOCl) alone or combined to each other on the E. faecalis biofilm, on artificial and human dentin surfaces. E. faecalis ATCC 29212 preformed biofilms, on polystyrene wells and on dentin discs, were treated with 880 nm NIR irradiation and NaOCl at 4%, 2.5%, 1% and 0.5% alone and combined to each other (NIR irradiation plus NaOCl 1% or 0.5%) at 5 and 10 min. Treated biofilms were compared to the controls for (i) biofilm biomass evaluation, (ii) CFU count for the quantification of cultivable cells and (iii) cells viability. All the detected experimental conditions displayed a significant reduction of biofilm biomass (p < 0.001) and CFUs/mL (p < 0.01) in respect to the controls on both tested surfaces. The effects on the E. faecalis biomass, colony count and cell viability were not time-dependent except for NaOCl 2.5% and 1% in the biofilm biomass reductions on human dentin discs. NIR-LED irradiation alone showed a reduction of E. faecalis aggregates without interfering with cell viability whereas NaOCl alone expressed a killing effect in a concentration dependent way. The combination of NIR-LED irradiation with NaOCl 1% and 0.5% displayed a double effect of cluster disaggregation and cell killing. In particular, NIR-LED irradiation combined with NaOCl 0.5% displayed an anti-biofilm activity major than those expressed by NaOCl 0.5% alone (p = 0.001) with a reduction of biomass 93% vs 71% and 97% vs 25% after 10 min, on polystyrene wells and human dentin discs, respectively. The innovative use of NIR-LED irradiation combined at short times with low concentration of NaOCl (1% and 0.5%) is capable to reach a significant effect on E. faecalis biofilm, especially on human dentin discs.

In Vitro Antibiofilm and Anti-Inflammatory Properties of Bacteriocins Produced by Pediococcus acidilactici Against Enterococcus faecalis

Although Enterococcus faecalis is known as a commensal microorganism in the gastrointestinal tract, it is linked to various foodborne infections. In addition, biofilm formation in E. faecalis is associated with the infections by exacerbating inflammation. Hence, we demonstrated that bacteriocins produced by Pediococcus acidilactici exhibited antibiofilm and anti-inflammatory activities against E. faecalis. Bacteriocins of P. acidilactici K10 and HW01 strains significantly reduced biofilm formation by E. faecalis on surfaces of polystyrene (p < 0.005 and p < 0.01 at 24 h, respectively) and stainless steel (p < 0.005 and p < 0.01 at 72 h, respectively), while both bacteriocins did not effectively reduce the growth of E. faecalis planktonic cells. Moreover, extracellular polymeric substances (EPSs) produced by E. faecalis were substantially decreased in the presence of P. acidilactici bacteriocin (p < 0.005), suggesting that E. faecalis biofilm formation was reduced by decreasing the production of EPSs, but not by killing bacteria. The bacteriocin of P. acidilactici also reduced the adhesion of E. faecalis to human intestinal epithelial cells (p < 0.005). Furthermore, both bacteriocins significantly inhibited E. faecalis-induced interleukin-8 production in human intestinal epithelial cells (p < 0.01 for K10 bacteriocin and p < 0.005 for HW01 bacteriocin). These results suggest that the bacteriocin of P. acidilactici can eradicate E. faecalis biofilms and inhibit the E. faecalis-induced inflammatory response in intestinal epithelial cells.

Enzymatic properties and physiological function of glutamate racemase from Thermus thermophilus

d-Amino acids are physiologically important components of peptidoglycan in the bacterial cell wall, maintaining cell structure and aiding adaptation to environmental changes through peptidoglycan remodelling. Therefore, the biosynthesis of d-amino acids is essential for bacteria to adapt to different environmental conditions. The peptidoglycan of the extremely thermophilic bacterium Thermus thermophilus contains d-alanine (d-Ala) and d-glutamate (d-Glu), but its d-amino acid metabolism remains poorly understood. Here, we investigated the enzyme activity and function of the product of the TTHA1643 gene, which is annotated to be a Glu racemase in the T. thermophilus HB8 genome. Among 21 amino acids tested, TTHA1643 showed highly specific activity toward Glu as the substrate. The catalytic efficiency (k_cat/K_m) of TTHA1643 toward d- and l-Glu was comparable; however, the k_cat value was 18-fold higher for l-Glu than for d-Glu. Temperature and pH profiles showed that the racemase activity of TTHA1643 is high under physiological conditions for T. thermophilus growth. To assess physiological relevance, we constructed a TTHA1643-deficient strain (∆TTHA1643) by replacing the TTHA1643 gene with the thermostable hygromycin resistance gene. Growth of the ∆TTHA1643 strain in synthetic medium without d-Glu was clearly diminished relative to wild type, although the TTHA1643 deletion was not lethal, suggesting that alternative d-Glu biosynthetic pathways may exist. The deterioration in growth was restored by adding d-Glu to the culture medium, showing that d-Glu is required for normal growth of T. thermophilus. Collectively, our findings show that TTHA1643 is a Glu racemase and has the physiological function of d-Glu production in T. thermophilus.

Involvement of penicillin-binding proteins in the metabolism of a bacterial peptidoglycan containing a non-canonical D-amino acid

Bacteria produce various D-amino acids, including non-canonical D-amino acids, to adapt to environmental changes and overcome a variety of threats. These D-amino acids are largely utilized as components of peptidoglycan, and they promote peptidoglycan remodeling and biofilm disassembly. The biosynthesis, maturation, and recycling of peptidoglycan are catalyzed by penicillin-binding proteins (PBPs). However, although non-canonical D-amino acids are known to be incorporated into peptidoglycan, the maturation and recycling of peptidoglycan containing such residues remain uncharacterized. Therefore, we investigated whether PBP4 and PBP5, low molecular mass (LMM) PBPs from Escherichia coli and Bacillus subtilis, are involved in these events of peptidoglycan metabolism. Enzyme assays using p-nitroaniline (pNA)-derivatized D-amino acids and peptidoglycan-mimicking peptides revealed that PBP4 and PBP5 from both species have peptidase activity toward substrates containing D-Asn, D-His, or D-Trp. These D-amino acids slowed the growth of dacA- or dacB-deficient E. coli (∆dacA or ∆dacB) relative to the wild-type strain. Additionally, these D-amino acids affected biofilm formation by the ∆dacB strain. Collectively, PBP4 and PBP5 are involved in the cleavage of peptidoglycan containing non-canonical D-amino acids, and these properties affect growth and biofilm formation.

d-Amino Acids and Lactic Acid Bacteria

Proteins are composed of l-amino acids except for glycine, which bears no asymmetric carbon atom. Accordingly, researchers have studied the function and metabolism of l-amino acids in living organisms but have paid less attention to the presence and roles of their d-enantiomers. However, with the recent developments in analytical techniques, the presence of various d-amino acids in the cells of various organisms and the importance of their roles have been revealed. For example, d-serine (d-Ser) and d-aspartate (d-Asp) act as neurotransmitters and hormone-like substances, respectively, in humans, whereas some kinds of d-amino acids act as a biofilm disassembly factor in bacteria. Interestingly, lactic acid bacteria produce various kinds of d-amino acids during fermentation, and many d-amino acids taste sweet, compared with the corresponding l-enantiomers. The influence of d-amino acids on human health and beauty has been reported in recent years. These facts suggest that the d-amino acids produced by lactic acid bacteria are important in terms of the taste and function of lactic-acid-fermented foods. Against this background, unique d-amino-acid-metabolizing enzymes have been searched for and observed in lactic acid bacteria. This review summarizes and introduces the importance of various d-amino acids in this regard.

Synergistic Actions of Benzyl Isothiocyanate with Ethylenediaminetetraacetic Acid and Efflux Pump Inhibitor Phenylalanine-Arginine β-Naphthylamide Against Multidrug-Resistant Escherichia coli

The aim of this study was to assess the efficacy of benzyl isothiocyanate (BITC) in combination with efflux inhibitors and metal chelators against multidrug-resistant Escherichia coli. In vitro synergism between testing molecules was observed based on the minimal inhibitory concentration (MIC), minimal bactericidal concentration (MBC), fractional inhibitory concentration index (FICI), bactericidal kinetics, and growth inhibition assay. BITC alone exhibited moderate antibacterial activity against E. coli strains with MIC and MBC values of 0.625-1.25 μM and 1.25-2.5 μM, respectively. In contrast, double and triple combinations of BITC, ethylenediaminetetraacetic acid (EDTA), and phenylalanine-arginine β-naphthylamide (PAβN) resulted in synergistic activities with FICI values between 0.18 and 0.5, whereas combination of BITC with carbonyl cyanide m-chlorophenyl hydrazone or 2, 2'-dipyridyl revealed additive or indifference effect with FICI values of 0.75-1.5 and 1-1.5, respectively. Results of bactericidal kinetics and growth inhibition assays also supported the synergistic effects of EDTA and PAβN with BITC against E. coli strains. Our data demonstrate the possible use of adjuvant agents, such as the chelating agent EDTA and the efflux inhibitor PAβN to improve the antibacterial potential of isothiocyanate and may help to develop an alternative strategy for reducing the occurrence of multidrug resistance.

Er,Cr:YSGG Laser-Activation Enhances Antimicrobial and Antibiofilm Action of Low Concentrations of Sodium Hypochlorite in Root Canals

The onset and persistence of endodontic infections due to residual biofilm after chemical disinfection promotes secondary bacterial infection. Alternative methods to disinfect operated root canals are a matter of great interest. The aim was to evaluate the antibacterial effectiveness of sodium hypochlorite (NaOCl) at low concentrations activated by the Er,Cr:YSGG laser-activated irrigation (LAI) against 10-day-old intracanal Enterococcusfaecalis biofilm. Biofilms were formed inside the root canals and divided into 7 groups (n13): 0.5% NaOCl + Er,Cr:YSGG; Saline + Er,Cr:YSGG; 0.5% NaOCl + syringe irrigation(SI); 2.5% NaOCl + SI; 5% NaOCl + SI; positive and negative controls. Bacterial survivors were counted and specimens visualized under scanning electron and confocal laser scanning microscopy. Treatments with 0.5% NaOCl + Er,Cr:YSGG and 2.5% NaOCl + SI gave a significant reduction in the number of CFU/mm². Moreover, scanning electron microscopy and confocal laser scanning microscopy imaging confirmed and reinforced bacteriological data. Thus, Er,Cr:YSGG LAI proved to be able to improve the intracanal distribution of 0.5% NaOCl after 60 s of activation, reaching the same level of effectiveness than 2.5% NaOCl. This is regarded as of clinical interest, since working with lower concentrations may contribute to reduce undesired effects.

Inhibition Activity of Compounds and Bacteriophages against Flavobacterium psychrophilum Biofilms In Vitro

Flavobacterium psychrophilum produces biofilms under laboratory conditions, and it has been inconclusively suggested that F. psychrophilum biofilms can be a potential reservoir for transmission of the pathogen to a fish population under fish farming conditions. Therefore, there is a need for anti-biofilm compounds. The main aim of this study was to determine the anti-biofilm properties of certain compounds and bacteriophages on F. psychrophilum biofilms under static conditions using a standard 96-well microtiter plate biofilm assay in vitro. Eight compounds (A-type proanthocyanidins, D-leucine, EDTA, emodin, fucoidan, L-alliin, parthenolide, and 2-aminoimidazole) at three sub-minimum inhibitory concentrations (sub-MICs), four bacteriophages (Fpv-3, Fpv-9, Fpv-10, and Fpv-21), and a phage combination (Fpv-9 + Fpv-10) were tested for inhibition of biofilm formation and reduction of the biomass of mature biofilms formed by two smooth isolates (P7-9/10 and P1-10B/10) and two rough isolates (P7-9/2R/10 and P1-10B/2R/10) of F. psychrophilum. The crystal violet staining method was used to stain the biofilms. Most of the compounds at sub-MICs inhibited the biofilm formation of mainly smooth isolates, attaining up to 80% inhibition. Additionally, the same reduction trend was also observed for 2-aminoimidazole, emodin, parthenolide, and D-leucine on the biomass of mature biofilms in a concentration-dependent manner. The anti-biofilm properties of the compounds are believed to lie in their ability to disturb the cellular interactions during biofilm formation and probably to cause cell dispersal in already formed biofilms. Lytic bacteriophages efficiently inhibited biofilm formation of F. psychrophilum, while they partially reduced the biomass of mature biofilms. However, the phage combination (Fpv-9 + Fpv-10) showed a successful reduction in the biomass of F. psychrophilum mature biofilms. We conclude that inhibiting compounds together with bacteriophages may supplement the use of disinfectants against bacterial biofilms (e.g., F. psychrophilum biofilms), leading to a reduced occurrence of bacterial coldwater disease outbreaks at fish farms.

Er,Cr:YSGG Laser-Activated Irrigation and Passive Ultrasonic Irrigation: Comparison of Two Strategies for Root Canal Disinfection

Objective: To compare the antibacterial effectiveness of 0.5% sodium hypochlorite (NaOCl) activated by the Er,Cr:YSGG laser-activated irrigation (LAI) and passive ultrasonic irrigation (PUI) against a 10-day-old intracanal Enterococcus faecalis biofilm. Background: LAI and PUI are regarded as alternative methods to release the irrigant in the inner regions of the root canal system achieving enhanced cleaning ability. Nevertheless, little evidence regarding the activation of low concentrations of NaOCl has been reported. Materials and methods: Seventy-two single-rooted teeth were instrumented, inoculated (E. faecalis ATCC 29212), and incubated for 10 days to allow biofilm formation. Specimens were randomly divided into six groups (n = 12 each): (1) 0.5% NaOCl+Er,Cr:YSGG LAI, (2) saline+Er,Cr:YSGG LAI, (3) 0.5% NaOCl+PUI, (4) saline+PUI, (5) positive control (no treatment), and (6) negative control (no bacteria). The activation time was distributed as follows: 30 sec of activation, followed by a rest phase of 30 sec, and ending with 30 sec of activation. The number of bacterial survivors was determined by plate counting. Results: Both irrigation regimens LAI and PUI reduced the number of colony-forming unit. Moreover, LAI +0.5% NaOCl and the rest of groups significantly differ (p < 0.001 for all comparisons). Conclusions: Er,Cr:YSGG LAI proved to be more effective than PUI in enhancing the antimicrobial activity of 0.5% NaOCl against 10-day-old intracanal E. faecalis biofilms.

Elucidation of the d-lysine biosynthetic pathway in the hyperthermophile Thermotoga maritima

Various d-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria, suggesting that these compounds are necessary for successful adaptation to environmental changes. In addition to the conventional d-alanine (d-Ala) and d-glutamate, the peptidoglycan of the hyperthermophilic bacterium Thermotoga maritima contains both l-lysine (l-Lys) and d-Lys, but not meso-diaminopimelate (meso-Dpm). d-Lys is an uncommon component of peptidoglycan, and its biosynthetic pathway remains unclear. In this study, we identified and characterized a novel Lys racemase (TM1597) and Dpm epimerase (TM1522) associated with the d-Lys biosynthetic pathway in T. maritima. The Lys racemase had a dimeric structure containing pyridoxal 5'-phosphate as a cofactor. Among the amino acids, it exhibited the highest racemase activity toward d- and l-Lys, and also had relatively high activity toward d- and l-enantiomers of ornithine and Ala. The Dpm epimerase had the highest epimerization activity toward ll- and meso-Dpm, and also measurably racemized certain amino acids, including Lys. These results suggest that Lys racemase contributes to production of d-Lys and d-Ala for use as peptidoglycan components, and that Dpm epimerase converts ll-Dpm to meso-Dpm, a precursor in the l-Lys biosynthetic pathway.

Cystathionine β-lyase is involved in d-amino acid metabolism

Non-canonical d-amino acids play important roles in bacteria including control of peptidoglycan metabolism and biofilm disassembly. Bacteria appear to produce non-canonical d-amino acids to adapt to various environmental changes, and understanding the biosynthetic pathways is important. We identified novel amino acid racemases possessing the ability to produce non-canonical d-amino acids in Escherichia coli and Bacillus subtilis in our previous study, whereas the biosynthetic pathways of these d-amino acids still remain unclear. In the present study, we demonstrated that two cystathionine β-lyases (MetC and MalY) from E. coli produce non-canonical d-amino acids including non-proteinogenic amino acids. Furthermore, MetC displayed d- and l-serine (Ser) dehydratase activity. We characterised amino acid racemase, Ser dehydratase and cysteine lyase activities, and all were higher for MetC. Interestingly, all three activities were at a comparable level for MetC, although optimal conditions for each reaction were distinct. These results indicate that MetC and MalY are multifunctional enzymes involved in l-methionine metabolism and the production of d-amino acids, as well as d- and l-Ser metabolism. To our knowledge, this is the first evidence that cystathionine β-lyase is a multifunctional enzyme with three different activities.

Application of D-Amino Acids as Biofilm Dispersing Agent in Dental Unit Waterlines

Aim and Purpose

Biofilms in dental unit waterlines (DUWLs) are extremely difficult to eliminate. Aim of this study is to evaluate the efficacy of a mixture of four D-amino acids on biofilm dispersion in DUWLs.

Materials and Methods

A mixture of four D-amino acids (D-methionine, D-tryptophan, D-leucine, and D-tyrosine, 10 mM each), distilled water (control), and 0.1 M hydrochloric acid (HCl) was used in the experiment. In laboratory, pieces of DUWLs covered with biofilms were submerged in different solutions for 5 days, flushed, and measured OD⁶⁰⁰ of the dispersed biofilms. Remnants of biofilms on the DUWLs were evaluated by SEM. In clinic, fifteen DCUs were incubated with test and control solutions, flushed, and measured OD⁶⁰⁰ of the dispersed biofilms. Microbial count of DUWL output water was enumerated twice a week for four weeks.

Results

There was a slight, but not significant, increase in OD⁶⁰⁰ of flushing water in D-amino acids group. D-amino acids effectively reduced bacterial plaque as demonstrated by SEM. Incubation with D-amino acids significantly reduced biofilms especially after the first day of flushing. Bacterial count in DUWL output water was significantly reduced after treatment with D-amino acids.

Conclusion

D-amino acids are applicable as biofilm dispersing agents in DUWLs.

Root canal irrigants influence the hydrophobicity and adherence of Staphylococcus epidermidis to root canal dentin: an in vitro study

Objectives

To determine the effect of root canal irrigants on the hydrophobicity and adherence of Staphylococcus epidermidis (S. epidermidis) to root canal dentin in vitro.

Materials and Methods

Root dentin blocks (n = 60) were randomly divided into 4 groups based on the irrigation regimen: group 1, saline; group 2, 5.25% sodium hypochlorite (NaOCl); group 3, 5.25% NaOCl followed by 17% ethylenediaminetetraacetic acid (EDTA); group 4, same as group 3 followed by 2% chlorhexidine (CHX). The hydrophobicity of S. epidermidis to root dentin was calculated by cell surface hydrophobicity while the adherence was observed by fluorescence microscopy, and bacteria were quantified using ImageJ software (National Institutes of Health). Statistical analysis of the data was done using Kruskal-Wallis test and Mann-Whitney U test (p = 0.05).

Results

The hydrophobicity and adherence of S. epidermidis to dentin were significantly increased after irrigating with group 3 (NaOCl-EDTA) (p < 0.05), whereas in group 4 (NaOCl-EDTA-CHX) both hydrophobicity and adherence were significantly reduced (p < 0.05).

Conclusions

The adherence of S. epidermidis to dentin was influenced differently by root canal irrigants. Final irrigation with CHX reduces the bacterial adherence and may impact biofilm formation.

Biofilms in Endodontics-Current Status and Future Directions

Microbiota are found in highly organized and complex entities, known as biofilms, the characteristics of which are fundamentally different from microbes in planktonic suspensions. Root canal infections are biofilm mediated. The complexity and variability of the root canal system, together with the multi-species nature of biofilms, make disinfection of this system extremely challenging. Microbial persistence appears to be the most important factor for failure of root canal treatment and this could further have an impact on pain and quality of life. Biofilm removal is accomplished by a chemo-mechanical process, using specific instruments and disinfecting chemicals in the form of irrigants and/or intracanal medicaments. Endodontic research has focused on the characterization of root canal biofilms and the clinical methods to disrupt the biofilms in addition to achieving microbial killing. In this narrative review, we discuss the role of microbial biofilms in endodontics and review the literature on the role of root canal disinfectants and disinfectant-activating methods on biofilm removal.