Unraveling the interplay between unicellular parasites and bacterial biofilms: Implications for disease persistence and antibiotic resistance

Bacterial biofilms have attracted significant attention due to their involvement in persistent infections, food and water contamination, and infrastructure corrosion. This review delves into the intricate interactions between bacterial biofilms and unicellular parasites, shedding light on their impact on biofilm formation, structure, and function. Unicellular parasites, including protozoa, influence bacterial biofilms through grazing activities, leading to adaptive changes in bacterial communities. Moreover, parasites like Leishmania and Giardia can shape biofilm composition in a grazing independent manner, potentially influencing disease outcomes. Biofilms, acting as reservoirs, enable the survival of protozoan parasites against environmental stressors and antimicrobial agents. Furthermore, these biofilms may influence parasite virulence and stress responses, posing challenges in disease treatment. Interactions between unicellular parasites and fungal-containing biofilms is also discussed, hinting at complex microbial relationships in various ecosystems. Understanding these interactions offers insights into disease mechanisms and antibiotic resistance dissemination, paving the way for innovative therapeutic strategies and ecosystem-level implications.

Proteus mirabilis biofilm expansion microscopy yields over 4-fold magnification for super-resolution of biofilm structure and subcellular DNA organization

Bacterial biofilms form when bacteria attach to surfaces and generate an extracellular matrix that embeds and stabilizes a growing community. Detailed visualization and quantitative analysis of biofilm architecture by optical microscopy are limited by the law of diffraction. Expansion Microscopy (ExM) is a novel Super-Resolution technique where specimens are physically enlarged by a factor of ∼4, prior to observation by conventional fluorescence microscopy. ExM requires homogenization of rigid constituents of biological components by enzymatic digestion. We developed an ExM approach capable of expanding 48-h old Proteus mirabilis biofilms 4.3-fold (termed PmbExM), close to the theoretic maximum expansion factor without gross shape distortions. Our protocol, based on lytic and glycoside-hydrolase enzymatic treatments, degrades rigid components in bacteria and extracellular matrix. Our results prove PmbExM to be a versatile and easy-to-use Super-Resolution approach for enabling studies of P. mirabilis biofilm architecture, assembly, and even intracellular features, such as DNA organization.

DeepSeeded: Volumetric Segmentation of Dense Cell Populations with a Cascade of Deep Neural Networks in Bacterial Biofilm Applications

Accurate and automatic segmentation of individual cell instances in microscopy images is a vital step for quantifying the cellular attributes, which can subsequently lead to new discoveries in biomedical research. In recent years, data-driven deep learning techniques have shown promising results in this task. Despite the success of these techniques, many fail to accurately segment cells in microscopy images with high cell density and low signal-to-noise ratio. In this paper, we propose a novel 3D cell segmentation approach DeepSeeded, a cascaded deep learning architecture that estimates seeds for a classical seeded watershed segmentation. The cascaded architecture enhances the cell interior and border information using Euclidean distance transforms and detects the cell seeds by performing voxel-wise classification. The data-driven seed estimation process proposed here allows segmenting touching cell instances from a dense, intensity-inhomogeneous microscopy image volume. We demonstrate the performance of the proposed method in segmenting 3D microscopy images of a particularly dense cell population called bacterial biofilms. Experimental results on synthetic and two real biofilm datasets suggest that the proposed method leads to superior segmentation results when compared to state-of-the-art deep learning methods and a classical method.

Integration of Lysin into Chitosan Nanoparticles for Improving Bacterial Biofilm Inhibition

Bacterial biofilms (BBFs) exhibit high drug resistance, antiphagocytosis, and extremely strong adhesion, and therefore can cause various diseases. They are also one of the important causes of bacterial infections. Thus, the effective removal of BBFs has attracted considerable research interest. Endolysins, which are efficient antibacterial bioactive macromolecules, have recently been receiving increasing attention. In this study, we overcame the deficiencies of endolysins via immobilization on chitosan nanoparticles (CS-NPs) by preparing LysST-3-CS-NPs using the ionic cross-linking reaction between CS-NPs and LysST-3, an endolysin purified using phage ST-3 expression. The obtained LysST-3-CS-NPs were verified and thoroughly characterized, their antimicrobial activity was investigated using microscopy, and their antibacterial efficacy on polystyrene surfaces was studied. The results obtained suggested that LysST-3-CS-NPs exhibit enhanced bactericidal properties and increased stability and can serve as reliable biocontrol agents for the prevention and treatment of Salmonella biofilm infections.

Biomaterials coated with zwitterionic polymer brush demonstrated significant resistance to bacterial adhesion and biofilm formation in comparison to brush coatings incorporated with antibiotics

A critical problem with the use of biomaterial implants is associated with bacterial adhesion on the surface of implants and in turn the biofilm formation. Among different strategies that have been reported to resolve this dilemma, surface design combined with both antiadhesive and antimicrobial properties has proven to be highly effective. Physiochemical properties of polymer brush coatings possess non-adhesive capability against bacterial adhesion and create a niche for further functionalization. The current study aims to evaluate the effect of antibiotics incorporated into the polymer brush on bacterial adhesion and biofilm formation. Brushes made of zwitterionic polymers were synthesized, functionalized with vancomycin via both physical and chemical conjugation, and grafted onto the silicon rubber surfaces. Antibacterial and antiadhesive measurements of designed coated biomaterials were mediated through the use of a parallel plate flow chamber against biofilm growth developed by Staphylococcus aureus and Escherichia coli over a period of 24 h. The analysis of biofilm growth on designed coated biomaterials showed that the pristine coated zwitterionic brushes are significantly resistant to bacterial adhesion and biofilm formation but not in the polymer brush coating incorporated with antibiotics.

Sensor system for analysis of biofilm sensitivity to ampicillin

The resistance of biofilms to antibiotics is a key factor that makes bacterial infections unsusceptible to antimicrobial therapy. The results of classical tests of cell sensitivity to antibiotics cannot be used to predict therapeutic success in infections associated with biofilm formation. We describe a simple and rapid method for the real-time evaluation of bacterial biofilm sensitivity to antibiotics, with Pseudomonas putida and ampicillin as examples. The method uses an electric biosensor to detect the difference between changes in the biofilm electric polarizability, thereby evaluating antibiotic sensitivity. The electric signals showed that P. putida biofilms were susceptible to ampicillin and that at high antibiotic concentrations, the biofilms differed markedly in their susceptibility (dose-dependent effect). The sensor also detected differences between biofilms before and after ampicillin treatment. The electric-signal changes enabled us to describe the physical picture of the processes occurring in bacterial biofilms in the presence of ampicillin. The approach used in this study is promising for evaluating the activity of various compounds against biofilms, because it permits a conclusion about the antibiotic sensitivity of biofilm bacteria to be made in real time and in a short period (analysis time, not longer than 20 min). An added strong point is that analysis can be done directly in liquid, without preliminary sample preparation. KEY POINTS: • Sensor system to analyze biofilm antimicrobial susceptibility is described. • The signal change depended on the ampicillin concentration (dose-dependent effect). • The sensor allows real-time determination of the antibiofilm effect of ampicillin.

Unravelling host-pathogen interactions by biofilm infected human wound models

Approximately 80 % of persistent wound infections are affected by the presence of bacterial biofilms, resulting in a severe clinical challenge associated with prolonged healing periods, increased morbidity, and high healthcare costs. Unfortunately, in vitro models for wound infection research almost exclusively focus on early infection stages with planktonic bacteria. In this study, we present a new approach to emulate biofilm-infected human wounds by three-dimensional human in vitro systems. For this purpose, a matured biofilm consisting of the clinical key wound pathogen Pseudomonas aeruginosa was pre-cultivated on electrospun scaffolds allowing for non-destructive transfer of the matured biofilm to human in vitro wound models. We infected tissue-engineered human in vitro skin models as well as ex vivo human skin explants with the biofilm and analyzed structural tissue characteristics, biofilm growth behavior, and biofilm-tissue interactions. The structural development of biofilms in close proximity to the tissue, resulting in high bacterial burden and in vivo-like morphology, confirmed a manifest wound infection on all tested wound models, validating their applicability for general investigations of biofilm growth and structure. The extent of bacterial colonization of the wound bed, as well as the subsequent changes in molecular composition of skin tissue, were inherently linked to the characteristics of the underlying wound models including their viability and origin. Notably, the immune response observed in viable ex vivo and in vitro models was consistent with previous in vivo reports. While ex vivo models offered greater complexity and closer similarity to the in vivo conditions, in vitro models consistently demonstrated higher reproducibility. As a consequence, when focusing on direct biofilm-skin interactions, the viability of the wound models as well as their advantages and limitations should be aligned to the particular research question of future studies. Altogether, the novel model allows for a systematic investigation of host-pathogen interactions of bacterial biofilms and human wound tissue, also paving the way for development and predictive testing of novel therapeutics to combat biofilm-infected wounds.

Bacteriophage Endolysin: A Powerful Weapon to Control Bacterial Biofilms

Bacterial biofilms are widespread in the environment, and bacteria in the biofilm are highly resistant to antibiotics and possess host immune defense mechanisms, which can lead to serious clinical and environmental health problems. The increasing problem of bacterial resistance caused by the irrational use of traditional antimicrobial drugs has prompted the search for better and novel antimicrobial substances. In this paper, we review the effects of phage endolysins, modified phage endolysins, and their combination with other substances on bacterial biofilms and provide an outlook on their practical applications. Phage endolysins can specifically and efficiently hydrolyze the cell walls of bacteria, causing bacterial lysis and death. Phage endolysins have shown superior bactericidal effects in vitro and in vivo, and no direct toxicity in humans has been reported to date. The properties of phage endolysins make them promising for the prevention and treatment of bacterial infections. Meanwhile, endolysins have been genetically engineered to exert a stronger scavenging effect on biological membranes when used in combination with antibiotics and drugs. Phage endolysins are powerful weapons for controlling bacterial biofilms.

Detection and imaging of bacterial biofilms with glutathione-stabilized gold nanoclusters

Bacterial biofilms colonize chronic wounds and surfaces of medical devices, thus making the development of reliable methods for imaging and detection of biofilms crucial. Although fluorescent identification of bacteria is sensitive and non-destructive, the lack of biofilm-specific fluorescent dyes limits the application of this technique to biofilm detection. Here, we demonstrate, for the first time, that fluorescent glutathione-stabilized gold nanoclusters (GSH-AuNCs) without targeting ligands can specifically interact with extracellular matrix components of Gram-negative and Gram-positive bacterial biofilms resulting in fluorescent staining of bacterial biofilms. By contrast, fluorescent bovine serum albumin-stabilized gold nanoclusters and 11-mercaptoundecanoic acid - stabilized gold nanoclusters do not stain the extracellular matrix of biofilms. According to molecular docking studies, GSH-AuNCs show affinity to several targets in extracellular matrix, including amyloid-anchoring proteins, matrix proteins and polysaccharides. Some experimental evidence was obtained for the interaction of GSH-AuNCs with the lipopolysaccharide (LPS) that was isolated from the matrix of Azospirillum baldaniorum biofilms. Based on GSH-AuNCs properties, we propose a new fluorescent method for the measurement of biofilm biomass with a limit of detection 1.7 × 10⁵ CFU/mL. The sensitivity of the method is 10-fold higher than the standard biofilm quantification with the crystal violet assay. There is a good linear relationship between the fluorescence intensity from the biofilms and the number of CFU from the biofilms in the range from 2.6 × 10⁵ to 6.7 × 10⁷ CFU/mL. The developed nanocluster-mediated method of biofilm staining was successfully applied for quantitative detection of biofilm formation on urinary catheter surface. The presented data suggest that fluorescent GSH-AuNCs can be used to diagnose medical device-associated infections.

Nanomotors-loaded microneedle patches for the treatment of bacterial biofilm-related infections of wound

The biofilms formed by bacteria at the wound site can effectively protect the bacteria, which greatly weakens the effect of antibiotics. Herein, a microneedle patch for wound treatment is designed, which can effectively penetrate the biofilms in a physical way because of the penetration ability of the microneedles and the motion behavior of the nanomotors, and deliver bacterial quorum sensing inhibitor luteolin (Le) and nanomotors with multiple antibacterial properties within biofilms. Firstly, the nanomotors-loaded microneedle patches are prepared and characterized. The results of in vitro and in vivo experiments show that the microneedle patches have good biosafety and antibacterial properties. Among them, Le can inhibit the growth of biofilms. Further, under near-infrared (NIR) irradiation, the nanomotors loaded with photosensitizer ICG and nitric oxide (NO) donor L-arginine (L-Arg) can move in the biofilms under the double driving effect of photothermal and NO, and can give full play to the multiple anti-biological infection effects of photothermal therapy (PTT), photodynamic therapy (PDT) and NO, and finally realize the effective removal of biofilms and promote wound healing. The intervention of nanomotor technology has brought about a new therapeutic strategy for bacterial biofilm-related infection of wound.

Tailored anti-biofilm activity - Liposomal delivery for mimic of small antimicrobial peptide

The eradication of bacteria embedded in biofilms is among the most challenging obstacles in the management of chronic wounds. These biofilms are found in most chronic wounds; moreover, the biofilm-embedded bacteria are considerably less susceptible to conventional antimicrobial treatment than the planktonic bacteria. Antimicrobial peptides and their mimics are considered attractive candidates in the pursuit of novel therapeutic options for the treatment of chronic wounds and general bacterial eradication. However, some limitations linked to these membrane-active antimicrobials are making their clinical use challenging. Novel innovative delivery systems addressing these limitations represent a smart solution. We hypothesized that incorporation of a novel synthetic mimic of an antimicrobial peptide in liposomes could improve its anti-biofilm effect as well as the anti-inflammatory activity. The small synthetic mimic of an antimicrobial peptide, 7e-SMAMP, was incorporated into liposomes (~280 nm) tailored for skin wounds and evaluated for its potential activity against both biofilm formation and eradication of pre-formed biofilms. The 7e-SMAMP-liposomes significantly lowered inflammatory response in murine macrophages (~30 % reduction) without affecting the viability of macrophages or keratinocytes. Importantly, the 7e-SMAMP-liposomes completely eradicated biofilms produced by Staphylococcus aureus and Escherichia coli above concentrations of 6.25 μg/mL, whereas in Pseudomonas aeruginosa the eradication reached 75 % at the same concentration. Incorporation of 7e-SMAMP in liposomes improved both the inhibition of biofilm formation as well as biofilm eradication in vitro, as compared to non-formulated antimicrobial, therefore confirming its potential as a novel therapeutic option for bacteria-infected chronic wounds.

Evaluation of photosensitizer-containing superhydrophobic surfaces for the antibacterial treatment of periodontal biofilms

Antimicrobial photodynamic therapy (aPDT) is a promising approach to control biofilms involved in periodontal diseases. However, certain challenges, such as staining of teeth, preferential interaction of photosensitizer (PS) with Gram-positive versus Gram-negative bacteria, and insufficient oxygen in hypoxic periodontal pockets have presented barriers to its use in the clinic. To overcome these challenges, a novel superhydrophobic (SH) film that generates airborne singlet oxygen has been developed. The SH-aPDT approach isolates the PS onto a topologically rough solid SH film on which channels allow air to diffuse to the PS surface, thus ensuring sufficient oxygen supply. Upon illumination, gas phase singlet oxygen (¹O₂) is produced and diffuses from the SH surface to the underlying biofilm. The killing efficacy was assessed as a function of transmitted fluence (17.9-89.5 J/cm²) and chorin e6 loading (96-1110 nmol/cm²) by counting of colony forming units, biofilm metabolism by XTT and confocal microscopy. The decrease in viability of both Gram-positive and Gram-negative bacteria in a multi-species biofilm was found to be linearly dependent on the fluence as well as the loading of the PS up to 71.6 J/cm² when 1110 nmols/cm² of chlorin e6 was used. A > 4.6 log bacterial reduction was observed under these conditions (p < 0.05). This novel SH-aPDT approach shows promise as an effective method to disinfect multi-species bacterial biofilms associated with periodontal disease and will be evaluated in animal models in future studies.

Bacterial extracellular matrix as a natural source of biotechnologically multivalent materials

The extracellular matrix (ECM) is an intricate megastructure made by bacterial cells to form architecturally complex biostructures called biofilms. Protection of cells, modulation of cell-to-cell signalling, cell differentiation and environmental sensing are functions of the ECM that reflect its diverse chemical composition. Proteins, polysaccharides and eDNA have specific functionalities while cooperatively interacting to sustain the architecture and biological relevance of the ECM. The accumulated evidence on the chemical heterogeneity and specific functionalities of ECM components has attracted attention because of their potential biotechnological applications, from agriculture to the water and food industries. This review compiles information on the most relevant bacterial ECM components, the biophysical and chemical features responsible for their biological roles, and their potential to be further translated into biotechnological applications.

Pyophage cocktail for the biocontrol of membrane fouling and its effect in aerobic microbial biofilm community during the treatment of antibiotics

Membrane bioreactor systems face an inevitable challenge that is biofouling, which not only hinders the operation of the system, but also poses an environmental and medical concern caused by the increased antibiotic resistance in bacterial biofilms. This study investigates the disruption of membrane fouling using bacteriophage cocktail (Pyophage) in an aerobic membrane bioreactor for treatment of wastewater containing high non-lethal concentration of erythromycin, tetracycline and sulfamethoxazole, while also considering the effect of the cocktail on performance. The results indicate that Pyophage cocktail contributes significantly to the decrease (45%) in transmembrane pressure while also suppressing biofilm-producing bacteria compared to the control reactors. It also reconstructed biodegradation mechanism of antibiotics especially increasing the relative abundance of gram-negative bacteria by enhancement the removal rate of erythromycin and sulfamethoxazole from the aerobic system to 99%.

Fate and effect of in-house synthesized tellurium based nanoparticles on bacterial biofilm biomass and architecture. Challenges for nanoparticles characterization in living systems

The unexpected impact of nanoparticles on environment and human health remains as a matter of concern. In this sense, understanding the interaction between nanoparticles and biological indicators such as microorganism may help to understand their fate and effect in environmental systems. However, the adverse effect of nanoparticles greatly depends on their properties and, therefore, a precise evaluation of nanoparticles physicochemical characteristics is mandatory as the first step in accurately elucidating their behaviour in different ecosystems. Here in this work, in house-synthesized tellurium-based nanoparticles have been fully characterized for first time by means of a multi-method approach. Once characterized, the effect of these nanoparticles on Staphylococcus aureus and Escherichia coli biofilm biomass and structure was explored and quantified for first time. Moreover, the morphological transformations of tellurium based nanoparticles within the confines of a biofilm are also highlighted. Architectural metric calculations evidenced that nanoparticles were able to reduce the biovolume of the biofilm produced for both bacteria. Interestingly, the interaction between nanoparticles and bacterial communities led to the transformation of tellurium nanoparticles from sphere to rod-shaped nanoparticles. These findings open new insights into the behaviour of a type of uncommon nanoparticles such as tellurium-based nanoparticles on microbial communities.

Synthesis of carbon quantum dot-poly lactic-co-glycolic acid hybrid nanoparticles for chemo-photothermal therapy against bacterial biofilms

Bacterial biofilm represents a protected mode of bacterial growth that significantly enhances the resistance to antibiotics. Poly lactic-co-glycolic acid (PLGA)-based nanoparticle delivery systems have been intensively investigated to combat the bacterial biofilms-associated infections. However, some drawbacks associated with current PLGA-based nanoformulations (e.g. the relatively low drug loading capability, premature burst release and/or incapability of on-demand release of cargos at the site of action) restrict the transition from the lab research to the clinical applications. One potent strategy to overcome the above-mentioned limitations is exploiting the unique properties of carbon quantum dots (CQDs) and combining CQDs with the conventional PLGA nanoparticles. In the present study, the CQDs were innovatively incorporated into PLGA nanoparticles by using a microfluidic method. The resulting CQD-PLGA hybrid nanoparticles presented good loading capability of azithromycin (a macrolide antibiotic, AZI) and tobramycin (an aminoglycoside antibiotic, TOB), and stimuli-responsive release of the cargos upon laser irradiation. Consequently, AZI-loaded CQD-PLGA hybrid nanoparticles showed chemo-photothermally synergistic anti-biofilm effects against P. aeruginosa biofilms. Additionally, the CQD-PLGA hybrid nanoparticles demonstrated good biocompatibility with the eukaryotic cells. Overall, the proof-of-concept of CQD-PLGA hybrid nanoparticles may open a new possibility in chemo-photothermal therapy against bacterial biofilms.

A surface spectroscopy study of a Pseudomonas fluorescens biofilm in the presence of an immobilized air bubble

A linear spectral mapping technique was applied to monitor the growth of biomolecular absorption bands at the bio-interface of a nascent Pseudomonas fluorescens biofilm during and after interaction with a surface-adhered air bubble. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectra were obtained in different locations in a microchannel with adequate spatial and temporal resolution to study the effect of a static bubble on the evolution of protein and lipid signals at the ATR crystal surface. The results reveal that the presence of a bubble during the lag phase modified levels of extracellular lipids and affected a surface restructuring process, many hours after the bubble's disappearance.

Electrochemical detection of food-spoiling bacteria using interdigitated platinum microelectrodes

The fast and non-destructive detection of bacterial attachment on food contact surfaces is important for the prevention of the unwanted formation of biofilms. Biofilms constitute a protected growth mode that allows bacteria to survive even in hostile environments. Therefore, the fast detection of bacterial attachment may be an effective strategy for biofilm control. In this study cyclic voltammetry (CV) was used to detect Bacillus subtilis ssp. subtilis, Paenibacillus polymyxa, Pseudomonas fragi attachment on interdigitated microelectrodes. The differences in current between the uncolonized sterile microelectrodes and the microelectrodes after bacterial attachment were determined. In addition, the surface coverage of microelectrodes was visualized using microscopy techniques. The results showed that the cyclic voltammetry in combination with interdigitated platinum microelectrodes can be used to detect bacterial biofilms.

Novel Polycationic Photosensitizers for Antibacterial Photodynamic Therapy

Antibacterial photodynamic therapy (APDT) is a promising method of treating local infected foci, in particular, surgical and burn wounds, trophic and diabetic ulcers. Photodynamic inactivation (PDI) is able to effectively destroy bacterial cells without them developing resistance in response to treatment.This work was dedicated to the study of photophysical and antibacterial properties of new photosensitizers (PS) based on polycationic phthalocyanines and synthetic bacteriochlorins for photodynamic inactivation of P. aeruginosa bacteria and their biofilms. Gram-negative bacteria P. aeruginosa are often found in infected wounds, presumably in biofilm state and are characterized by rather low susceptibility to APDT, which is a problem. PS were studied for possible aggregation at various concentrations by means of absorption and fluorescence spectroscopy. The results of studies of the ZnPcChol₈, (3-PyHp)₄BCBr₄ and (3-PyEBr)₄BCBr₄ in water and serum confirm the assumption of a low degree of their aggregation at high concentrations.Consequently, their photodynamic efficiency is high enabling to use these PS at high concentrations to sensitize pathological foci for APDT.It was shown that all the investigated PS had a high efficiency of photodynamic inactivation of Gram-negative bacteria P. aeruginosa, as well as their biofilms. Tetracationic hydrophilic near-infrared photosensitizer (3-PyEBr)₄BCBr₄ with reduced molecule size had significantly higher efficacy of photodynamic inactivation of P. aeruginosa biofilms compared with other studied photosensitizers.

Disentangling settlement responses to nutrient-rich contaminants: Elevated nutrients impact marine invertebrate recruitment via water-borne and substrate-bound cues

Anthropogenic contaminants, including nutrient enrichment, frequently alter environmental conditions in marine systems and affect the development of communities on hard-substrata. Biofilms can influence the settlement of marine invertebrates and hence impact on the structure of fouling communities. Few studies have examined bacteria, invertebrates and nutrient-rich contaminants in concert, with none yet to examine the effects of nutrient-rich contaminants on both biofilms and the recruitment of sessile invertebrate communities in-situ to ascertain the mechanistic basis behind observed impacts. Biofilm treatments were allowed to develop under manipulated environmental conditions of either ambient or enriched nutrient levels. Enrichment conditions were elevated via slow-release fertiliser and invertebrate recruitment was prevented during initial biofilm development. Biofilm treatments (including a no film control) were then subject to either ambient or enriched water-borne nutrients (in a fully-factorial design) during a period of invertebrate colonisation in the field. Effects of nutrient-rich contaminants on invertebrate recruitment were observed as changes to community composition and the abundances of taxonomic groups. Communities on no biofilm control treatments differed from those with pre-developed biofilms. Naturally developed biofilms promoted recruitment by all organisms, except barnacles, which preferred nutrient-enriched biofilms. Water-borne nutrients increased the recruitment of ascidians and barnacles, but suppressed bryozoan, serpulid polychaete and sponge recruitment. The direct and indirect impacts observed on biofilm and invertebrate communities suggest that increasing nutrient levels via nutrient-rich contaminants will result in structural community shifts that may ultimately impact ecosystem functioning within estuaries.

A systematic characterization of the distribution, biofilm-forming potential and the resistance of the biofilms to the CIP processes of the bacteria in a milk powder processing factory

Owing to the resistance to conventional cleaning and sanitizing agents, biofilms formed on surfaces of dairy processing equipment pose a hazard to the dairy industry. The objective of this study was to evaluate the diversity of the microflora attached to various surfaces of the processing lines of a milk powder processing factory based on 16S rRNA gene sequence analysis. The production of biofilms by the bacterial strains was evaluated on polystyrene (PS) and stainless-steel (SS) surfaces by crystal violet staining method. Especially, effects of temperatures (e.g., 37 °C and 55 °C) and growth mediums (e.g., nutrient broth, NB; tryptic soy broth, TSB) on the production of biofilms by these strains on PS surfaces were explored. Besides, the tolerance of the biofilms of the strains to CIP processes (1.5% v/v HNO₃ solution or 2.0% w/v NaOH solution at 80 °C) were analyzed. Forty-five isolates from eleven interior surfaces of the facilities were identified and the distribution of strains had high species diversity, which indicated that multiple spoilage and pathogenic microorganisms remained in milk powder processing lines after CIP processes. Bacteria showed higher biofilm-forming abilities on SS compared to PS surfaces under the same condition. Moreover, effects of the incubation temperature and growth medium on biofilm formation varied between genera, species, and strains. One strain of each species with biofilm-forming abilities on SS surfaces was selected to check the resistance of their biofilms formed on SS coupons to the CIP processes. Biofilms of all of the nine strains were highly or moderately alkali and acid resistant, posing a threat to the milk powder production. These results suggested that organisms within the biofilm might withstand temperature and pH changes better than planktonic organisms. More research is needed to investigate different species isolated from different facilities of the processing lines and to improve the key controlling points in the CIP processes.

Insights from the analysis of alginate lyase protein model from Pseudomonas fluorescens towards the understanding of mucoid biofilm disruption

Bacterial biofilm is a protective, slippery and slimy coat secreted by bacterial cells. It helps in attaching to moisturized surfaces during colonization. Alginate is an important component as it is essential for retention of water and nutrients in biofilms. It is a polysaccharide consisting of β-D-mannuronic acid (M) and α-L-guluronic acid (G) monomers with 1-4 linkage. The alginate lyase (AlgL) secreted by certain bacteria is capable of degrading alginate into oligo-uronides by β-elimination of the glycosidic bond. Therefore, it is of interest to analyze the simulated (GROMACS force filed) structure protein model (homology based on template 4OZV) of AlgL from Pseudomonas fluorescens to gain functional insight mucoid biofilm disruption. We report root mean square deviation (RMSD) and radius of gyration (Rg) profiles of the simulated (molecular dynamics) AlgL protein homology model in this context towards biofilm discruption.

Antimicrobial and antibiofilm efficacy of self-cleaning surfaces functionalized by TiO2 photocatalytic nanoparticles against Staphylococcus aureus and Pseudomonas putida

A photocatalytic sol of TiO₂ nanoparticles has been used for creating self-cleaning antimicrobial flat and porous glass surfaces. The substrates were irradiated to study their photocatalytic properties and behavior in the presence of biofilm-forming bacteria. Smooth glass surfaces and glass microfiber filters were covered with 1.98×10^-3±1.5×10^-4gcm^-2 and 8.55×10^-3±3.0×10^-4gcm^-2 densities, respectively. Self-cleaning properties were analyzed using the methylene blue 365nm UV-A photodegradation test. TiO₂-coated filters achieved rapid and complete photodegradation of methylene blue because of the better TiO₂ dispersion with respect to the glass slides. The effect of functionalized surfaces on the growth and viability of bacteria was studied using the strains Staphylococcus aureus and Pseudomonas putida. After irradiation (2h, 11.2Wm^-2, 290-400nm), the initially hydrophobic surface turned hydrophilic. The antibacterial effect led to extensive membrane damage and significant production of intracellular reactive oxygen species in all TiO₂-loaded irradiated specimens. The reduction of cell viability was over 99.9% (>3-log) for TiO₂ on glass surfaces. However, the polymeric extracellular matrix formed before the irradiation treatment was not removed. This study highlights the importance of bacterial colonization during dark periods and the difficulty of removing the structure of biofilms.

Multiple stressors in sediments impact adjacent hard substrate habitats and across biological domains

Coastal systems are increasingly impacted by human activities. While the direct effects of individual contaminants have been investigated, the potential for multiple contaminants to impact adjacent hard substrate habitats is poorly understood. Sediment-bound contaminants pose a risk to water column organisms through resuspension and the fluxing of dissolved nutrients and metals. This study experimentally manipulated contaminated coastal sediments in mesocosms with additions of a common fertiliser to investigate the impact on both bacterial biofilms and macrofouling communities on nearby hard substrates. Field mesocosms were deployed sub-tidally for two weeks in a fully crossed design with two levels of metal contamination (ambient or high) and three levels of organic enrichment (ambient, low and high). Developing biofilm and macrofaunal communities were collected on acetate settlement sheets above the mesocosm sediments and censused with a combination of high-throughput sequencing (biofilm) and microscopy (macrofauna). Organic enrichment of sediments induced compositional shifts in biofilm communities, reducing their diversity, evenness and richness. Furthermore, co-occurrence networks built from microbial assemblages exposed to contaminated sediments displayed reduced connectivity compared to controls, suggesting a more stochastic assembly dynamic, where microbial interactions are reduced. Macrofouling community composition shifted in response to increased enrichment with separate and interactive effects of metals also observed for individual taxa. Specifically, antagonistic stressor interactions were observed for colonial ascidians and arborescent bryozoans; metal contamination decreased abundances of these taxa, except under high enrichment conditions. Together these micro- and macrofaunal responses indicate selection for depauperate, but contaminant-tolerant, communities and a potential breakdown in biotic connectivity through multiple stressor impacts across habitat boundaries.

Riboswitches as Potential Targets for the Development of Anti-Biofilm Drugs

In nature, bacteria can exist as single motile cells or as sessile cellular community, known as microbial biofilms. Bacteria within biofilms are embedded in a self-produced extracellular matrix that makes them more resistant to antibiotic treatment and responses of the host immune system. Microbial biofilms are very important in medicine since they are associated with several human diseases such as dental caries, periodontitis, otitis media, infective endocarditis, infectious kidney stones, osteomyelitis or prostatitis. In addition, biofilms formed on the surface of clinical devices such as pacemakers, implants and catheters are difficult to treat, which underlines the clinical relevance of biofilm formation. At the molecular level, the switch from the planktonic state to biofilm formation is regulated primarily by bis- (3'-5)-cyclic dimeric guanosine monophosphate (c-di-GMP). C-di-GMP performs its function by binding to a wide variety of proteins, but also to riboswitches. C-di-GMP riboswitches are RNA regulatory elements located in the 5'-untranslated regions (5'-UTRs) of RNA messengers (mRNA) from genes involved in virulence, motility and biofilm formation, which are regulated by changes in the intracellular concentration of c-di-GMP. This review discusses the role of c-di-GMP responsive riboswitches as potential targets for the design of anti-biofilm agents.

Quantitative proteomic analysis of extracellular matrix extracted from mono- and dual-species biofilms of Fusobacterium nucleatum and Porphyromonas gingivalis

The Gram-negative bacteria Fusobacterium nucleatum and Porphyromonas gingivalis are members of a complex dental biofilm associated with periodontal disease. In this study, we cultured F. nucleatum and P. gingivalis as mono- and dual-species biofilms, and analyzed the protein composition of the biofilms extracellular polymeric matrix (EPM) by high-resolution liquid chromatography-tandem mass spectrometry. Label-free quantitative proteomic analysis was used for identification of proteins and sequence-based functional characterization for their classification and prediction of possible roles in EPM. We identified 542, 93 and 280 proteins in the matrix of F. nucleatum, P. gingivalis, and the dual-species biofilm, respectively. Nearly 70% of all EPM proteins in the dual-species biofilm originated from F. nucleatum, and a majority of these were cytoplasmic proteins, suggesting an enhanced lysis of F. nucleatum cells. The proteomic analysis also indicated an interaction between the two species: 22 F. nucleatum proteins showed differential levels between the mono and dual-species EPMs, and 11 proteins (8 and 3 from F. nucleatum and P. gingivalis, respectively) were exclusively detected in the dual-species EPM. Oxidoreductases and chaperones were among the most abundant proteins identified in all three EPMs. The biofilm matrices in addition contained several known and hypothetical virulence proteins, which can mediate adhesion to the host cells and disintegration of the periodontal tissues. This study demonstrated that the biofilm matrix of two important periodontal pathogens consists of a multitude of proteins whose amounts and functionalities vary largely. Relatively high levels of several of the detected proteins might facilitate their potential use as targets for the inhibition of biofilm development.

Protocols for Studying Inhibition and Eradication of Bacterial Biofilms by Antimicrobial Peptides

Many pathogenic microorganisms have the ability to form biofilms that are impervious to conventional antibiotics making these pathogens resistant to multiple antibiotics. This necessitates the development of novel antimicrobial compounds with less chance of resistance development and the ability to penetrate the extracellular polymer matrix of bacterial biofilms. In this report, simple assays to test the antibiofilm potential of antimicrobial peptides are described.

Novel Approaches to Manipulating Bacterial Pathogen Biofilms: Whole-Systems Design Philosophy and Steering Microbial Evolution

Understanding and manipulating bacterial biofilms is crucial in medicine, ecology and agriculture and has potential applications in bioproduction, bioremediation and bioenergy. Biofilms often resist standard therapies and the need to develop new means of intervention provides an opportunity to fundamentally rethink our strategies. Conventional approaches to working with biological systems are, for the most part, "brute force", attempting to effect control in an input and effort intensive manner and are often insufficient when dealing with the inherent non-linearity and complexity of living systems. Biological systems, by their very nature, are dynamic, adaptive and resilient and require management tools that interact with dynamic processes rather than inert artefacts. I present an overview of a novel engineering philosophy which aims to exploit rather than fight those properties, and hence provide a more efficient and robust alternative. Based on a combination of evolutionary theory and whole-systems design, its essence is what I will call systems aikido; the basic principle of aikido being to interact with the momentum of an attacker and redirect it with minimal energy expenditure, using the opponent's energy rather than one's own. In more conventional terms, this translates to a philosophy of equilibrium engineering, manipulating systems' own self-organisation and evolution so that the evolutionarily or dynamically stable state corresponds to a function which we require. I illustrate these ideas with a description of a proposed manipulation of environmental conditions to alter the stability of co-operation in the context of Pseudomonas aeruginosa biofilm infection of the cystic fibrosis lung.

High throughput screening methods for assessing antibiofilm and immunomodulatory activities of synthetic peptides

The recent observation that certain cationic peptides possess potent antibiofilm activity demonstrated that small peptides could be used to treat biofilm-associated infections. Other so-called innate defense regulator peptides possess potent immunomodulatory properties such as leukocyte recruitment and suppression of harmful inflammation. A peptide that directly targets biofilm cells while favorably modulating the immune response would be particularly advantageous for treating serious skin infections caused by Staphylococcus aureus. In the present work, using SPOT-synthesized peptide arrays on cellulose membranes, we outline a strategy for systematically assessing the antibiofilm activity of hundreds of IDR-1002 (VQRWLIVWRIRK-NH2) and IDR-HH2 (VQLRIRVAVIRA-NH2) peptide variants against MRSA biofilms. In addition, the ability of these peptides to stimulate production of a monocyte chemoattractant protein (MCP-1) and suppress LPS-induced interleukin (IL)-1β production in human peripheral blood mononuclear cells (PBMCs) was evaluated. These results informed the synthesis of second-generation peptides resulting in a new peptide, IDR-2009 (KWRLLIRWRIQK-NH2), with enhanced MCP-1 stimulatory activity, favorable IL-1β suppression characteristics and strong antibiofilm activity against MRSA and Pseudomonas aeruginosa biofilms. This work provides a proof-of-concept that multiple peptide activities can be optimized simultaneously to generate novel sequences that possess a variety of biological properties.

Effect of repeated tracheostomy tube reprocessing on biofilm formation

Objectives/Hypothesis

To determine the effect of repeated reprocessing of pediatric tracheostomy tubes (TTs) on biofilm formation.

Study Design

In vitro microbiological study.

Methods

Pediatric, uncuffed, polyvinyl chloride (PVC) TTs from two different manufacturers (Tracoe Mini and Shiley) were reprocessed mechanically with household detergent and soaked in sodium hypochlorite (bleach). Two TTs of each brand were reprocessed 0 (control), 10, or 20 times. Twenty 2‐mm coupons were then obtained from each TT, immersed in human mucus, and cultured with either Staphylococcus aureus or Pseudomonas aeruginosa. Biofilm formation was evaluated with bacterial counts.

Results

Bacterial counts of S. aureus for both brands were significantly higher on the TTs that were reprocessed 20 times compared to those that were not reprocessed (Tracoe: P = .040, Shiley: P  <  .0001) or those that were reprocessed 10 times (Tracoe: P = .022, Shiley: P = .0002). There was no difference between controls and TTs reprocessed 10 times (Tracoe: P = .76, Shiley: P = .24). P. aeuruginosa counts were not significantly different among the varying numbers of reprocessing cycles for either Tracoe or Shiley TTs (P = .08 and P = .97, respectively).

Conclusions

Repeated reprocessing of PVC TTs with detergent and bleach paradoxically promotes S. aureus biofilm development, possibly due to degradation of the tube surface that facilitates bacterial attachment. Further investigation is needed to determine the optimal technique and limits of reprocessing TTs in clinical practice.

Level of Evidence

NA Laryngoscope, 126:996–999, 2016

Bottom-up and top-down solid-state NMR approaches for bacterial biofilm matrix composition

The genomics and proteomics revolutions have been enormously successful in providing crucial "parts lists" for biological systems. Yet, formidable challenges exist in generating complete descriptions of how the parts function and assemble into macromolecular complexes and whole-cell assemblies. Bacterial biofilms are complex multicellular bacterial communities protected by a slime-like extracellular matrix that confers protection to environmental stress and enhances resistance to antibiotics and host defenses. As a non-crystalline, insoluble, heterogeneous assembly, the biofilm extracellular matrix poses a challenge to compositional analysis by conventional methods. In this perspective, bottom-up and top-down solid-state NMR approaches are described for defining chemical composition in complex macrosystems. The "sum-of-the-parts" bottom-up approach was introduced to examine the amyloid-integrated biofilms formed by Escherichia coli and permitted the first determination of the composition of the intact extracellular matrix from a bacterial biofilm. An alternative top-down approach was developed to define composition in Vibrio cholerae biofilms and relied on an extensive panel of NMR measurements to tease out specific carbon pools from a single sample of the intact extracellular matrix. These two approaches are widely applicable to other heterogeneous assemblies. For bacterial biofilms, quantitative parameters of matrix composition are needed to understand how biofilms are assembled, to improve the development of biofilm inhibitors, and to dissect inhibitor modes of action. Solid-state NMR approaches will also be invaluable in obtaining parameters of matrix architecture.

Strategies to prevent biofilm-based tympanostomy tube infections

OBJECTIVE

To review the potential contributory role of biofilms to post-tympanstomy tube otorrhea and plugging as well as the available interventions currently utilized to prevent biofilm formation on tympanostomy tubes.

DATA SOURCES

A literature review was performed utilizing the MEDLINE/Pubmed database from 1980 to 2013.

REVIEW METHODS

Electronic database was searched with combinations of keywords "biofilm", "tympanostomy tube", "ventilation tube", and "post-tympanostomy tube otorrhea".

RESULTS

Two of the most common sequelae that occur after tympanostomy tube insertion are otorrhea and tube occlusion. There is an increased evidence supporting a role for biofilms in the pathogenesis of otitis media. In this review, we have shown a multitude of novel approaches for prevention of biofilm associated sequelae of otitis media with effusion. These interventions include (i) changing the inherent composition of the tube itself, (ii) coating the tubes with antibiotics, polymers, plant extracts, or other biofilm-resistant materials, (iii) tubal impregnation with antimicrobial compounds, and (iv) surface alterations of the tube by ion-bombardment or surface ionization.

CONCLUSION

Currently, there is not one type of tympanostomy tube in which bacteria will not adhere. The challenges of treating chronic post-tympanostomy tube otorrhea and tube occlusion indicate the need for further research in optimization of tympanostomy tube design in addition to development of novel therapies.