In vitro and in vivo model systems to study microbial biofilm formation

Fungal Biofilms as a Valuable Target for the Discovery of Natural Products That Cope with the Resistance of Medically Important Fungi-Latest Findings

The development of new antifungal agents that target biofilms is an urgent need. Natural products, mainly from the plant kingdom, represent an invaluable source of these entities. The present review provides an update (2017-May 2021) on the available information on essential oils, propolis, extracts from plants, algae, lichens and microorganisms, compounds from different natural sources and nanosystems containing natural products with the capacity to in vitro or in vivo modulate fungal biofilms. The search yielded 42 articles; seven involved essential oils, two Brazilian propolis, six plant extracts and one of each, extracts from lichens and algae/cyanobacteria. Twenty articles deal with the antibiofilm effect of pure natural compounds, with 10 of them including studies of the mechanism of action and five dealing with natural compounds included in nanosystems. Thirty-seven manuscripts evaluated Candida spp. biofilms and two tested Fusarium and Cryptococcus spp. Only one manuscript involved Aspergillus fumigatus. From the data presented here, it is clear that the search of natural products with activity against fungal biofilms has been a highly active area of research in recent years. However, it also reveals the necessity of deepening the studies by (i) evaluating the effect of natural products on biofilms formed by the newly emerged and worrisome health-care associated fungi, C. auris, as well as on other non-albicans Candida spp., Cryptococcus sp. and filamentous fungi; (ii) elucidating the mechanisms of action of the most active natural products; (iii) increasing the in vivo testing.

Quantification of Staphylococcus aureus Biofilm Formation by Crystal Violet and Confocal Microscopy

Most Staphylococcus aureus strains can grow as a multicellular biofilm, a phenotype of utmost importance to clinical infections such as endocarditis, osteomyelitis, and implanted medical device infection. As biofilms are inherently more tolerant to the host immune system and antibiotics, understanding the S. aureus genes and regulatory circuits that contribute to biofilm development is an active and on-going field of research. This chapter details a high-throughput and standardized way to grow S. aureus biofilms using a classical microtiter plate assay. Biofilms can be quantified using crystal violet or by confocal microscopy imaging and COMSTAT analysis.

Development and Quantitation of Pseudomonas aeruginosa Biofilms after in vitro Cultivation in Flow-reactors

Characterization of biofilm formation and metabolic activities is critical to investigating biofilm interactions with environmental factors and illustrating biofilm regulatory mechanisms. An appropriate in vitro model that mimics biofilm in vivo habitats therefore demands accurate quantitation and investigation of biofilm-associated activities. Current methodologies commonly involve static biofilm setups (such as biofilm assays in microplates, bead biofilms, or biofilms on glass-slides) and fluidic flow biofilm systems (such as drip-flow biofilm reactors, 3-channel biofilm reactors, or tubing biofilm reactors). Continuous flow systems take into consideration the contribution of hydrodynamic shear forces, nutrient supply, and physical transport of dispersed cells, which define the habitat for biofilm development in most natural and engineered systems. This protocol describes the assembly of 3 flow-system setups to cultivate Pseudomonas aeruginosa PAO1 and Shewanella oneidensis MR-1 model biofilms, including the respective quantitation and observation approaches. The standardized flow systems promise productive and reproducible biofilm experimental results, which can be further modified according to specific research projects.

Critical parameters in cultivation of experimental biofilms using the example of Pseudomonas fluorescens

Formation and treatment of biofilms present a great challenge for health care and industry. About 80% of human infections are associated with biofilms including biomaterial centered infections, like infections of prosthetic heart valves, central venous catheters, or urinary catheters. Additionally, biofilms can cause food and drinking water contamination. Biofilm research focusses on application of experimental biofilm models to study initial adherence processes, to optimize physico-chemical properties of medical materials for reducing interactions between materials and bacteria, and to investigate biofilm treatment under controlled conditions. Exploring new antimicrobial strategies plays a key role in a variety of scientific disciplines, like medical material research, anti-infectious research, plant engineering, or wastewater treatment. Although a variety of biofilm models exist, there is a lack of standardization for experimental protocols, and designing experimental setups remains a challenge. In this study, a number of experimental parameters critical for material research have been tested that influence formation and stability of an experimental biofilm using the non-pathogenic model strain of Pseudomonas fluorescens. These parameters include experimental time frame, nutrient supply, inoculum concentration, static and dynamic cultivation conditions, material properties, and sample treatment during staining for visualization of the biofilm. It was shown, that all tested parameters critically influence the experimental biofilm formation process. The results obtained in this study shall support material researchers in designing experimental biofilm setups.

The Chemistry of Antibiofilm Phytocompounds

Phytocompounds are long known for their therapeutic uses due to their competence as antimicrobial agents. The antimicrobial activity of these bioactive compounds manifests their ability as an antibiofilm agent and is thereby proved to be competent to treat the widespread biofilm-associated chronic infections. The rapid development of antibiotic resistance in bacteria has made the treatment of these infections almost impossible by conventional antibiotic therapy, which forced a switch-over to the use of phytocompounds. The present overview deals with the classification of a huge array of phytocompounds according to their chemical nature, detection of their target pathogen, and elucidation of their mode of action.

Isolation and characterization of a strain with high microbial attachment in aerobic granular sludge

Aerobic granule is a special microbial aggregate associated with biofilm structure. The formation of aerobic granular sludge is primarily depending on its bacterial community and relevant microbiological properties. In this experiment, a strain with high microbial attachment was isolated from aerobic granular sludge, and the detailed characteristics were examined. Its high attachment ability could reach 2.34 (OD_600nm), while other low attachment values were only around 0.06-0.32, which indicated a big variation among the different bacteria. The strain exhibited a very special morphology with many fibric fingers under SEM observation. A distinctive behaviour was to form a spherical particle by themselves, which would be very beneficial for the formation and development of granular sludge. The EPS measurement showed that its PN content was higher than low attachment bacteria, and 3D-EEM confirmed that there were some different components. Based on the 16S rRNA analysis, it was identified to mostly belong to Stenotrophomonas. Its augmentation to particle sludge cultivation demonstrated that the strain could significantly promote the formation of aerobic granule. Conclusively, it was strongly suggested that it might be used as a good and potential model strain or chassis organism for the aerobic granular sludge formation and development.

Polymeric nano- and microparticulate drug delivery systems for treatment of biofilms

Now-a-days healthcare systems face great challenges with antibiotic resistance and low efficacy of antibiotics when combating pathogenic bacteria and bacterial biofilms. Administration of an antibiotic in its free form is often ineffective due to lack of selectivity to the infectious site and breakdown of the antibiotic before it exerts its effect. Therefore, polymeric delivery systems, where the antibiotic is encapsulated into a formulation, have shown great promise, facilitating a high local drug concentration at the site of infection, a controlled drug release and less drug degradation. All this leads to improved therapeutic effects and fewer systemic side effects together with a lower risk of developing antibiotic resistance. Here, we review and provide a comprehensive overview of polymer-based nano- and microparticles as carriers for antimicrobial agents and their effect on eradicating bacterial biofilms. We have a main focus on polymeric particulates containing poly(lactic-co-glycolic acid), chitosan and polycaprolactone, but also strategies involving combinations of these polymers are included. Different production techniques are reviewed and important parameters for biofilm treatment are discussed such as drug loading capacity, control of drug release, influence of particle size and mobility in biofilms. Additionally, we reflect on other promising future strategies for combating biofilms such as lipid-polymer hybrid particles, enzymatic biofilm degradation, targeted/triggered antibiotic delivery and future alternatives to the conventional particles.

Anti-biofilm Approach in Infective Endocarditis Exposes New Treatment Strategies for Improved Outcome

Infective endocarditis (IE) is a life-threatening infective disease with increasing incidence worldwide. From early on, in the antibiotic era, it was recognized that high-dose and long-term antibiotic therapy was correlated to improved outcome. In addition, for several of the common microbial IE etiologies, the use of combination antibiotic therapy further improves outcome. IE vegetations on affected heart valves from patients and experimental animal models resemble biofilm infections. Besides the recalcitrant nature of IE, the microorganisms often present in an aggregated form, and gradients of bacterial activity in the vegetations can be observed. Even after appropriate antibiotic therapy, such microbial formations can often be identified in surgically removed, infected heart valves. Therefore, persistent or recurrent cases of IE, after apparent initial infection control, can be related to biofilm formation in the heart valve vegetations. On this background, the present review will describe potentially novel non-antibiotic, antimicrobial approaches in IE, with special focus on anti-thrombotic strategies and hyperbaric oxygen therapy targeting the biofilm formation of the infected heart valves caused by Staphylococcus aureus. The format is translational from preclinical models to actual clinical treatment strategies.

The Role of PK/PD Analysis in the Development and Evaluation of Antimicrobials

Pharmacokinetic/pharmacodynamic (PK/PD) analysis has proved to be very useful to establish rational dosage regimens of antimicrobial agents in human and veterinary medicine. Actually, PK/PD studies are included in the European Medicines Agency (EMA) guidelines for the evaluation of medicinal products. The PK/PD approach implies the use of in vitro, ex vivo, and in vivo models, as well as mathematical models to describe the relationship between the kinetics and the dynamic to determine the optimal dosing regimens of antimicrobials, but also to establish susceptibility breakpoints, and prevention of resistance. The final goal is to optimize therapy in order to maximize efficacy and minimize side effects and emergence of resistance. In this review, we revise the PK/PD principles and the models to investigate the relationship between the PK and the PD of antibiotics. Additionally, we highlight the outstanding role of the PK/PD analysis at different levels, from the development and evaluation of new antibiotics to the optimization of the dosage regimens of currently available drugs, both for human and animal use.

Mimicking biofilm formation and development: Recent progress in in vitro and in vivo biofilm models

Biofilm formation in living organisms is associated to tissue and implant infections, and it has also been linked to the contribution of antibiotic resistance. Thus, understanding biofilm development and being able to mimic such processes is vital for the successful development of antibiofilm treatments and therapies. Several decades of research have contributed to building the foundation for developing in vitro and in vivo biofilm models. However, no such thing as an "all fit" in vitro or in vivo biofilm models is currently available. In this review, in addition to presenting an updated overview of biofilm formation, we critically revise recent approaches for the improvement of in vitro and in vivo biofilm models.

Biofilm-Infected Human Clusteroid Three-Dimensional Coculture Platform to Replace Animal Models in Testing Antimicrobial Nanotechnologies

Microbial biofilms are a major concern in wound care, implant devices, and organ infections. Biofilms allow higher tolerance to antimicrobial drugs, can impair wound healing, and potentially lead to sepsis. There has been a recent focus on developing novel nanocarrier-based delivery vehicles to enhance the biofilm penetration of traditional antibacterial drugs. However, a feasible in vitro human skin model to mimic the biofilm formation and its treatment for clearance have not yet been reported. This study describes the benefits of using an innovative bacterial biofilm-infected keratinocyte clusteroid model for the first time. It paves a new way for testing innovative nanomedicine delivery systems in a rapid and reproducible way on a realistic human cell-based platform, free of any animal testing. Herein, we have developed a novel composite 3D biofilm/human keratinocyte clusteroid coculture platform, which was used to measure biofilm clearance efficiency of nanoparticle (NP)-based therapeutics. We tested this model by treating the biofilm-infected 3D coculture layers by a ciprofloxacin-loaded Carbopol nanogel particles, surface-functionalized by the cationic protease Alcalase. We measured the antibacterial efficiency of the NP treatment on clearing Staphylococcus aureus and Pseudomonas aeruginosa biofilms on the 3D keratinocyte clusteroid/biofilm coculture model. Our experiments showed that these bacteria can infect the 3D layer of keratinocyte clusteroids and produce a stable biofilm. The biofilms were efficiently cleared by treatment with a formulation of 0.0032 wt % ciprofloxacin-loaded in 0.2 wt % Carbopol NPs surface-functionalized with 0.2 wt % Alcalase. Taken together, these promising results demonstrate that our coculture model can be exploited as a novel platform for testing the biofilm-eliminating efficiency of various NP formulations emulating skin and wound infections and could have wider applicability to replace animal models in similar experiments. This 3D cell culture-based platform could help in developing and testing of more effective antibacterial agents for clinical applications of antiplaque dental treatments, implants, infection control, and wound dressings.

Influence of sugars on biofilm formation of Staphylococcus epidermidis

The problem of biofilm formation by clinical strains of opportunistic bacteria is one of the most significant for medicine, because in a state of biofilm bacteria become more resistant to environmental factors, including antibiotics, a situation that can cause failure of treatment. Among opportunistic pathogens staphylococci are of special interest. Knowledge about the peculiarities of biofilm formation of these strains, in particular the polysaccharide biosynthesis, can be used for creation of a strategy of prophylaxis of different lesions that bind with staphylococci. The effect of different concentrations of the most widespread sugars (glucose, sucrose, lactose, galactose) on the activity of biofilm formation by strains of Staphylococcus epidermidis was investigated. Strains of S. epidermidis (n = 7) were isolated from the reproductive tract of women with dysbiosis. The cultures were grown in universal synthetic media with concentration of one of the listed sugars (0.5–3.0%) during 72 h. Results were obtained colorimetrically. We studied the number of cells in biofilm and the index of biofilm formation. The largest number of cells in the biofilm was observed when the culture incubated in a medium with 2.0% of glucose (increase of 25.3 times compared to control). The amount of CFU in the control biofilm was 9.96 lg CFU/mL. The glucose concentration of 3.0% inhibited the biofilm formation: the number of cells in the biofilm was 569 times less compared to the control. The highest value of biofilm formation index was 7.2, which was 1.3 times higher than the control (5.4). In the presence of lactose and galactose in nutrient medium in concentrations from 1.0% a decrease in the number of cells and biofilm formation index were observed. The received data show that process of biofilm formation is significantly dependent on external sources of sugars, which can indicate the possibility of their use as antibiofilm drug compounds, which inhibit membrane transport of sugars in bacteria.

An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents

Bacterial biofilms are complex and highly antibiotic-resistant aggregates of microbes that form on surfaces in the environment and body including medical devices. They are key contributors to the growing antibiotic resistance crisis and account for two-thirds of all infections. Thus, there is a critical need to develop anti-biofilm specific therapeutics. Here we discuss mechanisms of biofilm formation, current anti-biofilm agents, and strategies for developing, discovering, and testing new anti-biofilm agents. Biofilm formation involves many factors and is broadly regulated by the stringent response, quorum sensing, and c-di-GMP signaling, processes that have been targeted by anti-biofilm agents. Developing new anti-biofilm agents requires a comprehensive systems-level understanding of these mechanisms, as well as the discovery of new mechanisms. This can be accomplished through omics approaches such as transcriptomics, metabolomics, and proteomics, which can also be integrated to better understand biofilm biology. Guided by mechanistic understanding, in silico techniques such as virtual screening and machine learning can discover small molecules that can inhibit key biofilm regulators. To increase the likelihood that these candidate agents selected from in silico approaches are efficacious in humans, they must be tested in biologically relevant biofilm models. We discuss the benefits and drawbacks of in vitro and in vivo biofilm models and highlight organoids as a new biofilm model. This review offers a comprehensive guide of current and future biological and computational approaches of anti-biofilm therapeutic discovery for investigators to utilize to combat the antibiotic resistance crisis.

Microbiota and cancer: In vitro and in vivo models to evaluate nanomedicines

Nanomedicine implication in cancer treatment and diagnosis studies witness huge attention, especially with the promising results obtained in preclinical studies. Despite this, only few nanomedicines succeeded to pass clinical phase. The human microbiota plays obvious roles in cancer development. Nanoparticles have been successfully used to modulate human microbiota and notably tumor associated microbiota. Taking the microbiota involvement under consideration when testing nanomedicines for cancer treatment might be a way to improve the poor translation from preclinical to clinical trials. Co-culture models of bacteria and cancer cells, as well as animal cancer-microbiota models offer a better representation for the tumor microenvironment and so potentially better platforms to test nanomedicine efficacy in cancer treatment. These models would allow closer representation of human cancer and might smoothen the passage from preclinical to clinical cancer studies for nanomedicine efficacy.

Antibiofilm Peptides: Relevant Preclinical Animal Infection Models and Translational Potential

Biofilm-forming bacteria may be 10-1000 times more resistant to antibiotics than planktonic bacteria and represent about 75% of bacterial infections in humans. Antibiofilm treatments are scarce, and no effective therapies have been reported so far. In this context, antibiofilm peptides (ABPs) represent an exciting class of agents with potent activity against biofilms both in vitro and in vivo. Moreover, murine models of bacterial biofilm infections have been used to evaluate the in vivo effectiveness of ABPs. Therefore, here we highlight the translational potential of ABPs and provide an overview of the different clinically relevant murine models to assess ABP efficacy, including wound, foreign body, chronic lung, and oral models of infection. We discuss key challenges to translate ABPs to the clinic and the pros and cons of the existing murine biofilm models for reliable assessment of the efficacy of ABPs.

Persistent inhibition of Candida albicans biofilm and hyphae growth on titanium by graphene nanocoating

OBJECTIVES

Candida albicanscolonizes biomaterial surfaces and are highly resistant to therapeutics. Graphene nanocoating on titanium compromises initial biofilm formation. However, its sustained antibiofilm potential is unknown. The objective of this study was to investigate the potential of graphene nanocoating to decrease long-term fungal biofilm development and hyphae growth on titanium.

METHODS

Graphene nanocoating was deposited twice (TiGD) or five times (TiGV) on grade 4 titanium with vacuum assisted technique and characterized with Raman spectroscopy and atomic force microscope. The biofilm formation and hyphae growth of C. albicans was monitored for seven days by CFU, XTT, confocal, mean cell density and scanning electronic microscopy (SEM). Uncoated titanium was the Control. All tests had three independent biological samples and were performed in independent triplicates. Data was analyzed with one- or two-way ANOVA and Tukey's HSD (α = 0.05).

RESULTS

Both TiGD and TiGV presented less biofilms at all times points compared with Control. The confocal and SEM images revealed few adhered cells on graphene coated samples, absence of hyphae and no features of a mature biofilm architecture. The increase in number of layers of graphene nanocoating did not improve its antibiofilm potential.

SIGNIFICANCE

The graphene nanocoating exerted a long-term persistent inhibitory effect on the biofilm formation on titanium. The fewer cells that were able to attach on graphene coated titanium were scattered and unable to form a mature biofilm with hyphae elements. The findings open opportunities to prevent microbial attachment and proliferation on implantable materials without the use of antibiotics.

The classification of Staphylococcus aureus strains by biofilm production differs depending on the method used

INTRODUCTION

Strains can be classified in terms of biofilm production from quantitative absorbance values collectively by dividing strains into tertile ranks or individually by calculating the optical density for the negative control. However, these methods have not been compared in a large sample of Staphylococcus aureus strains. Therefore, our objective was to analyze the agreement between both methods in terms of biomass production and metabolic activity of their biofilm.

METHODS

We classified 233 S. aureus strains by biomass production and metabolic activity using the crystal violet and XTT assays, respectively. Strains were classified as low, moderate, or high biofilm producers according to tertile or optical density.

RESULTS

We found no agreement between both methods (p<0.001 and p=0.028, respectively).

CONCLUSIONS

We consider strains' biofilm classification by optical density to be a more reliable method, as it depends on the individual absorbance of each strain.

Effect of host-mimicking medium and biofilm growth on the ability of colistin to kill Pseudomonas aeruginosa

In vivo biofilms cause recalcitrant infections with extensive and unpredictable antibiotic tolerance. Here, we demonstrate increased tolerance of colistin by Pseudomonas aeruginosa when grown in medium that mimics cystic fibrosis (CF) sputum versus standard medium in in vitro biofilm assays, and drastically increased tolerance when grown in an ex vivo CF model versus the in vitro assay. We used colistin conjugated to the fluorescent dye BODIPY to assess the penetration of the antibiotic into ex vivo biofilms and showed that poor penetration partly explains the high doses of drug necessary to kill bacteria in these biofilms. The ability of antibiotics to penetrate the biofilm matrix is key to their clinical success, but hard to measure. Our results demonstrate both the importance of reduced entry into the matrix in in vivo-like biofilm, and the tractability of using a fluorescent tag and benchtop fluorimeter to assess antibiotic entry into biofilms. This method could be a relatively quick, cheap and useful addition to diagnostic and drug development pipelines, allowing the assessment of drug entry into biofilms, in in vivo-like conditions, prior to more detailed tests of biofilm killing.

Advantages and limitations of microtiter biofilm assays in the model of antibiofilm activity of Klebsiella phage KP34 and its depolymerase

One of the potential antibiofilm strategies is to use lytic phages and phage-derived polysaccharide depolymerases. The idea is to uncover bacteria embedded in the biofilm matrix making them accessible and vulnerable to antibacterials and the immune system. Here we present the antibiofilm efficiency of lytic phage KP34 equipped with virion-associated capsule degrading enzyme (depolymerase) and its recombinant depolymerase KP34p57, depolymerase-non-bearing phage KP15, and ciprofloxacin, separately and in combination, using a multidrug-resistant K. pneumoniae biofilm model. The most effective antibiofilm agents were (1) phage KP34 alone or in combination with ciprofloxacin/phage KP15, and (2) depolymerase KP34p57 with phage KP15 and ciprofloxacin. Secondly, applying the commonly used biofilm microtiter assays: (1) colony count, (2) LIVE/DEAD BacLight Bacterial Viability Kit, and (3) crystal violet (CV) biofilm staining, we unravelled the main advantages and limitations of the above methods in antibiofilm testing. The diverse mode of action of selected antimicrobials strongly influenced obtained results, including a false positive enlargement of biofilm mass (CV staining) while applying polysaccharide degrading agents. We suggest that to get a proper picture of antimicrobials' effectiveness, multiple examination methods should be used and the results must be read considering the principle of each technique and the antibacterial mechanism.

Unraveling Pseudomonas aeruginosa and Candida albicans Communication in Coinfection Scenarios: Insights Through Network Analysis

Modern medicine is currently facing huge setbacks concerning infection therapeutics as microorganisms are consistently knocking down every antimicrobial wall set before them. The situation becomes more worrying when taking into account that, in both environmental and disease scenarios, microorganisms present themselves as biofilm communities that are often polymicrobial. This comprises a competitive advantage, with interactions between different species altering host responses, antimicrobial effectiveness, microbial pathogenesis and virulence, usually augmenting the severity of the infection and contributing for the recalcitrance towards conventional therapy. Pseudomonas aeruginosa and Candida albicans are two opportunistic pathogens often co-isolated from infections, mainly from mucosal tissues like the lung. Despite the billions of years of co-existence, this pair of microorganisms is a great example on how little is known about cross-kingdom interactions, particularly within the context of coinfections. Given the described scenario, this study aimed to collect, curate, and analyze all published experimental information on the molecular basis of P. aeruginosa and C. albicans interactions in biofilms, in order to shed light into key mechanisms that may affect infection prognosis, increasing this area of knowledge. Publications were optimally retrieved from PubMed and Web of Science and classified as to their relevance. Data was then systematically and manually curated, analyzed, and further reconstructed as networks. A total of 641 interactions between the two pathogens were annotated, outputting knowledge on important molecular players affecting key virulence mechanisms, such as hyphal growth, and related genes and proteins, constituting potential therapeutic targets for infections related to these bacterial-fungal consortia. Contrasting interactions were also analyzed, and quorum-sensing inhibition approaches were highlighted. All annotated data was made publicly available at www.ceb.uminho.pt/ISCTD, a database already containing similar data for P. aeruginosa and Staphylococcus aureus communication. This will allow researchers to cut on time and effort when studying this particular subject, facilitating the understanding of the basis of the inter-species and inter-kingdom interactions and how it can be modulated to help design alternative and more effective tailored therapies. Finally, data deposition will serve as base for future dataset integration, whose analysis will hopefully give insights into communications in more complex and varied biofilm communities.

Interaction between bovine mammary epithelial cells and planktonic or biofilm Staphylococcus aureus: The bacterial lifestyle determines its internalization ability and the pathogen recognition

The main cause of mastitis, one of the most costly diseases in the dairy industry, is bacterial intramammary infection. Many of these bacteria are biofilm formers. Biofilms have been associated with resistance to antibiotics and to the host immune system. Here, we evaluated different experimental models representing bacterial biofilm lifestyle with the aim to study bacterial invasion into bovine mammary epithelial cells and the interaction of these cells with planktonic or biofilm Staphylococcus aureus. Staphylococcus aureus V329, its nonbiofilm-forming mutant and bovine mammary alveolar cells (MAC-T) were used. Bacterial invasion was studied using the gentamicin exclusion test, cell viability by trypan blue exclusion technique, TLR2 expression by flow cytometry, IL1β/IL6 production by ELISA and IL8/TNFα gene expression by real-time polymerase chain reaction. Biofilm and planktonic S. aureus showed differences in their invasion ability, with the biofilm mode showing a lower ability. Planktonic S. aureus reduced MAC-T viability after 6 h of co-culture, while biofilms did so at 24 h. MAC-T infected with planktonic bacteria showed increased TLR2 expression. Both lifestyles increased IL8 expression and IL1β/IL6 production but did not modify TNFα expression. Our results demonstrate that the bacterial lifestyle affects the invasion behavior, suggesting that biofilms reduce the bacteria-epithelial cell interaction. Planktonic cultures seem to induce higher cellular activation than biofilms. Further knowledge about the complex host-biofilm interaction is necessary to design more efficient therapies against bovine mastitis.

Staphylococcus epidermidis and Cutibacterium acnes: Two Major Sentinels of Skin Microbiota and the Influence of Cosmetics

Dermatological and cosmetics fields have recently started to focus on the human skin microbiome and microbiota, since the skin microbiota is involved in the health and dysbiosis of the skin ecosystem. Amongst the skin microorganisms, Staphylococcus epidermidis and Cutibacterium acnes, both commensal bacteria, appear as skin microbiota sentinels. These sentinels have a key role in the skin ecosystem since they protect and prevent microbiota disequilibrium by fighting pathogens and participate in skin homeostasis through the production of beneficial bacterial metabolites. These bacteria adapt to changing skin microenvironments and can shift to being opportunistic pathogens, forming biofilms, and thus are involved in common skin dysbiosis, such as acne or atopic dermatitis. The current evaluation methods for cosmetic active ingredient development are discussed targeting these two sentinels with their assets and limits. After identification of these objectives, research of the active cosmetic ingredients and products that maintain and promote these commensal metabolisms, or reduce their pathogenic forms, are now the new challenges of the skincare industry in correlation with the constant development of adapted evaluation methods.

Mini-review: from in vitro to ex vivo studies: an overview of alternative methods for the study of medical biofilms

Microbial biofilms are a natural adaptation of microorganisms, typically composed of multiple microbial species, exhibiting complex community organization and cooperation. Biofilm dynamics and their complex architecture are challenging for basic analyses, including the number of viable cells, biomass accumulation, biofilm morphology, among others. The methods used to study biofilms range from in vitro techniques to complex in vivo models. However, animal welfare has become a major concern, not only in society, but also in the academic and scientific field. Thus, the pursuit for alternatives to in vivo biofilm analyses presenting characteristics that mimic in vivo conditions has become essential. In this context, the present review proposes to provide an overview of strategies to study biofilms of medical interest, with emphasis on alternatives that approximate experimental conditions to host-associated environments, such as the use of medical devices as substrata for biofilm formation, microcosm and ex vivo models.

Evaluation of non-traditional visualization methods to detect surface attachment of biofilms

In food safety and food quality, biofilm research is of great importance for mitigating food-borne pathogens in food processing environments. To supplement the traditional staining techniques for biofilm characterization, we introduce several non-traditional imaging methods for detecting biofilm attachment to the solid-liquid and air-liquid interfaces. For strains of Pseudomonas aeruginosa (the positive control), Acinetobacter baumanii, Listeria monocytogenes and Salmonella enterica, the traditional crystal violet assay showed evidence of biofilm attachment to the well plate base as well as inferred the presence of an air-liquid biofilm attached on the upper well walls where the meniscus was present. However, air-liquid biofilms and solid-surface-attached biofilms were not detected for all of these strains using the non-traditional imaging methods. For L. monocytogenes, we were unable to detect biofilms at a particle-laden, air-liquid interface as evidenced through microscopy, which contradicts the meniscus staining test and suggests that the coffee-ring effect may lead to false positives when using meniscus staining. Furthermore, when L. monocytogenes was cultivated in a pendant droplet in air, only microbial sediment at the droplet apex was observed without any apparent bacterial colonization of the droplet surface. All other strains showed clear evidence of air-liquid biofilms at the air-liquid interface of a pendant droplet. To non-invasively detect if and when air-liquid pellicles form in a well plate, we also present a novel in situ reflection assay that demonstrates the capacity to do this quantitatively.

Establishment of a quality control circle to reduce biofilm formation in flexible endoscopes by improvement of qualified cleaning rate

Objective

In recent years, the Emergency Care Research Institute has advised that endoscope cleaning is of considerable importance. In the present study, a quality control circle (QCC) was used to reduce the formation of biofilms in flexible endoscopes within one hospital in Guangdong Province, China.

Methods

During reprocessing of 235 flexible endoscopes in the urology surgical suite, adenosine triphosphate (ATP) detection was used to monitor the efficacy of biofilm removal. The internal and external parts of flexible endoscopes were used as sampling sites by means of the flushing and smudge methods, respectively. When the two results reached the standard of less than 500 relative light units/piece at the same time, endoscopic biofilm clearance was considered to be qualified. A QCC was established to implement a 10-step plan-do-check-act model.

Results

The baseline qualified rate (i.e., ATP monitoring pass rate) during reprocessing of 235 flexible endoscopes was 50%. During the study, the qualified rate increased to 85.29% after establishment of the QCC. During reprocessing of 150 flexible endoscopes in the following 6 months, the qualified rate remained at 90%.

Conclusion

Establishment of the QCC improved the removal of biofilm from flexible endoscopes in the urology surgical suite.

Phenotypic and genetic properties of susceptible and multidrug-resistant Pseudomonas aeruginosa isolates in Southern Serbia

Drug resistance of Pseudomonas aeruginosa is a leading problem in hospital infections. The aim of this study was to determine the best molecular genetic discrimination method for Pseudomonas spp. isolates among 94 outpatients and inpatients and see their grouping by phenotype characteristics (biofilm formation, frequency of serotypes, pigmentation, production of different class of beta-lactamases, and susceptibility to different antibiotic classes) and genotype. The most common serotypes were P1, P6, and P11, while co-productions of pyoverdine and pyocyanin were observed in 70 % of isolates. A total of 77.66 % isolates were mostly weak and moderate biofilm producers. Isolates were susceptible to colistin (100 %), aztreonam (97.87 %), imipenem (91.49 %), doripenem (90.43 %), and meropenem (84.04 %). MICs values confirmed susceptibility to ceftazidime and cefepime and singled out meripenem as the most effective inhibitor. Most isolates were resistant to aminoglycosides and fluoroquinolones. Only two isolates produced ESBL, eight were carbapenemase producers, and five isolates produced MBLs. Twenty-nine isolates were multidrug-resistant; 82.8 % of which produced both pigments, 58.3 % were non-typeable, while the P6 and P11 serotypes were equally distributed (16.7 %). Thirteen MDR isolates were strong enzyme producers. RAPD PCR analysis using primer 272 proved the best at discriminatory fingerprinting for Pseudomonas isolates, as it allocated 12 clusters. A correlation between DNA patterns and antibiotic resistance, production of pigments, serotypes distribution, and biofilm formation was not observed, and only confirmed higher genetic heterogeneity among P. aeruginosa isolates, which suggests that other molecular methods are needed to reveal potential relations between genotypic patterns and phenotypic characteristics.

Detection and Categorization of Biofilm-forming Staphylococcus aureus, Viridans streptococcus, Klebsiella pneumoniae, and Escherichia coli Isolated from Complete Denture Patients and Visualization Using Scanning Electron Microscopy

Aims:

Complete denture patients have a plethora of microorganisms inhabiting their complete dentures. Some bacteria are capable of causing systemic illness such as aspiration pneumonia and infective endocarditis. Hence, detection as well as the categorization of biofilms, which form on the denture surface is vital in the study of denture biofilm-associated local and systemic diseases. This study aimed at the detection and categorization of biofilm-forming Staphylococcus aureus, Viridans streptococcus, Klebsiella pneumoniae, and Escherichia coli isolated from complete dentures and visualization of biofilms using scanning electron microscopy (SEM).

Materials and Methods:

Thirty complete denture patients were selected for the study and swabs were collected from their complete denture surfaces. Isolation of the bacteria was done using selective media and confirmed using biochemical tests and 16SrRNA sequencing. The bacteria were subjected to biofilm assays via Microtiter plate assay. The biofilm-forming bacteria were categorized as weak, moderate, and strong biofilm formers based on optical density (OD) values. As a visual confirmation of the biofilms, scanning electron microscopic (SEM) images were taken for each of the strong biofilm-forming bacteria. Descriptive statistical analysis was carried out with the help of Statistical Package for the Social Sciences (SPSS) statistical package version 20.0.

Results:

The average OD of S. aureus was 1. 333±0. 015 and the average OD of V. streptococcus species was 1. 304 ± 0.023. The average OD value of K. pneumoniae was 0.8 ± 0.012 and the average value of E. coli was 1.014 ± 0.01.

Conclusions:

The study of biofilms especially the strongly biofilm formers is very useful to understand the potential pathogenic effect of biofilms. These biofilms cause the systemic spread of the planktonic bacteria which could lead to systemic diseases that are resistant to conventional treatment. This could be due to the inherent nature of the biofilm to offer drug resistance to existing antibacterial agents.

Ex Vivo Murine Skin Model for B. burgdorferi Biofilm

Borrelia burgdorferi, the causative agent of Lyme disease, has been recently shown to form biofilm structures in vitro and in vivo. Biofilms are tightly clustered microbes characterized as resistant aggregations that allow bacteria to withstand harsh environmental conditions, including the administration of antibiotics. Novel antibiotic combinations have recently been identified for B. burgdorferi in vitro, however, due to prohibiting costs, those agents have not been tested in an environment that can mimic the host tissue. Therefore, researchers cannot evaluate their true effectiveness against B. burgdorferi, especially its biofilm form. A skin ex vivo model system could be ideal for these types of experiments due to its cost effectiveness, reproducibility, and ability to investigate host-microbial interactions. Therefore, the main goal of this study was the establishment of a novel ex vivo murine skin biopsy model for B. burgdorferi biofilm research. Murine skin biopsies were inoculated with B. burgdorferi at various concentrations and cultured in different culture media. Two weeks post-infection, murine skin biopsies were analyzed utilizing immunohistochemical (IHC), reverse transcription PCR (RT-PCR), and various microscopy methods to determine B. burgdorferi presence and forms adopted as well as whether it remained live in the skin tissue explants. Our results showed that murine skin biopsies inoculated with 1 × 107 cells of B. burgdorferi and cultured in BSK-H + 6% rabbit serum media for two weeks yielded not just significant amounts of live B. burgdorferi spirochetes but biofilm forms as well. IHC combined with confocal and atomic force microscopy techniques identified specific biofilm markers and spatial distribution of B. burgdorferi aggregates in the infected skin tissues, confirming that they are indeed biofilms. In the future, this ex vivo skin model can be used to study development and antibiotic susceptibility of B. burgdorferi biofilms in efforts to treat Lyme disease effectively.

Repurposing Antispasmodic Agent Otilonium Bromide for Treatment of Staphylococcus aureus Infections

Recently, the problem of bacterial resistance has been brought into focus, which makes the development of new antibiotics become a necessity. Compared with traditional development approaches, drug repurposing provides a faster and more effective approach to find new antimicrobial agents. In this study, we found that antispasmodic agent otilonium bromide had strong antibacterial ability and bactericidal activity against Staphylococcus aureus, with minimal inhibitory concentrations (MICs) of 4-8 μg/ml, and bacteria could be killed completely after treatment with 2× MIC of otilonium bromide for 5 h. Furthermore, it had a potent effect on eradicating biofilm at concentrations ranging from 16 to 64 μg/ml. At the same time, it had low tendency to develop resistance and possessed limited cytotoxicity. In the methicillin-resistant S. aureus-infected mouse peritonitis model, it was also effective to cure mice and improve their survival rate. In addition, we observed that otilonium bromide changed the permeability of bacterial membrane and caused membrane damage, and it is probably the antibacterial mechanism of otilonium bromide. Taken together, our results indicated that otilonium bromide could be a new antimicrobial agent to treat S. aureus infections more safely and efficiently.

CxxC Zinc Finger Protein Derived Peptide, MF18 Functions Against Biofilm Formation

The major threat in modern medicine was biofilm forming bacterial related infections and they were highly tolerant to conventional antibiotics and a boundless demand for new drugs. In this regard, antimicrobial peptide (AMP) have been considered as potential alternative agents to conventional antibiotics. In this study, we have reported a CxxC zinc finger protein derived peptide, MF18 and its various biological role including activity against biofilm forming bacteria. Zinc finger protein are important in regulation of several cellular processes and wide range of molecular functions. The CxxC zinc finger protein identified from the cDNA library of a teleost fish; further it was characterised using various online bioinformatics programs. During the in-silico analysis, an AMP named MF18 was identified from the CxxC zinc finger protein, then it was synthesised for further biological activity studies. The antimicrobial activity of MF18 was confirmed against the biofilm clinical isolates such as Staphylococcus aureus and Escherichia coli. The MIC of the antimicrobial peptide at the concentration of 320 µM was observed against these two biofilm bacteria. The mechanism of the peptides was determined using bacteria on its membrane permeabilization ability by scanning electron microscopy. It is exhibited that the MF18 potentially influenced in damaging the morphology of the bacteria. The toxicity of MF18 against the continuous cell line (RAW 264.7) was demonstrated by MTT assay and also using peripheral red blood cells by haemolytic assay; both assays showed that the peptide have no toxicity on the cells at lower concentration. Overall, the study showed the potential therapeutic application of the peptide in pharma industry.

A multimodel regime for evaluating effectiveness of antimicrobial wound care products in microbial biofilms

Microbial biofilms have become increasingly recognized as a cause of wound chronicity. There are several topical antimicrobial wound care products available for use; however, their effectiveness has routinely been demonstrated with planktonic microorganisms. There is no target reference value for antimicrobial effectiveness of wound care products in biofilm models. In addition, data on antimicrobial activity of products in biofilm models are scattered across many test methods in a variety of studies. The aim of this work is to directly compare commercial products containing the commonly used topical antimicrobial agents iodine, silver, polyhexamethylene biguanide, octenidine, hypochlorous acid, benzalkonium chloride, and a surfactant-based topical containing poloxamer 188. Five different in vitro biofilm models of varied complexity were used, incorporating several bacterial pathogens such as Staphylococcus, Enterococcus, Streptococcus, Pseudomonas, Acinetobacter, Klebsiella, and Enterobacter. The fungal pathogens Candida albicans and Candida auris were also evaluated. A multispecies bacterial biofilm model was also used to evaluate the products. Additionally, C. albicans was used in combination with S. aureus and P. aeruginosa in a multikingdom version of the polymicrobial biofilm model. Statistically significant differences in antimicrobial performance were observed between treatments in each model and changing microbial growth conditions or combinations of organisms resulted in significant performance differences for some treatments. The iodine and benzalkonium chloride-containing products were overall the most effective in vitro and were then selected for in vivo evaluation in an infected immunocompromised murine model. Unexpectedly, the iodine product was statistically (P > .05) no different than the untreated control, while the benzalkonium chloride containing product significantly (P < .05) reduced the biofilm compared to untreated control. This body of work demonstrates the importance of not only evaluating antimicrobial wound care products in biofilm models but also the importance of using several different models to gain a comprehensive understanding of products' effectiveness.

Proposal for a microcosm biofilm model for the study of vulvovaginal candidiasis

This study proposes a microcosm biofilm (MiB) model for the study of vulvovaginal candidiasis (VVC). Different conditions that mimic the vaginal environment were tested for MiB formation. The best growth conditions were obtained with samples incubated in vaginal fluid simulator medium pH 4.5 at 35 °C under a microaerophilic atmosphere. MiBs were evaluated for growth kinetics, fluconazole susceptibility and morphology. Samples containing high numbers of bacteria were analyzed for metagenomics. At 48 h, MiBs presented a higher cell density (CFU ml^-1), a higher biomass and tolerance to fluconazole than their corresponding monospecies biofilms. Morphological analysis of MiBs revealed blastoconidia preferentially adhered to epithelial cells. Abundant Lactobacillus spp. were detected in two clinical samples; their MiBs showed a lower biomass and a higher fluconazole susceptibility. The proposed model proved to be a useful tool for the study of the complex microbial relationship in the vaginal environment, and may help to find new strategies for VVC control.

Three-Dimensional In Vitro Oral Mucosa Models of Fungal and Bacterial Infections

Oral mucosa is the target tissue for many microorganisms involved in periodontitis and other infectious diseases affecting the oral cavity. Three-dimensional (3D) in vitro and ex vivo oral mucosa equivalents have been used for oral disease modeling and investigation of the mechanisms of oral bacterial and fungal infections. This review was conducted to analyze different studies using 3D oral mucosa models for the evaluation of the interactions of different microorganisms with oral mucosa. In this study, based on our inclusion criteria, 43 articles were selected and analyzed. Different types of 3D oral mucosa models of bacterial and fungal infections were discussed in terms of the biological system used, culture conditions, method of infection, and the biological endpoints assessed in each study. The critical analysis revealed some contradictory reports in this field of research in the literature. Challenges in recovering bacteria from oral mucosa models were further discussed, suggesting possible future directions in microbiomics, including the use of oral mucosa-on-a-chip. The potential use of these 3D tissue models for the evaluation of the effects of antiseptic agents on bacteria and oral mucosa was also addressed. This review concluded that there were many aspects that would require optimization and standardization with regard to using oral mucosal models for infection by microorganisms. Using new technologies-such as microfluidics and bioreactors-could help to reproduce some of the physiologically relevant conditions and further simulate the clinical situation. Impact statement Tissue-engineered or commercial models of the oral mucosa are very useful for the study of diseases that involve the interaction of microorganisms and oral epithelium. In this review, challenges in recovering bacteria from oral mucosa models, the potential use of these three-dimensional tissue models for the evaluation of the effects of antiseptic agents, and future directions in microbiomics are discussed.

Current Concepts of Osteomyelitis: From Pathologic Mechanisms to Advanced Research Methods

Osteomyelitis is an inflammation of the bone and bone marrow that is most commonly caused by a Staphylococcus aureus infection. Much of our understanding of the underlying pathophysiology of osteomyelitis, from the perspective of both host and pathogen, has been revised in recent years, with notable discoveries including the role played by osteocytes in the recruitment of immune cells, the invasion and persistence of S. aureus in submicron channels of cortical bone, and the diagnostic role of polymorphonuclear cells in implant-associated osteomyelitis. Advanced in vitro cell culture models, such as ex vivo culture models or organoids, have also been developed over the past decade, and have become widespread in many fields, including infectious diseases. These models better mimic the in vivo environment, allow the use of human cells, and can reduce our reliance on animals in osteomyelitis research. In this review, we provide an overview of the main pathologic concepts in osteomyelitis, with a focus on the new discoveries in recent years. Furthermore, we outline the value of modern in vitro cell culture techniques, with a focus on their current application to infectious diseases and osteomyelitis in particular.

Antifungal susceptibility pattern and biofilm-related genes expression in planktonic and biofilm cells of Candida parapsilosis species complex

Background and Purpose:

Candida parapsilosis complex isolates are mainly responsible for nosocomial catheter-related infection in immunocompromised patients. Biofilm formation is regarded as one of the most pertinent key virulence factors in the development of these emerging infections. The present study aimed to compare in vitro antifungal susceptibility patterns and biofilm-related genes expression ratio in planktonic and biofilm’s cells of clinically C. parapsilosis complex isolates.

Materials and Methods:

The current study was conducted on a number of 17 clinical C. parapsilosis complex (10 C. parapsilosis sensu stricto, 5 C. orthopsilosis, and 2 C. metapsilosis). The antifungal susceptibility patterns of amphotericin B, fluconazole, itraconazole, voriconazole, posaconazole, and caspofungin in planktonic and biofilm forms were closely examined using CLSI M27-A3 broth microdilution method. The expression levels of biofilm-related genes (BCR1, EFG1, and FKS1) were evaluated in planktonic and biofilm’s cells using Real-time polymerase chain reaction (PCR) technique.

Results:

The obtained results indicated that all C. parapsilosis complex isolates were able to produce high and moderate amounts of biofilm forms. In addition, the sessile minimum inhibitory concentrations were reported to be high for fluconazole (≥ 64 µg/ml), itraconazole, voriconazole, and posaconazole (≥ 16 µg/ml), as compared to planktonic minimum inhibitory concentrations. Moreover, a significant difference was observed between antifungal susceptibility patterns for all azole antifungal agents (P<0.05). Furthermore, the BCR1 overexpression was considered significant in biofilms with regard to planktonic cells in C. parapsilosis species complex (P=0.002).

Conclusion:

C. parapsilosis complex isolates were found susceptible to most of the tested antifungal drugs, while biofilms demonstrated a noticeable resistant to azoles. The marked discrepancy noted in antifungal susceptibility patterns among these species should be highlighted to achieve effective therapeutic treatment.

A Simple Polymicrobial Biofilm Keratinocyte Colonization Model for Exploring Interactions Between Commensals, Pathogens and Antimicrobials

Skin offers protection against external insults, with the skin microbiota playing a crucial defensive role against pathogens that gain access when the skin barrier is breached. Linkages between skin microbes, biofilms and disease have not been well established although single-species biofilm formation by skin microbiota in vitro has been extensively studied. Consequently, the purpose of this work was to optimize and validate a simple polymicrobial biofilm keratinocyte model for investigating commensal, pathogen and keratinocyte interactions and for evaluating therapeutic agents or health promoting interventions. The model incorporates the commensals (Staphylococcus epidermidis and Micrococcus luteus) and pathogens (Staphylococcus aureus and Pseudomonas aeruginosa) which form robust polymicrobial biofilms on immortalized keratinocytes (HaCat cells). We observed that the commensals reduce the damage caused to the keratinocyte monolayer by either pathogen. When the commensals were combined with P. aeruginosa and S. aureus, much thinner biofilms were observed than those formed by the pathogens alone. When P. aeruginosa was inoculated with S. epidermidis in the presence or absence of M. luteus, the commensals formed a layer between the keratinocytes and pathogen. Although S. aureus completely inhibited the growth of M. luteus in dual-species biofilms, inclusion of S. epidermidis in triple or quadruple species biofilms, enabled M. luteus to retain viability. Using this polymicrobial biofilm keratinocyte model, we demonstrate that a quorum sensing (QS) deficient S. aureus agr mutant, in contrast to the parent, failed to damage the keratinocyte monolayer unless supplied with the exogenous cognate autoinducing peptide. In addition, we show that treatment of the polymicrobial keratinocyte model with nanoparticles containing an inhibitor of the PQS QS system reduced biofilm thickness and P. aeruginosa localization in mono- and polymicrobial biofilms.

Sonobactericide: An Emerging Treatment Strategy for Bacterial Infections

Ultrasound has been developed as both a diagnostic tool and a potent promoter of beneficial bio-effects for the treatment of chronic bacterial infections. Bacterial infections, especially those involving biofilm on implants, indwelling catheters and heart valves, affect millions of people each year, and many deaths occur as a consequence. Exposure of microbubbles or droplets to ultrasound can directly affect bacteria and enhance the efficacy of antibiotics or other therapeutics, which we have termed sonobactericide. This review summarizes investigations that have provided evidence for ultrasound-activated microbubble or droplet treatment of bacteria and biofilm. In particular, we review the types of bacteria and therapeutics used for treatment and the in vitro and pre-clinical experimental setups employed in sonobactericide research. Mechanisms for ultrasound enhancement of sonobactericide, with a special emphasis on acoustic cavitation and radiation force, are reviewed, and the potential for clinical translation is discussed.

Biofilm Formation and Quantification Using the 96-Microtiter Plate

Biofilm formation in microtiter plates is certainly the most commonly used method to grow and study biofilm. This simple design is very popular due to its high-throughput screening capacities, low cost, and easy handling. In the protocol described here, we focus on the use of 96-well optically clear, polystyrene flat-bottom plate to study biofilm formation by Leptospira spp. and quantify the biofilm formation by crystal violet (CV) staining. We also describe an alternative method, based on phase contrast image analysis that we believe is more suitable for accurately quantifying biofilm growth by reducing handling of this fragile structure.

An in vitro collagen perfusion wound biofilm model; with applications for antimicrobial studies and microbial metabolomics

Background

The majority of in vitro studies of medically relevant biofilms involve the development of biofilm on an inanimate solid surface. However, infection in vivo consists of biofilm growth on, or suspended within, the semi-solid matrix of the tissue, whereby current models do not effectively simulate the nature of the in vivo environment. This paper describes development of an in vitro method for culturing wound associated microorganisms in a system that combines a semi-solid collagen gel matrix with continuous flow of simulated wound fluid. This enables culture of wound associated reproducible steady state biofilms under conditions that more closely simulate the dynamic wound environment. To demonstrate the use of this model the antimicrobial kinetics of ceftazidime, against both mature and developing Pseudomonas aeruginosa biofilms, was assessed. In addition, we have shown the potential application of this model system for investigating microbial metabolomics by employing selected ion flow tube mass spectrometry (SIFT-MS) to monitor ammonia and hydrogen cyanide production by Pseudomonas aeruginosa biofilms in real-time.

Results

The collagen wound biofilm model facilitates growth of steady-state reproducible Pseudomonas aeruginosa biofilms under wound like conditions. A maximum biofilm density of 10¹⁰ cfu slide^− 1 was achieved by 30 h of continuous culture and maintained throughout the remainder of the experiment. Treatment with ceftazidime at a clinically relevant dose resulted in a 1.2–1.6 log reduction in biofilm density at 72 h compared to untreated controls. Treatment resulted in loss of complex biofilm architecture and morphological changes to bacterial cells, visualised using confocal microscopy. When monitoring the biofilms using SIFT-MS, ammonia and hydrogen cyanide levels peaked at 12 h at 2273 ppb (±826.4) and 138 ppb (±49.1) respectively and were detectable throughout experimentation.

Conclusions

The collagen wound biofilm model has been developed to facilitate growth of reproducible biofilms under wound-like conditions. We have successfully used this method to: (1) evaluate antimicrobial efficacy and kinetics, clearly demonstrating the development of antimicrobial tolerance in biofilm cultures; (2) characterise volatile metabolite production by P. aeruginosa biofilms, demonstrating the potential use of this method in metabolomics studies.

The future of biofilm research - Report on the '2019 Biofilm Bash'

In May 2019, 29 scientists with expertise in various subdisciplines of biofilm research got together in Leavenworth (WA, USA) at an event designated as the ‘2019 Biofilm Bash’. The goal of this informal two-day meeting was first to identify gaps in our knowledge, and then to come up with ways how the biofilm community can fill these gaps. The meeting was organized around six questions that covered the most important items brought forward by the organizers and participants. The outcome of these discussions is summarized in the present paper. We are aware that these views represent a small subset of our field, and that inevitably we will have inadvertently overlooked important developing research areas and ideas. We are nevertheless hopeful that this report will stimulate discussions and help create new ways of how we can advance our field.

Phenazine Antibiotic-Inspired Discovery of Bacterial Biofilm-Eradicating Agents

Bacterial biofilms are surface-attached communities of slow-growing and non-replicating persister cells that demonstrate high levels of antibiotic tolerance. Biofilms occur in nearly 80 % of infections and present unique challenges to our current arsenal of antibiotic therapies, all of which were initially discovered for their abilities to target rapidly dividing, free-floating planktonic bacteria. Bacterial biofilms are credited as the underlying cause of chronic and recurring bacterial infections. Innovative approaches are required to identify new small molecules that operate through bacterial growth-independent mechanisms to effectively eradicate biofilms. One source of inspiration comes from within the lungs of young cystic fibrosis (CF) patients, who often endure persistent Staphylococcus aureus infections. As these CF patients age, Pseudomonas aeruginosa co-infects the lungs and utilizes phenazine antibiotics to eradicate the established S. aureus infection. Our group has taken a special interest in this microbial competition strategy and we are investigating the potential of phenazine antibiotic-inspired compounds and synthetic analogues thereof to eradicate persistent bacterial biofilms. To discover new biofilm-eradicating agents, we have established an interdisciplinary research program involving synthetic medicinal chemistry, microbiology and molecular biology. From these efforts, we have identified a series of halogenated phenazines (HPs) that potently eradicate bacterial biofilms, and future work aims to translate these preliminary findings into ground-breaking clinical advances for the treatment of persistent biofilm infections.

Pathogen displacement during intermittent catheter insertion: a novel in vitro urethra model

AIM

To develop a novel in vitro urethra model and use it to determine if insertion of an intermittent urinary catheter (IC) displaces pathogenic bacteria from the urethral meatus along the urethra.

METHODS

Displacement of microbial growth after catheter insertion was assessed using a novel in vitro urethra model. The in vitro urethra model utilized chromogenic agar and was inoculated with bacteria at one side of the artificial urethra channel, to act as a contaminated urethral meatus, before an IC was inserted into the channel. Three ICs types were used to validate the in vitro urethra model and methodology.

RESULTS

When compared to the bacterial growth control, a significant difference in bacterial growth was found after insertion of the uncoated (P ≤ 0·001) and hydrophilic coated (P ≤ 0·009) catheters; no significant difference when a prototype catheter was inserted into the in vitro urethra model with either bacterial species tested (P ≥ 0·423).

CONCLUSION

The results presented support the hypothesis that a single catheter insertion can initiate a catheter-associated urinary tract infection.

SIGNIFICANCE AND IMPACT OF THE STUDY

The in vitro urethra model and associated methodology were found to be reliable and reproducible (P ≥ 0·265) providing new research tool for the development and validation of emerging technologies in urological healthcare.

New advances on the Brettanomyces bruxellensis biofilm mode of life

The wine spoilage yeast Brettanomyces bruxellensis can be found at several steps in the winemaking process due to its resistance to multiple stress conditions. The ability to form biofilm is a potential resistance strategy, although it has been given little attention so far for this yeast. In this work, the capacity to form biofilm and its structure were explored in YPD medium and in wine. Using microsatellite analysis, 65 isolates were discriminated into 5 different genetic groups from which 12 strains were selected. All 12 strains were able to form biofilm in YPD medium on a polystyrene surface. The presence of microcolonies, filamentous cells and extracellular polymeric substances, constituting the structure of the biofilm despite a small thickness, were highlighted using confocal and electronic microscopy. Moreover, different cell morphologies according to genetic groups were highlighted. The capacity to form biofilm in wine was also revealed for two selected strains. The impact of wine on biofilms was demonstrated with firstly considerable biofilm cell release and secondly growth of these released biofilm cells, both in a strain dependent manner. Finally, B. bruxellensis has been newly described as a producer of chlamydospore-like structures in wine, for both planktonic and biofilm lifestyles.

Anti-quorum Sensing and Antimicrobial Effect of Mediterranean Plant Essential Oils Against Phytopathogenic Bacteria

Essential oils (EOs) are one of the most interesting natural products extracted from different aromatic plants. For centuries, EOs have been considered an essential part of the traditional pharmacopeia. Many plant EOs have been reported as possible effective alternatives for commercial pesticides, and their single constituents have been used efficiently in food preservation for their promising anti-QS activity against several food pathogenic microorganisms. The current mini review gives a general overview over the microbicide effect as well as anti-quorum sensing and the anti-biofilm formation of some common plant EOs, especially those of Lamiaceae and Verbanaceae families; these are commonly grown in the Mediterranean region and are effective against some serious food phytopathogenic bacteria.

Bactericidal and Anti-biofilm Activity of the Retinoid Compound CD437 Against Enterococcus faecalis

Enterococcus faecalis (E. faecalis), a biofilm-forming pathogen, causes nosocomial infections. In recent years, drug resistance by enterococci has become increasingly severe due to widespread antibiotic abuse. Therefore, novel antibacterial agents are urgently needed. In this study, the synthetic retinoid compound CD437 was found to have potent bactericidal effect on E. faecalis. In addition, CD437 exhibited synergistic effects when administered in combination with gentamicin and additive effects when combined with ceftriaxone sodium. CD437 also inhibited biofilm formation by E. faecalis and exerted bactericidal effect on mature biofilm. Moreover, CD437 exhibited antibacterial and anti-biofilm effects against Staphylococcus. No bactericidal action of CD437 was observed against the gram-negative bacillus, but Pseudomonas aeruginosa biofilm extracellular polymeric substances (EPS) matrix formation was reduced. Overall, these findings indicate that CD437 has the potential to be developed as a novel antibacterial drug.

Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing

The selective regulation of bacteria in complex microbial populations is key to controlling pathogenic bacteria. CRISPR nucleases can be programmed to kill bacteria, but require an efficient and broad-host range delivery system to be effective. Here, using an Escherichia coli and Salmonella enterica co-culture system, we show that plasmids based on the IncP RK2 conjugative system can be used as delivery vectors for a TevSpCas9 dual nuclease. Notably, a cis-acting plasmid that encodes the conjugation and CRISPR machinery conjugates from E. coli to S. enterica with high frequency compared to a trans system that separates conjugation and CRISPR machinery. In culture conditions that enhance cell-to-cell contact, conjugation rates approach 100% with the cis-acting plasmid. Targeting of single or multiplexed sgRNAs to non-essential genes results in high S. enterica killing efficiencies. Our data highlight the potential of cis-acting conjugative plasmids as a delivery system for CRISPR nucleases or other microbial-altering agents for targeted bacterial killing.