Microbial Interkingdom Biofilms and the Quest for Novel Therapeutic Strategies

Cross-kingdom pathogen detection via duplex universal PCR and high-resolution melt

Infectious diseases caused by pathogenic bacteria and fungi continuously pose a significant threat worldwide. The occurrence of polymicrobial infections, including polybacterial, polyfungal or bacteria-fungal co-infections further complicates diagnosis and treatment. Current diagnostic methods, heavily reliant on culture methods, are slow and often inefficient. This inefficiency underscores the urgent need for new diagnostic approaches that can swiftly identify a wide array of pathogens across both the bacterial and fungal kingdoms. In response to this need, our study introduces a duplex universal PCR and high-resolution melt (HRM) method that enables the detection of both bacterial and fungal pathogens within a single PCR-HRM procedure. This method uses two universal primer sets designed to target bacterial and fungal genomic DNA respectively, facilitating broad-range detection of 16 pathogens flagged by the World Health Organization (WHO). Moreover, this assay can be adapted in microfluidic-based digital reaction format and when analyzed via a one-versus-one support vector machine classifier achieved a detection accuracy exceeding 99.9%. This digital duplex PCR-HRM method has the capacity to quantitatively detect co-infections with varying pathogen ratios in simulated samples, demonstrating its versatility and multiplexed capacity. When applied to clinical bronchoalveolar lavage (BAL) samples, digital duplex PCR-HRM successfully identified both monomicrobial and polymicrobial infections. This development marks a significant advancement in the field of infectious disease diagnostics, offering a rapid, accurate, and comprehensive method for identifying a broad spectrum of bacterial and fungal pathogens, thus potentially improving patient management and outcomes.

Surface-Charge Tuned Polymeric Nanoemulsions for Carvacrol Delivery in Interkingdom Biofilms

Biofilms, intricate microbial communities entrenched in extracellular polymeric substance (EPS) matrices, pose formidable challenges in infectious disease treatment, especially in the context of interkingdom biofilms prevalent in the oral environment. This study investigates the potential of carvacrol-loaded biodegradable nanoemulsions (NEs) with systematically varied surface charges─cationic guanidinium (GMT-NE) and anionic carboxylate (CMT-NE). Zeta potentials of +25 mV (GMT-NE) and -33 mV (CMT-NE) underscore successful nanoemulsion fabrication (∼250 nm). Fluorescent labeling and dynamic tracking across three dimensions expose GMT-NE's superior diffusion into oral biofilms, yielding a robust antimicrobial effect with 99.99% killing for both streptococcal and Candida species and marked reductions in bacterial cell viability compared to CMT-NE (∼4-log reduction). Oral mucosa tissue cultures affirm the biocompatibility of both NEs with no morphological or structural changes, showcasing their potential for combating intractable biofilm infections in oral environment. This study advances our understanding of NE surface charges and their interactions within interkingdom biofilms, providing insights crucial for addressing complex infections involving bacteria and fungi in the demanding oral context.

Nanomaterials Regulate Bacterial Quorum Sensing: Applications, Mechanisms, and Optimization Strategies

Anti-virulence therapy that interferes with bacterial communication, known as "quorum sensing (QS)", is a promising strategy for circumventing bacterial resistance. Using nanomaterials to regulate bacterial QS in anti-virulence therapy has attracted much attention, which is mainly attributed to unique physicochemical properties and excellent designability of nanomaterials. However, bacterial QS is a dynamic and multistep process, and there are significant differences in the specific regulatory mechanisms and related influencing factors of nanomaterials in different steps of the QS process. An in-depth understanding of the specific regulatory mechanisms and related influencing factors of nanomaterials in each step can significantly optimize QS regulatory activity and enhance the development of novel nanomaterials with better comprehensive performance. Therefore, this review focuses on the mechanisms by which nanomaterials regulate bacterial QS in the signal supply (including signal synthesis, secretion, and accumulation) and signal transduction cascade (including signal perception and response) processes. Moreover, based on the two key influencing factors (i.e., the nanomaterial itself and the environment), optimization strategies to enhance the QS regulatory activity are comprehensively summarized. Collectively, applying nanomaterials to regulate bacterial QS is a promising strategy for anti-virulence therapy. This review provides reference and inspiration for further research on the anti-virulence application of nanomaterials.

Supramolecular Self-Associating Amphiphiles Inhibit Biofilm Formation by the Critical Pathogens, Pseudomonas aeruginosa and Candida albicans

In 2019, 4.95 million deaths were directly attributed to antimicrobial-resistant bacterial infections globally. In addition, the mortality associated with fungal infections is estimated at 1.7 million annually, with many of these deaths attributed to species that are no longer susceptible to traditional therapeutic regimes. Herein, we demonstrate the use of a novel class of supramolecular self-associating amphiphilic (SSA) salts as antimicrobial agents against the critical pathogens Pseudomonas aeruginosa and Candida albicans. We also identify preliminary structure-activity relationships for this class of compound that will aid the development of next-generation SSAs demonstrating enhanced antibiofilm activity. To gain insight into the possible mode of action for these agents, a series of microscopy studies were performed, taking advantage of the intrinsic fluorescent nature of benzothiazole-substituted SSAs. Analysis of these data showed that the SSAs interact with the cell surface and that a benzothiazole-containing SSA inhibits hyphal formation by C. albicans.

Bioactive Compounds from an Endophytic Pezicula sp. Showing Antagonistic Effects against the Ash Dieback Pathogen

A fungal endophyte originating from the Canary Islands was identified as a potent antagonist against the fungal phytopathogen Hymenoscyphus fraxineus, which causes the devastating ash dieback disease. This endophyte was tentatively identified as Pezicula cf. ericae, using molecular barcoding. Isolation of secondary metabolites by preparative high-performance liquid chromatography (HPLC) yielded the known compounds CJ-17,572 (1), mycorrhizin A (3) and cryptosporioptides A-C (4-6), besides a new N-acetylated dihydroxyphenylalanin derivative 2, named peziculastatin. Planar structures were elucidated by NMR and HRMS data, while the relative stereochemistry of 2 was assigned by H,H and C,H coupling constants. The assignment of the unknown stereochemistry of CJ-17,572 (1) was hampered by the broadening of NMR signals. Nevertheless, after semisynthetic conversion of 1 into its methyl derivatives 7 and 8, presumably preventing tautomeric effects, the relative configuration could be assigned, whereas comparison of ECD data to those of related compounds determined the absolute configuration. Metabolites 1 and 3 showed significant antifungal effects in vitro against H. fraxineus. Furthermore, 4-6 exhibited significant dispersive effects on preformed biofilms of S. aureus at concentrations up to 2 µg/mL, while the biofilm formation of C. albicans was also inhibited. Thus, cryptosporioptides might constitute a potential source for the development of novel antibiofilm agents.

Lung microbiota and potential treatment of respiratory diseases

The unique microbiome found in the lungs has been studied and shown to be associated with both pulmonary homeostasis and lung diseases. The lung microbiome has the potential to produce metabolites that modulate host-microbe interactions. Specifically, short-chain fatty acids (SCFAs) produced by certain strains of the lung microbiota have been shown to regulate immune function and maintain gut mucosal health. In response, this review described the distribution and composition of the microbiota in lung diseases and discussed the impact of the lung microbiota on health and lung disease. In addition, the review further elaborated on the mechanism of microbial metabolites in microbial-host interaction and their application in the treatment of lung diseases. A better understanding of the interaction between the microbiota, metabolites, and host will provide potential strategies for the development of novel methods for the treatment of pulmonary microbial induced lung diseases.

In vitro evaluation of biofilm formation by Candida parapsilosis and Enterobacter cloacae. Scanning electron microscopy and efficacy of antimicrobial combinations study

Fungal-bacterial infections are being increasingly recognized in clinical settings, and the interaction between these species in polymicrobial biofilms often lead to infections that are highly resistant to treatment. In this in vitro study, we analyzed the formation of mixed biofilms using clinically isolated Candida parapsilosis and Enterobacter cloacae. Additionally, we assessed the potential of conventional antimicrobials, both alone and in combination, for treating polymicrobial biofilms built by these human pathogens. Our results demonstrate that C. parapsilosis and E. cloacae are capable of forming mixed biofilms, as confirmed by scanning electron microscopy. Interestingly, we found that colistin alone or in combination with antifungal drugs was highly effective reducing up to 80% of the total biomass of polymicrobial biofilms.

Mitigation and use of biofilms in space for the benefit of human space exploration

Biofilms are self-organized communities of microorganisms that are encased in an extracellular polymeric matrix and often found attached to surfaces. Biofilms are widely present on Earth, often found in diverse and sometimes extreme environments. These microbial communities have been described as recalcitrant or protective when facing adversity and environmental exposures. On the International Space Station, biofilms were found in human-inhabited environments on a multitude of hardware surfaces. Moreover, studies have identified phenotypic and genetic changes in the microorganisms under microgravity conditions including changes in microbe surface colonization and pathogenicity traits. Lack of consistent research in microgravity-grown biofilms can lead to deficient understanding of altered microbial behavior in space. This could subsequently create problems in engineered systems or negatively impact human health on crewed spaceflights. It is especially relevant to long-term and remote space missions that will lack resupply and service. Conversely, biofilms are also known to benefit plant growth and are essential for human health (i.e., gut microbiome). Eventually, biofilms may be used to supply metabolic pathways that produce organic and inorganic components useful to sustaining life on celestial bodies beyond Earth. This article will explore what is currently known about biofilms in space and will identify gaps in the aerospace industry's knowledge that should be filled in order to mitigate or to leverage biofilms to the advantage of spaceflight.

Candida albicans-enteric viral interactions-The prostaglandin E2 connection and host immune responses

The human microbiome comprises trillions of microorganisms residing within different mucosal cavities and across the body surface. The gut microbiota modulates host susceptibility to viral infections in several ways, and microbial interkingdom interactions increase viral infectivity within the gut. Candida albicans, a frequently encountered fungal species in the gut, produces highly structured biofilms and eicosanoids such as prostaglandin E₂ (PGE₂), which aid in viral protection and replication. These biofilms encompass viruses and provide a shield from antiviral drugs or the immune system. PGE₂ is a key modulator of active inflammation with the potential to regulate interferon signaling upon microbial invasion or viral infections. In this review, we raise the perspective of gut interkingdom interactions involving C. albicans and enteric viruses, with a special focus on biofilms, PGE₂, and viral replication. Ultimately, we discuss the possible implications of C. albicans-enteric virus associations on host immune responses, particularly the interferon signaling pathway.

Valorization of Invasive Plant Extracts against the Bispecies Biofilm Staphylococcus aureus-Candida albicans by a Bioguided Molecular Networking Screening

Invasive plants efficiently colonize non-native territories, suggesting a great production of bioactive metabolites which could be effective antibiofilm weapons. Our study aimed to look for original molecules able to inhibit bispecies biofilm formed by S. aureus and C. albicans. Extracts from five invasive macrophytes (Ludwigia peploides, Ludwigia grandiflora, Myriophyllum aquaticum, Lagarosiphon major and Egeria densa) were prepared and tested in vitro against 24 h old bispecies biofilms using a crystal violet staining (CVS) assay. The activities of the extracts reducing the biofilm total biomass by 50% or more were comparatively analyzed against each microbial species forming the biofilm by flow cytometry (FCM) and scanning electron microscopy. Extracts active against both species were fractionated. Obtained fractions were analyzed by UHPLC-MS/MS and evaluated by the CVS assay. Chemical and biological data were combined into a bioactivity-based molecular networking (BBMN) to identify active compounds. The aerial stem extract of L. grandiflora showed the highest antibiofilm activity (>50% inhibition at 50 µg∙mL−1). The biological, chemical and BBMN investigations of its fractions highlighted nine ions correlated with the antibiofilm activity. The most correlated compound, identified as betulinic acid (BA), inhibited bispecies biofilms regardless of the three tested couples of strains (ATCC strains: >40% inhibition, clinical isolates: ≈27% inhibition), confirming its antibiofilm interest.

Nanoparticle-Based Inhalation Therapy for Pulmonary Diseases

The lung is exposed to various pollutants and is the primary site for the onset of various diseases, including infections, allergies, and cancers. One possible treatment approach for such pulmonary diseases involves direct administration of therapeutics to the lung so as to maintain the topical concentration of the drug. Particles with nanoscale diameters tend to reach the pulmonary region. Nanoparticles (NPs) have garnered significant interest for applications in biomedical and pharmaceutical industries because of their unique physicochemical properties and biological activities. In this article, we describe the biological and pharmacological activities of NPs as well as summarize their potential in the formulation of drugs employed to treat pulmonary diseases. Recent advances in the use of NPs in inhalation chemotherapy for the treatment of lung diseases have also been highlighted.

An Overview of Biofilm Formation-Combating Strategies and Mechanisms of Action of Antibiofilm Agents

Biofilm formation on surfaces via microbial colonization causes infections and has become a major health issue globally. The biofilm lifestyle provides resistance to environmental stresses and antimicrobial therapies. Biofilms can cause several chronic conditions, and effective treatment has become a challenge due to increased antimicrobial resistance. Antibiotics available for treating biofilm-associated infections are generally not very effective and require high doses that may cause toxicity in the host. Therefore, it is essential to study and develop efficient anti-biofilm strategies that can significantly reduce the rate of biofilm-associated healthcare problems. In this context, some effective combating strategies with potential anti-biofilm agents, including plant extracts, peptides, enzymes, lantibiotics, chelating agents, biosurfactants, polysaccharides, organic, inorganic, and metal nanoparticles, etc., have been reviewed to overcome biofilm-associated healthcare problems. From their extensive literature survey, it can be concluded that these molecules with considerable structural alterations might be applied to the treatment of biofilm-associated infections, by evaluating their significant delivery to the target site of the host. To design effective anti-biofilm molecules, it must be assured that the minimum inhibitory concentrations of these anti-biofilm compounds can eradicate biofilm-associated infections without causing toxic effects at a significant rate.

Poly(DL-lactic acid) scaffolds as a bone targeting platform for the co-delivery of antimicrobial agents against S. aureus-C. albicans mixed biofilms

New strategies for the treatment of polymicrobial bone infections are required. In this study, the co-delivery of two antimicrobials by poly(D,L-lactic acid) (PDLLA) scaffolds was investigated in a polymicrobial biofilm model. PDLLA scaffolds were prepared by solvent casting/particulate leaching methodology, incorporating minocycline and voriconazole as clinically relevant antimicrobial agents. The scaffolds presented a sponge-like appearance, suitable to support cell proliferation and drug release. Single- and dual-species biofilm models of Staphylococcus aureus and Candida albicans were developed and characterized. S. aureus presented a higher ability to form single-species biofilms, compared to C. albicans. Minocycline and voriconazole-loaded PDLLA scaffolds showed activity against S. aureus and C. albicans single- and dual-biofilms. Ultimately, the cytocompatibility/functional activity of PDLLA scaffolds observed in human MG-63 osteosarcoma cells unveil their potential as a next-generation co-delivery system for antimicrobial therapy in bone infections.

A novel antibacterial and antifouling nanocomposite coated endotracheal tube to prevent ventilator-associated pneumonia

Background

The endotracheal tube (ETT) is an essential medical device to secure the airway patency in patients undergoing mechanical ventilation or general anesthesia. However, long-term intubation eventually leads to complete occlusion, ETTs potentiate biofilm-related infections, such as ventilator-associated pneumonia. ETTs are mainly composed of medical polyvinyl chloride (PVC), which adheres to microorganisms to form biofilms. Thus, a simple and efficient method was developed to fabricate CS-AgNPs@PAAm-Gelatin nanocomposite coating to achieve dual antibacterial and antifouling effects.

Results

The PAAm-Gelatin (PAAm = polyacrylamide) molecular chain gel has an interpenetrating network with a good hydrophilicity and formed strong covalent bonds with PVC-ETTs, wherein silver nanoparticles were used as antibacterial agents. The CS-AgNPs@PAAm-Gelatin coating showed great resistance and antibacterial effects against Staphylococcus aureus and Pseudomonas aeruginosa. Its antifouling ability was tested using cell, protein, and platelet adhesion assays. Additionally, both properties were comprehensively evaluated using an artificial broncho-lung model in vitro and a porcine mechanical ventilation model in vivo. These remarkable results were further confirmed that the CS-AgNPs@PAAm-Gelatin coating exhibited an excellent antibacterial capacity, an excellent stain resistance, and a good biocompatibility.

Conclusions

The CS-AgNPs@PAAm-Gelatin nanocomposite coating effectively prevents the occlusion and biofilm-related infection of PVC-ETTs by enhancing the antibacterial and antifouling properties, and so has great potential for future clinical applications.

Graphical Abstract

Quorum sensing: a new perspective to reveal the interaction between gut microbiota and host

Quorum sensing (QS), a chemical communication process between bacteria, depends on the synthesis, secretion and detection of signal molecules. It can synchronize the gene expression of bacteria to promote cooperation within the population and improve competitiveness among populations. The preliminary exploration of bacterial QS has been completed under ideal and highly controllable conditions. There is an urgent need to investigate the QS of bacteria under natural conditions, especially the QS of intestinal flora, which is closely related to health. Excitingly, growing evidence has shown that QS also exists in the intestinal flora. The crosstalk of QS between gut microbiota and the host is systematically clarified in this review.

Facile Biofilm Penetration of Cationic Liposomes Loaded with DNase I/Proteinase K to Eradicate Cutibacterium acnes for Treating Cutaneous and Catheter Infections

Background

The biofilm produced by Cutibacterium acnes is a major infection threat for skin and implanted catheters. Nanoparticles provide a new approach to eradicate biofilms. The present study evaluated the capability of cationic liposomes loaded with DNase I (DNS) and proteinase K (PK) to remove preformed C. acnes biofilms.

Methods

DNS and PK were able to target and disassemble the biofilm by degrading extracellular polymer substances (EPS). Soyaethyl morpholinium ethosulfate (SME) was used to render a positive charge and enhance the antibacterial activity of the liposomes.

Results

The cationic liposomes containing enzymes yielded monodisperse nanovesicles ranging between 95 and 150 nm. The entrapment efficiency of the enzymes in the liposomes achieved a value of 67–83%. All liposomal formulations suppressed planktonic C. acnes growth at a minimum inhibitory concentration (MIC) equal to the free SME in the solution. The enzyme in the liposomal form inhibited biofilm growth much better than that in the free form, with the dual enzyme-loaded liposomes demonstrating the greatest inhibition of 54% based on a crystal violet assay. The biofilm-related virulence genes PA380 and PA1035 were downregulated by the combined enzymes in the liposomes but not the individual DNS or PK. Scanning electron microscopy (SEM) and confocal microscopy displayed reduced C. acnes aggregates and biofilm thickness by the liposomal system. The liposomes could penetrate through about 85% of the biofilm thickness. The in vitro pig skin permeation also showed a facile delivery of liposomes into the epidermis, deeper skin strata, and hair follicles. The liposomes exhibited potent activity to eliminate C. acnes colonization in mouse skin and catheters in vivo. The colony-forming units (CFUs) in the catheter treated with the liposomes were reduced by 2 logs compared to the untreated control.

Conclusion

The data suggested a safe application of the enzyme-loaded cationic liposomes as antibacterial and antibiofilm agents.

The Antibiofilm Nanosystems for Improved Infection Inhibition of Microbes in Skin

Biofilm formation is an important virulence factor for the opportunistic microorganisms that elicit skin infections. The recalcitrant feature of biofilms and their antibiotic tolerance impose a great challenge on the use of conventional therapies. Most antibacterial agents have difficulty penetrating the matrix produced by a biofilm. One novel approach to address these concerns is to prevent or inhibit the formation of biofilms using nanoparticles. The advantages of using nanosystems for antibiofilm applications include high drug loading efficiency, sustained or prolonged drug release, increased drug stability, improved bioavailability, close contact with bacteria, and enhanced accumulation or targeting to biomasses. Topically applied nanoparticles can act as a strategy for enhancing antibiotic delivery into the skin. Various types of nanoparticles, including metal oxide nanoparticles, polymeric nanoparticles, liposomes, and lipid-based nanoparticles, have been employed for topical delivery to treat biofilm infections on the skin. Moreover, nanoparticles can be designed to combine with external stimuli to produce magnetic, photothermal, or photodynamic effects to ablate the biofilm matrix. This study focuses on advanced antibiofilm approaches based on nanomedicine for treating skin infections. We provide in-depth descriptions on how the nanoparticles could effectively eliminate biofilms and any pathogens inside them. We then describe cases of using nanoparticles for antibiofilm treatment of the skin. Most of the studies included in this review were supported by in vivo animal infection models. This article offers an overview of the benefits of nanosystems for treating biofilms grown on the skin.

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.

Synthesis of the fungal macrolide berkeleylactone A and its inhibition of microbial biofilm formation

The fungal macrolide berkeleylactone A was synthesised in 13 steps and 24% yield using (R)-propylene oxide and an asymmetric Noyori hydrogenation of a β-ketoester to install the stereogenic centres. A domino addition-Wittig olefination of a 13-hydroxytetradecanal intermediate with the cumulated ylide Ph3PCCO closed the macrocyle by establishing the α,β-unsaturated ester group, necessary for the attachment of the sidechain thiol via a thia-Michael reaction. The synthetic berkeleylactone A inhibited the formation of Staphylococcus aureus biofilms and showed significant dispersive effects on preformed biofilms of Candida albicans by at least 45% relative to untreated controls at concentrations as low as 1.3 μg mL-1.