Targeting Acyl Homoserine Lactones (AHLs) by the quorum quenching bacterial strains to control biofilm formation in Pseudomonas aeruginosa

E.PathDash, pathway activation analysis of publicly available pathogen gene expression data

E.PathDash facilitates re-analysis of gene expression data from pathogens clinically relevant to chronic respiratory diseases, including a total of 48 studies, 548 samples, and 404 unique treatment comparisons. The application enables users to assess broad biological stress responses at the KEGG pathway or gene ontology level and also provides data for individual genes. E.PathDash reduces the time required to gain access to data from multiple hours per data set to seconds. Users can download high-quality images such as volcano plots and boxplots, differential gene expression results, and raw count data, making it fully interoperable with other tools. Importantly, users can rapidly toggle between experimental comparisons and different studies of the same phenomenon, enabling them to judge the extent to which observed responses are reproducible. As a proof of principle, we invited two cystic fibrosis scientists to use the application to explore scientific questions relevant to their specific research areas. Reassuringly, pathway activation analysis recapitulated results reported in original publications, but it also yielded new insights into pathogen responses to changes in their environments, validating the utility of the application. All software and data are freely accessible, and the application is available at scangeo.dartmouth.edu/EPathDash.

IMPORTANCE

Chronic respiratory illnesses impose a high disease burden on our communities and people with respiratory diseases are susceptible to robust bacterial infections from pathogens, including Pseudomonas aeruginosa and Staphylococcus aureus, that contribute to morbidity and mortality. Public gene expression datasets generated from these and other pathogens are abundantly available and an important resource for synthesizing existing pathogenic research, leading to interventions that improve patient outcomes. However, it can take many hours or weeks to render publicly available datasets usable; significant time and skills are needed to clean, standardize, and apply reproducible and robust bioinformatic pipelines to the data. Through collaboration with two microbiologists, we have shown that E.PathDash addresses this problem, enabling them to elucidate pathogen responses to a variety of over 400 experimental conditions and generate mechanistic hypotheses for cell-level behavior in response to disease-relevant exposures, all in a fraction of the time.

Marine-derived bioactive materials as antibiofilm and antivirulence agents

Microbial infections are major human health issues, and, recently, the mortality rate owing to bacterial and fungal infections has been increasing. In addition to intrinsic and extrinsic antimicrobial resistance mechanisms, biofilm formation is a key adaptive resistance mechanism. Several bioactive compounds from marine organisms have been identified for use in biofilm therapy owing to their structural complexity, biocompatibility, and economic viability. In this review, we discuss recent trends in the application of marine natural compounds, marine-bioinspired nanomaterials, and marine polymer conjugates as possible therapeutic agents for controlling biofilms and virulence factors. We also comprehensively discuss the mechanisms underlying biofilm formation and inhibition of virulence factors by marine-derived materials and propose possible applications of novel and effective antibiofilm and antivirulence agents.

An insight on the powerful of bacterial quorum sensing inhibition

Bacteria have their own language through which they communicate with one another like all higher organisms. So, many researchers are working hard to identify and comprehend the components of this bacterial communication, known as quorum sensing (QS). In quorum sensing, bacteria use signaling molecules called autoinducers (AIs) to exchange information. Many natural compounds and extraction techniques have been intensively studied to disrupt bacterial signaling and examine their effectiveness for bacterial pathogenesis control. Quorum sensing inhibitors can interfere with QS and block the action of AI signaling molecules. Recent research indicates that quorum sensing inhibitors (QSIs) and quorum quenching enzymes (QQEs) show great promise in reducing the pathogenicity of bacteria and inhibiting biofilm synthesis. In addition, the effectiveness of QQEs and QSIs in experimental animal models was demonstrated. These are taken into account in the development of innovative medical devices, such as dressings and catheters, to prevent bacterial infections. The present review highlights this aspect with a prospective vision for its development and application.

DHTPY-Cu@ZOL-Enhanced Photodynamic Therapy: A Strategic Platform for Advanced Treatment of Drug-Resistant Bacterial Wound Infections

Purpose

This research was to innovate a nanozyme-based therapeutic strategy that combines aggregation-induced emission (AIE) photosensitizers with copper nanozymes. This approach is designed to address the hypoxic conditions often found in bacterial infections and aims to boost the effectiveness of photodynamic therapy (PDT) by ensuring sufficient oxygen supply for reactive oxygen species (ROS) generation.

Methods

Our approach involved the synthesis of dihydroxyl triphenyl vinyl pyridine (DHTPY)-Cu@zoledronic acid (ZOL) nanozyme particles. We initially synthesized DHTPY and then combined it with copper nanozymes to form the DHTPY-Cu@ZOL composite. The nanozyme's size, morphology, and chemical properties were characterized using various techniques, including dynamic light scattering, transmission electron microscopy, and X-ray photoelectron spectroscopy. We conducted a series of in vitro and in vivo tests to evaluate the photodynamic, antibacterial, and wound-healing properties of the DHTPY-Cu@ZOL nanozymes, including their oxygen-generation capacity, ROS production, and antibacterial efficacy against methicillin-resistant Staphylococcus aureus (MRSA).

Results

The DHTPY-Cu@ZOL exhibited proficient H2O2 scavenging and oxygen generation, crucial for enhancing PDT in oxygen-deprived infection environments. Our in vitro analysis revealed a notable antibacterial effect against MRSA, suggesting the nanozymes' potential to disrupt bacterial cell membranes. Further, in vivo studies using a diabetic rat model with MRSA-infected wounds showed that DHTPY-Cu@ZOL markedly improved wound healing and reduced bacterial presence, underscoring its efficacy as a non-antibiotic approach for chronic infections.

Conclusion

Our study suggests that DHTPY-Cu@ZOL is a highly promising approach for combating antibiotic-resistant microbial pathogens and biofilms. The biocompatibility and stability of these nanozyme particles, coupled with their improved PDT efficacy position them as a promising candidate for clinical applications.

Anti-Biofilm Strategies: A Focused Review on Innovative Approaches

Biofilm (BF) can give rise to systemic infections, prolonged hospitalization times, and, in the worst case, death. This review aims to provide an overview of recent strategies for the prevention and destruction of pathogenic BFs. First, the main phases of the life cycle of BF and maturation will be described to identify potential targets for anti-BF approaches. Then, an approach acting on bacterial adhesion, quorum sensing (QS), and the extracellular polymeric substance (EPS) matrix will be introduced and discussed. Finally, bacteriophage-mediated strategies will be presented as innovative approaches against BF inhibition/destruction.

Emerging trends in the inhibition of bacterial molecular communication: An overview

Quorum sensing (QS) is a molecular cell-cell communication utilized by several bacteria and some fungi. It involves cell density dependent gene expression that includes extra polymeric substance production, sporulation, antibiotic production, motility, competence, symbiosis and conjugation. These expressions were carried out by different signaling molecules like acyl homo-serine lactone (AHL) and auto-inducing peptides (AIPs) which was effluxed by gram negative and gram positive bacteria. Pathogenic bacteria and biofilms often exhibit high resistance to antibiotics, attributed to the presence of antibiotic efflux pumps, reduced membrane permeability, and enzymes that deactivate quorum sensing (QS) inhibitors. To counteract virulence and multi-drug resistance (MDR), novel strategies such as employing quorum sensing (QS) inhibitors and quorum quenchers are employed. It targets signaling molecules with synthesis and prevents the signal from binding to receptors. In this present review, the mechanisms of QS along with inhibitors from different sources are described. These strategies potentially interfere with QS and it can be applied in different fields, mainly in hospitals and marine environments where the pathogenic infections and biofilm formation are highly involved.

Strategies and materials for the prevention and treatment of biofilms

Biofilms are aggregates of organized microbial growth that function as barriers and create a stable internal environment for cell survival. The bacteria in the biofilms exhibit characteristics that are quite different from the planktonic bacteria, such as strong resistance to antibiotics and other bactericides, getting out of host immunity, and developing in harsh environments, which all contribute to the persistent and intractable treatment. Hence, there is an urgent need to develop novel materials and strategies to combat biofilms. However, most of the reviews on anti-biofilms published in recent years are based on specific fields or materials. Microorganisms are ubiquitous, except in the context of medical and health issues; however, biofilms exert detrimental effects on the advancement and progress of various fields. Therefore, this review aims to provide a comprehensive summary of effective strategies and methodologies applicable across all industries. Firstly, the process of biofilms formation was introduced to enhance our comprehension of the "enemy". Secondly, strategies to intervene in the important links of biofilms formation were discussed, taking timely action during the early weak stages of the "enemy". Thirdly, treatment strategies for mature biofilms were summarized to deal with biofilms that break through the defense line. Finally, several substances with antibacterial properties were presented. The review concludes with the standpoint of the author about potential developments of anti-biofilms strategies. This review may help researchers quickly understand the research progress and challenges in the field of anti-biofilms to design more efficient methods and strategies to combat biofilms.

Nano-immunomodulators: prospective applications to combat drug resistant bacterial infections and related complications

Antimicrobial resistance (AMR) is a growing problem in our healthcare sector, it can make infections more difficult and expensive to treat and lead to treatment failure and increased risk of death. Currently, at least 700,000 people worldwide die each year from AMR. Alternative methods for mitigating drug-resistant bacterial infections are desperately needed because of the unacceptably low rate of conventional antibiotic discovery. Therefore, the implementation of various therapeutic strategies is necessary to deal with drug-resistant bacteria and immunomodulation is one of them which is highly encouraged through various studies. Immunomodulators are different biological or synthetic substances that possess the capability of inducing, suppressing, or overall modulating the innate and adaptive immune system. Some phytochemicals, including flavonoids, glycosides, polysaccharides, terpenoids, essential oils, peptides, synthetic molecules, and synthetic biomaterials, can play a crucial role in the fight against bacterial infections directly or indirectly by enhancing the activity of existing antibiotics or by boosting immunity. Nanotechnology can be used to modulate immune responses through various fabrication methods and strategies of design and for drug formulation by encapsulating potential compounds/molecules in the form of nanoparticles and by surface modification or capping of nanomaterials. This approach can improve drug solubility, stability, and bioavailability, reduce toxicity, and help to increase the effectiveness of drugs against resistant microorganisms. This review aims to provide current developments in the field of immunomodulators of different origins that can be combined with nanotechnology and exploited as potential future drugs or adjuvants to fight drug-resistant bacterial pathogens.

Biofouling in Membrane Bioreactors-Mitigation and Current Status: a Review

Biological fouling as termed biofouling is caused by varied living organisms and is difficult to eliminate from the environment thus becoming a major issue during membrane bioreactors. Biofouling in membrane bioreactors (MBRs) is a crucial problem in increasing liquid pressure due to reduced pore diameter, clogging of the membrane pores, and alteration of the chemical composition of the water which greatly limits the growth of MBRs. Thus, membrane biofouling and/or microbial biofilms is a hot research topic to improve the market competitiveness of the MBR technology. Though several antibiofouling strategies (addition of bioflocculant or sponge into MBRs) came to light, biological approaches are sustainable and more practicable. Among the biological approaches, quorum sensing-based biofouling control (so-called quorum quenching) is an interesting and promising tool in combating biofouling issues in the MBRs. Several review articles have been published in the area of membrane biofouling and mitigation approaches. However, there is no single source of information about biofouling and/or biofilm formation in different environmental settings and respective problems, antibiofilm strategies and current status, quorum quenching, and its futurity. Thus, the objectives of the present review were to provide latest insights on mechanism of membrane biofouling, quorum sensing molecules, biofilm-associated problems in different environmental setting and antibiofilm strategies, special emphasis on quorum quenching, and its futurity in the biofilm/biofouling control. We believe that these insights greatly help in the better understanding of biofouling and aid in the development of sustainable antibiofouling strategies.

A method establishment and application for biofilm quorum quenching activity assay

The existence of quorum sensing (QS) and quorum quenching (QQ) plays important roles in biofilm formation. However, direct detection of QS ability is difficult due to the low concentrations of signal molecules inside the biofilm. Therefore, QQ activity is typically used to indicate the attribution of QS/QQ to the biofilm. Nevertheless, current detection methods of QQ activity based on biosensors present undesirable operability and accuracy. In this study, the 96-well plate assay based on a specific biosensor, Agrobacterium tumefaciens A136, and a colorimetric substance, X-gal was established. The reliable fitting results were obtained by standardizing the composition of the A136 X-gal assay solution and optimizing the operating conditions. This method improved the accuracy of QQ activity detection and reduced time and cost consumption. Finally, the 96-well plate assay was successfully applied to detect the QQ activities of biofilm samples and explore possible environmental influencing factors. In general, this study provided a new strategy for understanding the QQ effect in biofilm systems.

Two legume fatty acid amide hydrolase isoforms with distinct preferences for microbial- and plant-derived acylamides

Fatty acid amide hydrolase (FAAH) is a widely conserved amidase in eukaryotes, perhaps best known for inactivating N-acylethanolamine lipid mediators. However, FAAH enzymes hydrolyze a wide range of acylamide substrates. Analysis of FAAHs from multiple angiosperm species revealed two conserved phylogenetic groups that differed in key conserved residues in the substrate binding pocket. While the foundation group of plant FAAHs, designated FAAH1, has been studied at the structural and functional level in Arabidopsis thaliana, nothing is known about FAAH2 members. Here, we combined computational and biochemical approaches to compare the structural and enzymatic properties of two FAAH isoforms in the legume Medicago truncatula designated MtFAAH1 and MtFAAH2a. Differences in structural and physicochemical properties of the substrate binding pockets, predicted from homology modeling, molecular docking, and molecular dynamic simulation experiments, suggested that these two FAAH isoforms would exhibit differences in their amidohydrolase activity profiles. Indeed, kinetic studies of purified, recombinant MtFAAHs indicated a reciprocal preference for acylamide substrates with MtFAAH1 more efficiently utilizing long-chain acylamides, and MtFAAH2a more efficiently hydrolyzing short-chain and aromatic acylamides. This first report of the enzymatic behavior of two phylogenetically distinct plant FAAHs will provide a foundation for further investigations regarding FAAH isoforms in legumes and other plant species.

Quorum-quenching potential of recombinant PvdQ-engineered bacteria for biofilm formation

Quorum sensing (QS) is a core mechanism for bacteria to regulate biofilm formation, and therefore, QS inhibition or quorum quenching (QQ) is used as an effective and economically feasible strategy against biofilms. In this study, the PvdQ gene encoding AHL acylase was introduced into Escherichia coli (DE3), and a PvdQ-engineered bacterium with highly efficient QQ activity was obtained and used to inhibit biofilm formation. Gene sequencing and western blot analysis showed that the recombinant pET-PvdQ strain was successfully constructed. The color reaction of Agrobacterium tumefaciens A136 indicated that PvdQ engineering bacteria had shown strong AHL signal molecule quenching activity and significantly inhibited the adhesion (motility) of Pseudomonas aeruginosa and biofilm formation of activated sludge bacteria in Membrane Bio-Reactor (MBR; inhibition rate 51-85%, p < 0.05). In addition, qRT-PCR testing revealed that recombinant PvdQ acylase significantly reduced the transcription level of QS biofilm formation-related genes (cdrA, pqsA, and lasR; p < 0.05). In this study, QQ genetically engineered bacteria enhanced by genetic engineering could effectively inhibit the QS signal transduction mechanism and have the potential to control biofilm formation of pathogenic bacteria in the aquaculture environment, providing an environmentally friendly and alternative antibiotic strategy to suppress biofilm contamination.

Innovative microbial disease biocontrol strategies mediated by quorum quenching and their multifaceted applications: A review

With the increasing resistance exhibited by undesirable bacteria to traditional antibiotics, the need to discover alternative (or, at least, supplementary) treatments to combat chemically resistant bacteria is becoming urgent. Quorum sensing (QS) refers to a novel bacterial communication system for monitoring cell density and regulation of a network of gene expression that is mediated by a group of signaling molecules called autoinducers (AIs). QS-regulated multicellular behaviors include biofilm formation, horizontal gene transfer, and antibiotic synthesis, which are demonstrating increasing pathogenicity to plants and aquacultural animals as well as contamination of wastewater treatment devices. To inhibit QS-regulated microbial behaviors, the strategy of quorum quenching (QQ) has been developed. Different quorum quenchers interfere with QS through different mechanisms, such as competitively inhibiting AI perception (e.g., by QS inhibitors) and AI degradation (e.g., by QQ enzymes). In this review, we first introduce different signaling molecules, including diffusible signal factor (DSF) and acyl homoserine lactones (AHLs) for Gram-negative bacteria, AIPs for Gram-positive bacteria, and AI-2 for interspecies communication, thus demonstrating the mode of action of the QS system. We next exemplify the QQ mechanisms of various quorum quenchers, such as chemical QS inhibitors, and the physical/enzymatic degradation of QS signals. We devote special attention to AHL-degrading enzymes, which are categorized in detail according to their diverse catalytic mechanisms and enzymatic properties. In the final part, the applications and advantages of quorum quenchers (especially QQ enzymes and bacteria) are summarized in the context of agricultural/aquacultural pathogen biocontrol, membrane bioreactors for wastewater treatment, and the attenuation of human pathogenic bacteria. Taken together, we present the state-of-the-art in research considering QS and QQ, providing theoretical evidence and support for wider application of this promising environmentally friendly biocontrol strategy.