Engineering microbial physiology with synthetic polymers: cationic polymers induce biofilm formation in Vibrio cholerae and downregulate the expression of virulence genes

Bacterial clustering biomaterials as anti-infective therapies

In Nature, bacterial clustering by host-released peptides or nucleic acids is an evolutionarily conserved immune defense strategy employed to prevent adhesion of pathogenic microbes, which is prerequisite for most infections. Synthetic anti-adhesion strategies present as non-lethal means of targeting bacteria and may potentially be used to avoid resistance against antimicrobial therapies. From bacteria-agglutinating biomolecules discovered in nature to synthetic designs involving peptides, cationic polymers and nanoparticles, the modes of actions appear broad and unconsolidated. Herein, we present a critical review and update of the state-of-the-art in synthetic bacteria-clustering designs with proposition of a more streamlined nomenclature and classification. Overall, this review aims to consolidate the conceptual framework in the field of bacterial clustering and highlight its potentials as an avenue for discovering novel antibacterial biomaterials.

Sodium butyrate inhibits the expression of virulence factors in Vibrio cholerae by targeting ToxT protein

Cholera, a diarrheal disease caused by the gram-negative bacterium Vibrio cholerae, remains a global health threat in developing countries due to its high transmissibility and increased antibiotic resistance. There is a pressing need for alternative strategies, with an emphasis on anti-virulent approaches to alter the outcome of bacterial infections, given the increase in antimicrobial-resistant strains. V. cholerae causes cholera by secreting virulence factors in the intestinal epithelial cells. These virulence factors facilitate bacterial colonization and cholera toxin production during infection. Here, we demonstrate that sodium butyrate (SB), a small molecule, had no effect on bacterial viability but was effective in suppressing the virulence attributes of V. cholerae. The production of cholera toxin (CT) was significantly reduced in a standard V. cholerae El Tor strain and two clinical isolates when grown in the presence of SB. Analysis of mRNA and protein levels further revealed that SB reduced the expression of the ToxT-dependent virulence genes like tcpA and ctxAB. DNA-protein interaction assays, conducted at cellular (ChIP) and in vitro conditions (EMSA), indicated that SB weakens the binding between ToxT and its downstream promoter DNA, likely by blocking DNA binding. Furthermore, the anti-virulence efficacy of SB was confirmed in animal models. These findings suggest that SB could be developed as an anti-virulence agent against V. cholerae, serving as a potential alternative to conventional antibiotics or as an adjunctive therapy to combat cholera.

IMPORTANCE

The world has been facing an upsurge in cholera cases since 2021, a similar trend continuing into 2022, with over 29 countries reporting cholera outbreaks (World Health Organization, 16 December 2022, Disease Outbreak News, Cholera-global situation). Treatment of cholera involves oral rehydration therapy coupled with antibiotics to reduce the duration of the illness. However, in recent years, indiscriminate use of antibiotics has contributed to the emergence of antibiotic-resistant strains. In this study, we have addressed the problem of antibiotic resistance by targeting virulence factors. Screening various compounds using in silico methods led to the identification of a small molecule, SB, that inhibits the virulence cascade in V. cholerae. We demonstrated that (i) SB intervened in ToxT protein-DNA binding and subsequently affected the expression of ToxT-regulated virulence genes (ctxAB and tcpA) and (ii) SB is a potential therapeutic candidate for the development of a novel antimicrobial agent.

Deciphering the Dilemma of Community Behavior Promotion and Inhibition by Cationic Bactericide-coated Nanoparticles in Gram-Negative Bacteria

Cationic bactericidal-coated gold nanoparticles are known to effectively prevent Gram-negative bacterial initial adhesion and community behavior development by strongly binding to bacterial surfaces and disrupting the cell membranes. However, such nanoparticles have been recently shown to unintentionally promote community behavior in Gram-negative bacteria because of the bacterial stress response. To find whether these contradictory findings are due to emerging stress response or poorly understood nanoparticle interactions of Gram-negative bacteria, in this work, we treated high population curli-producing Gram-negative Escherichia coli with cationic antibiotic/antiseptic-coated gold nanoparticles and followed the consequences in details using a variety of physical methods and controls. Parallelly, we employed standard biological assays commonly used to detect community behavior in bacteria. Biological assays yielded contradictory results some inferring promotion while others inferring inhibition. However, physical methods revealed that promotion and inhibition observations resulted from physical interactions without any bacterial response being involved. Using physical methods, we further demonstrated that macromolecules of cationic antibiotics and antiseptics exhibit similar consequences as nanoparticles, independent of inhibitory concentration. Overall, the results emphasize the need to consider physical interactions, rather than relying solely on standard biological assays, when evaluating the inhibition or promotion of community behavior by cationic antibiotic/antiseptic-coated nanoparticles or free cationic antibiotics/antiseptics against Gram-negative bacteria.

Host-guest chemistry on living cells enabling recyclable photobiocatalytic cascade

Combining chemical and whole-cell catalysts enables sustainable chemoenzymatic cascade reactions. However, their traditional combination faces challenges in catalyst recycling and maintaining cell viability. Here, we introduce a supramolecular host-guest strategy that efficiently attaches photocatalysts to bacterial cells, facilitating recyclable photobiocatalysis. This method involves attaching a cationic polyethylenimine (PEI) polymer, functionalized with β-cyclodextrin (β-CD), to E. coli cells. The polymer attachment is biocompatible and protective, safeguarding the cells from harsh conditions such as UV radiation and organic solvents, without causing cell death. Additionally, the presence of β-CD imparts a plug-and-play capability to the cells, enabling the straightforward integration of guest photocatalysts - specifically anthraquinone - onto the cell surface through host-guest interactions. This effective combination of cellular and chemical catalysts promotes efficient photobiocatalytic cascades and supports the photocatalyst's recycling and reuse. This supramolecular system thus represents a promising platform for advancing photobiocatalysis in cascade synthesis.

A Supramolecular Approach to Engineering Living Cells with Enzymes for Adaptive and Recyclable Cascade Synthesis

Biocatalytic transformation in nature is inherently dynamic, spontaneous, and adaptive, enabling complex chemical synthesis and metabolism. These processes often involve supramolecular recognition among cells, enzymes, and biomacromolecules, far surpassing the capabilities of isolated cells and enzymes used in industrial synthesis. Inspired by nature, here we design a supramolecular approach to equip living cells with these capacities, enabling recyclable, efficient cascade reactions. Our two-step "plug-and-play" methodology begins by coating Escherichia coli cells with guest-containing polymers (SupraBAC) via supramolecular charge interactions, followed by the introduction of β-cyclodextrin-functionalized host enzymes through host-guest chemistry, creating a robust cell-enzyme complex. This supramolecular coating not only protects cells from various stresses, such as UV radiation, heat, and organic solvents, but also facilitates the overexpression of intracellular enzymes and the attachment of extracellular enzymes within and on SupraBAC. This combination results in efficient multienzyme cascade synthesis, enabling two- and three-step reactions in one pot. Importantly, the multienzyme system can be recycled up to five times without significant loss of activity. Our findings introduce a versatile, adaptive supramolecular coating for whole-cell catalysts, offering a sustainable and efficient solution for complex synthesis in both chemistry and industrial biotechnology.

A simple and efficient fluorescent labeling method in Staphylococcus aureus for real-time tracking of invasive bacteria

Bacterial fluorescent labeling is a powerful tool for the diagnosis and treatment of bacterial infections. Here, we present a simple and efficient labeling strategy for Staphylococcus aureus. Intracellular labeling of bacteria was achieved by heat shock using Cyanine 5.5 (Cy5.5) near-infrared-I dyes in S. aureus (Cy5.5@S. aureus). Several key factors, such as Cy5.5 concentration and labeling time, were systematically evaluated. Further, the cytotoxicity of Cy5.5 and the stability of Cy5.5@S. aureus was evaluated by flow cytometry, inverted fluorescence microscopy, and transmission electron microscopy. In addition, Cy5.5@S. aureus were used to explore the phagocytic behavior of RAW264.7 macrophages. These results proved that Cy5.5@S. aureus had a uniform fluorescence intensity and high luminance; additionally, our method had no significant adverse effects on S. aureus compared to unlabeled S. aureus infections. Our method provides researchers with a useful option for analyzing the behavior of S. aureus as an infectious agent. This technique can be broadly applied to study host cell-bacteria interactions at the molecular level, and to in vivo tracing of bacterial infections.

Polymer-induced biofilms for enhanced biocatalysis

The intrinsic resilience of biofilms to environmental conditions makes them an attractive platform for biocatalysis, bioremediation, agriculture or consumer health. However, one of the main challenges in these areas is that beneficial bacteria are not necessarily good at biofilm formation. Currently, this problem is solved by genetic engineering or experimental evolution, techniques that can be costly and time consuming, require expertise in molecular biology and/or microbiology and, more importantly, are not suitable for all types of microorganisms or applications. Here we show that synthetic polymers can be used as an alternative, working as simple additives to nucleate the formation of biofilms. Using a combination of controlled radical polymerization and dynamic covalent chemistry, we prepare a set of synthetic polymers carrying mildly cationic, aromatic, heteroaromatic or aliphatic moieties. We then demonstrate that hydrophobic polymers induce clustering and promote biofilm formation in MC4100, a strain of Escherichia coli that forms biofilms poorly, with aromatic and heteroaromatic moieties leading to the best performing polymers. Moreover, we compare the effect of the polymers on MC4100 against PHL644, an E. coli strain that forms biofilms well due to a single point mutation which increases expression of the adhesin curli. In the presence of selected polymers, MC4100 can reach levels of biomass production and curli expression similar or higher than PHL644, demonstrating that synthetic polymers promote similar changes in microbial physiology than those introduced following genetic modification. Finally, we demonstrate that these polymers can be used to improve the performance of MC4100 biofilms in the biocatalytic transformation of 5-fluoroindole into 5-fluorotryptophan. Our results show that incubation with these synthetic polymers helps MC4100 match and even outperform PHL644 in this biotransformation, demonstrating that synthetic polymers can underpin the development of beneficial applications of biofilms.

Approaches for the inhibition and elimination of microbial biofilms using macromolecular agents

Biofilms are complex three-dimensional structures formed at interfaces by the vast majority of bacteria and fungi. These robust communities have an important detrimental impact on a wide range of industries and other facets of our daily lives, yet their removal is challenging owing to the high tolerance of biofilms towards conventional antimicrobial agents. This key issue has driven an urgent search for new innovative antibiofilm materials. Amongst these emerging approaches are highly promising materials that employ aqueous-soluble macromolecules, including peptides, proteins, synthetic polymers, and nanomaterials thereof, which exhibit a range of functionalities that can inhibit biofilm formation or detach and destroy organisms residing within established biofilms. In this Review, we outline the progress made in inhibiting and removing biofilms using macromolecular approaches, including a spotlight on cutting-edge materials that respond to environmental stimuli for "on-demand" antibiofilm activity, as well as synergistic multi-action antibiofilm materials. We also highlight materials that imitate and harness naturally derived species to achieve new and improved biomimetic and biohybrid antibiofilm materials. Finally, we share some speculative insights into possible future directions for this exciting and highly significant field of research.

Deep eutectic solvent-assisted phase separation in chitosan solutions for the production of 3D monoliths and films with tailored porosities

A facile and greener methodology to obtain pure chitosan-based 3D porous structures in the form of monoliths and films is proposed. It is based on a modified evaporation-induced phase separation process in a chitosan solution precursor. In this approach, a deep eutectic solvent (DES) is used as the nonsolvent system and an ecofriendly, cost effective, simple and versatile alternative for the production of highly structured chitosan materials. The porous heterogeneous structure can be fine-tuned by varying the chitosan content in the precursor solution and chitosan/DES ratio, and enabled the structured polymer to absorb large amounts of water to form hydrogels. This is a versatile and unexplored approach to design porous chitosan with tailored morphology in the absence of crosslinkers, which, based on preliminary studies on V. cholerae biofilm formation, is expected to open new avenues for various applications in biomedical, catalysis, water purification, filtration and other areas where the control of bacterial biofilm formation is critical.

Characteristic profiles of biofilm, enterotoxins and virulence of Staphylococcus aureus isolates from dairy cows in Xinjiang Province, China

As an important zoonotic pathogen, Staphylococcus aureus has led to serious mastitis and endometritis in infected dairy cows. In this study, a total of 164 strains of S. aureus were isolated from dairy cows in Xinjiang Province, China, and subjected to assays to determine drug susceptibility and biofilm (BF) formation ability. Enterotoxin-related genes were detected, and the transcription levels of genes related to BF formation were determined by using reverse transcription-quantitative polymerase chain reaction. Moreover, the pathogenicity of isolates with different BF formation abilities was determined by measuring their hemolysis activity, half lethal dose (LD₅₀) and organ bacterial load. The results showed that 86.0% of S. aureus isolates could form BF. Among them, 42.1% of the strains had weak BF formation ability, and most strains with a strong BF formation ability were ica gene carriers. The S. aureus isolates displayed multidrug resistance and their drug resistance was positively correlated with their BF formation ability. Moreover, 96.3% of the S. aureus isolates carried enterotoxin genes. Among them, the detection rates of the novel enterotoxin genes were higher than those of conventional enterotoxin genes. Furthermore, isolates with a strong BF formation ability had higher LD50 but lower hemolysis ability and organ bacterial load than those of the isolates with weak or no BF ability. However, isolates without BF ability produced more severe pathological changes than those of isolates with strong BF formation ability. These findings suggest that higher BF ability and presence of novel enterotoxin genes are important characteristics of S. aureus isolates from dairy cows in Xinjiang Province, China, and such isolates may pose potential threats to food safety.

Dual bioresponsive antibiotic and quorum sensing inhibitor combination nanoparticles for treatment of Pseudomonas aeruginosa biofilms in vitro and ex vivo

Many debilitating infections result from persistent microbial biofilms that do not respond to conventional antibiotic regimens. A potential method to treat such chronic infections is to combine agents which interfere with bacterial biofilm development together with an antibiotic in a single formulation. Here, we explore the use of a new bioresponsive polymer formulation derived from specifically modified alginate nanoparticles (NPs) in order to deliver ciprofloxacin (CIP) in combination with the quorum sensing inhibitor (QSI) 3-amino-7-chloro-2-nonylquinazolin-4(3H)-one (ACNQ) to mature Pseudomonas aeruginosa biofilms. The alginate NPs were engineered to incorporate a pH-responsive linker between the polysaccharide backbone and the QSI, and to encapsulate CIP via charge-charge interactions of the positively-charged drug with the carboxyl residues of the alginate matrix. In this way, a dual-action release of antibiotic and QSI was designed for the low-pH regions of a biofilm, involving cleavage of the QSI-linker to the alginate matrix and reduced charge-charge interactions between CIP and the polysaccharide as the alginate carboxyl side-chains protonated. When tested in a biofilm model the concomitant release of CIP + QSI from the pH-responsive nanoparticles significantly reduced the viability of the biofilm compared with CIP treatment alone. In addition, the alginate NPs were shown to penetrate deeply into P. aeruginosa biofilms, which we attribute in part to the charges of the NPs and the release of the QSI agent. Finally, we tested the formulation in both a 2D keratinocyte and a 3D ex vivo skin infection model. The dual-action bio-responsive QSI and CIP release nanoparticles effectively cleared the infection in the latter, suggesting considerable promise for combination therapeutics which prevent biofilm formation as well as effectively killing mature P. aeruginosa biofilms.

1-Amino-2'-fucosyllactose inhibits biofilm formation by Streptococcus agalactiae

2'-Fucosyllactose (2'-FL) is a ubiquitous oligosaccharide in human milk. Importantly, this carbohydrate promotes the growth of several strains of Bifidobacteria, a class of beneficial gut commensal, and inhibits epithelial binding of pathogens. In light of these protective effects, we elected to evaluate the potential of 2'-FL to serve as an antibacterial agent against Group B Streptococcus (GBS). While 2'-FL was devoid of any substantial antimicrobial or antibiofilm activity, conversion of 2'-FL to its reducing end β-amine provided a novel antibiofilm compound.

Aggregation of Vibrio cholerae by Cationic Polymers Enhances Quorum Sensing but Overrides Biofilm Dissipation in Response to Autoinduction

Vibrio cholerae is a Gram-negative bacterium found in aquatic environments and a human pathogen of global significance. Its transition between host-associated and environmental lifestyles involves the tight regulation of niche-specific phenotypes such as motility, biofilm formation, and virulence. V. cholerae's transition from the host to environmental dispersal usually involves suppression of virulence and dispersion of biofilm communities. In contrast to this naturally occurring transition, bacterial aggregation by cationic polymers triggers a unique response, which is to suppress virulence gene expression while also triggering biofilm formation by V. cholerae, an artificial combination of traits that is potentially very useful to bind and neutralize the pathogen from contaminated water. Here, we set out to uncover the mechanistic basis of this polymer-triggered bacterial behavior. We found that bacteria-polymer aggregates undergo rapid autoinduction and achieve quorum sensing at bacterial densities far below those required for autoinduction in the absence of polymers. We demonstrate this induction of quorum sensing is due both to a rapid formation of autoinducer gradients and local enhancement of autoinducer concentrations within bacterial clusters as well as the stimulation of CAI-1 and AI-2 production by aggregated bacteria. We further found that polymers cause an induction of the biofilm-specific regulator VpsR and the biofilm structural protein RbmA, bypassing the usual suppression of biofilm during autoinduction. Overall, this study highlights that synthetic materials can be used to cross-wire natural bacterial responses to achieve a combination of phenotypes with potentially useful applications.