Nanoscale analysis of the effects of antibiotics and CX1 on a Pseudomonas aeruginosa multidrug-resistant strain

Nanomechanical characterization of soft nanomaterial using atomic force microscopy

Atomic force microscopy (AFM) is a promising method for generating high-spatial-resolution images, providing insightful perspectives on the nanomechanical attributes of soft matter, including cells, bacteria, viruses, proteins, and nanoparticles. AFM is widely used in biological and pharmaceutical sciences because it can scrutinize mechanical properties under physiological conditions. We comprehensively reviewed experimental techniques and fundamental mathematical models to investigate the mechanical properties, including elastic moduli and binding forces, of soft materials. To determine these mechanical properties, two-dimensional arrays of force-distance (f-d) curves are obtained through AFM indentation experiments using the force volume technique. For elasticity determination, models are divided into approach f-d curve-based models, represented by the Hertz model, and retract f-d curve-based models, exemplified by the Johnson-Kendall-Roberts and Derjaguin-Müller-Toporov models. Especially, the Chen, Tu, and Cappella models, developed from the Hertz model, are used for thin samples on hard substrates. Additionally, the establishment of physical or chemical bonds during indentation experiments, observable in retract f-d curves, is crucial for the adhesive properties of samples and binding affinity between antibodies (receptors) and antigens (ligands). Chemical force microscopy, single-molecule force spectroscopy, and single-cell force spectroscopy are primary AFM methods that provide a comprehensive view of such properties through retract curve analysis. Furthermore, this paper, structured into key thematic sections, also reviews the exemplary application of AFM across multiple scientific disciplines. Notably, cancer cells are softer than healthy cells, although more sophisticated investigations are required for prognostic applications. AFM also investigates how bacteria adapt to antibiotics, addressing antimicrobial resistance, and reveals that stiffer virus capsids indicate reduced infectivity, aiding in the development of new strategies to combat viral infections. Moreover, AFM paves the way for innovative therapeutic approaches in designing effective drug delivery systems by providing insights into the physical properties of soft nanoparticles and the binding affinity of target moieties. Our review provides researchers with representative studies applying AFM to a wide range of cross-disciplinary research.

Pseudomonas aeruginosa assembles H1-T6SS in response to physical and chemical damage of the outer membrane

Bacteria respond to environmental stimuli and attacks from competing organisms. Pseudomonas aeruginosa assembles the type VI secretion system (H1-T6SS) to precisely retaliate against aggressive competing bacteria. However, we lack an understanding of how the H1-T6SS assembly dynamically responds to nanomechanical forces. To address this, we analyzed live cells using correlative atomic force microscopy (AFM) and fluorescence microscopy. We show that indentation forces above 7 nanonewtons trigger local, repeated and targeted H1-T6SS assemblies within seconds of impact by the AFM tip. Analysis of the corresponding AFM force curves shows that a breach of a single layer of the cell envelope is necessary and sufficient for triggering H1-T6SS assembly. Accordingly, polymyxin B nonapeptide, which damages the outer membrane, also triggers H1-T6SS assembly. This suggests that P. aeruginosa has evolved a danger-sensing mechanism that enables rapid and precise deployment of its antibacterial H1-T6SS in response to breaches in the outer membrane.

Investigating the role of extracellular polymeric substances produced by Parachlorella kessleri in Zn(II) bioremediation using atomic force microscopy

Microalgae, such as Parachlorella kessleri, have significant potential for environmental remediation, especially in removing heavy metals like zinc from water. This study investigates how P. kessleri, isolated from a polluted river in Argentina, can remediate zinc. Using atomic force microscopy (AFM), the research examined the interactions between Zn particles and cells grown with different nitrogen sources-nitrate or ammonium. The results showed that cells grown with nitrate produced extracellular polymeric substances (EPS), while those grown with ammonium did not. Raman spectroscopy revealed distinct metabolic responses based on the nitrogen source, with nitrate-grown cells showing altered profiles after zinc exposure. Zinc exposure also changed the surface roughness and nanomechanical properties of the cells, particularly in those producing EPS. AFM force spectroscopy experiments then confirmed strong Zn binding to EPS in nitrate-grown cells, while interactions were weaker in ammonium-grown cells that lacked EPS. Overall, our results elucidate the critical role of EPS in Zn removal by P. kessleri cells and show that Zn remediation is mediated by EPS adsorption. This study underscores the significance of regulating nitrogen sources to stimulate EPS production, offering insights that are essential for subsequent bioremediation applications.

Insight into the outer membrane asymmetry of P. aeruginosa and the role of MlaA in modulating the lipidic composition, mechanical, biophysical, and functional membrane properties of the cell envelope

In Gram-negative bacteria, the outer membrane (OM) is asymmetric, with lipopolysaccharides (LPS) in the outer leaflet and glycerophospholipids (GPLs) in the inner leaflet. The asymmetry is maintained by the Mla system (MlaA-MlaBCDEF), which contributes to lipid homeostasis by removing mislocalized GPLs from the outer leaflet of the OM. Here, we ascribed how Pseudomonas aeruginosa ATCC 27853 coordinately regulates pathways to provide defense against the threats posed by the deletion of mlaA. Especially, we explored (i) the effects on membrane lipid composition including LPS, GPLs, and lysophospholipids, (ii) the biophysical properties of the OM such as stiffness and fluidity, and (iii) the impact of these changes on permeability, antibiotic susceptibility, and membrane vesicles (MVs) generation. Deletion of mlaA induced an increase in total GPLs and a decrease in LPS level while also triggering alterations in lipid A structures (arabinosylation and palmitoylation), likely to be induced by a two-component system (PhoPQ-PmrAB). Altered lipid composition may serve a physiological purpose in regulating the mechanobiological and functional properties of P. aeruginosa. We demonstrated an increase in cell stiffness without alteration of turgor pressure and inner membrane (IM) fluidity in ∆mlaA. In addition, membrane vesiculation increased without any change in OM/IM permeability. An amphiphilic aminoglycoside derivative (3',6-dinonyl neamine) that targets P. aeruginosa membranes induced an opposite effect on ∆mlaA strain with a trend toward a return to the situation observed for the WT strain. Efforts dedicated to understanding the crosstalk between the OM lipid composition, and the mechanical behavior of bacterial envelope, is one needed step for designing new targets or new drugs to fight P. aeruginosa infections.IMPORTANCEPseudomonas aeruginosa is a Gram-negative bacterium responsible for severe hospital-acquired infections. The outer membrane (OM) of Gram-negative bacteria acts as an effective barrier against toxic compounds, and therefore, compromising this structure could increase sensitivity to antibiotics. The OM is asymmetric with the highly packed lipopolysaccharide monolayer at the outer leaflet and glycerophospholipids at the inner leaflet. OM asymmetry is maintained by the Mla pathway resulting in the retrograde transport of glycerophospholipids from the OM to the inner membrane. In this study, we show that deleting mlaA, the membrane component of Mla system located at the OM, affects the mechanical and functional properties of P. aeruginosa cell envelope. Our results provide insights into the role of MlaA, involved in the Mla transport pathway in P. aeruginosa.

Bacterial eradication by a low-energy pulsed electron beam generator

Low-energy electron beams (LEEB) are a safe and practical sterilization solution for in-line industrial applications, such as sterilizing medical products. However, their low dose rate induces product degradation, and the limited maximal energy prohibits high-throughput applications. To address this, we developed a low-energy 'pulsed' electron beam generator (LEPEB) and evaluated its efficacy and mechanism of action. Bacillus pumilus vegetative cells and spores were irradiated with a 250 keV LEPEB system at a 100 Hz pulse repetition frequency and a pulse duration of only 10 ns. This produced highly efficient bacterial inactivation at a rate of >6 log10, the level required for sterilization in industrial applications, with only two pulses for vegetative bacteria (20 ms) and eight pulses for spores (80 ms). LEPEB induced no morphological or structural defects, but decreased cell wall hydrophobicity in vegetative cells, which may inhibit biofilm formation. Single- and double-strand DNA breaks and pyrimidine dimer formation were also observed, likely causing cell death. Together, the unique combination of high dose rate and nanosecond delivery of LEPEB enable effective and high-throughput bacterial eradication for direct integration into production lines in a wide range of industrial applications.

Functionalized Calixarenes as Promising Antibacterial Drugs to Face Antimicrobial Resistance

Since the discovery of polyphenolic resins 150 years ago, the study of polymeric compounds named calix[n]arene has continued to progress, and those skilled in the art perfectly know now how to modulate this phenolic ring. Consequently, calix[n]arenes are now used in a large range of applications and notably in therapeutic fields. In particular, the calix[4]arene exhibits multiple possibilities for regioselective polyfunctionalization on both of its rims and offers researchers the possibility of precisely tuning the geometry of their structures. Thus, in the crucial research of new antibacterial active ingredients, the design of calixarenes finds its place perfectly. This review provides an overview of the work carried out in this aim towards the development of intrinsically active prodrogues or metallic calixarene complexes. Out of all the work of the community, there are some excellent activities emerging that could potentially place these original structures in a very good position for the development of new active ingredients.

Antimicrobial activity of water-soluble tetra-cationic porphyrins on Pseudomonas aeruginosa

This manuscript presents the cytotoxicity, antimicrobial activity, antibiofilm preliminary properties, and associated therapy with commercial drugs using water-soluble tetra-cationic porphyrins against Pseudomonas aeruginosa. Two commercial tetra-cationic porphyrins were tested against a standard strain of P. aeruginosa 01 (PA01) in antibacterial activity assays under dark conditions and irradiated with white light for 120 min. Porphyrin 4-H₂TMePor showed better antimicrobial activity and was chosen for further tests. Increased minimum inhibitory concentration was observed in the presence of reactive oxygen species, suggesting that photooxidation was mediated by the singlet oxygen production. In the time-kill curve assay, 4-H₂TMePor inhibited bacterial growth in 90 min of irradiation. The checkerboard assay revealed synergistic interactions. Biofilms of the standard PA01 strain and three clinical isolates were formed. The biofilm destruction assay was more efficient for PA01, significantly reducing the biofilm biomass formed compared to the positive control. The associated treatment to destroy the biofilm potentiated a significant decrease in the biofilm biomass compared to the positive control. The photosensitizer did not damage human keratinocytes or mouse fibroblasts in the cytotoxicity assays, demonstrating the safety of using 4-H₂TMePor. Atomic force microscopy indicated lower adhesion force, higher cell wall deformation, and higher dissipation energy in the treated control compared to untreated PA01. Given our findings, it is evident that water-soluble tetra-cationic porphyrins have excellent antimicrobial and a preliminary antibiofilm activity against Gram-negative bacteria, proving to be a potential photosensitizer for clinical use.

Use of Atomic Force Microscopy to Characterize LPS Perturbations

Lipopolysaccharide (LPS) on Gram-negative bacterial outer membranes is the first target for antimicrobial agents, due to their spatial proximity to outer environments of microorganisms. To understand the molecular nature and their interaction with antimicrobial agents, establishing a model LPS structure is of key importance. Here, we describe procedures for following LPS layer attachment to a solid surface and provide protocols for measuring bacterial membrane morphology after adding antibiotics. Using atomic force microscopy (AFM), we show methods to characterize the effects of antibiotic polymyxin B to the LPS layers at the nanoscale.

Adhesion heterogeneity of individual bacterial cells in an axenic culture studied by atomic force microscopy

The evaluation of bacterial adhesive properties at a single-cell level is critical for under standing the role of phenotypic heterogeneity in bacterial attachment and community formation. Bacterial population exhibits a wide variety of adhesive properties at the single-cell level, suggesting that bacterial adhesion is a rather complex process and some bacteria are prone to phenotypic heterogeneity. This heterogeneity was more pronounced for Escherichia coli, where two subpopulations were detected. Subpopulations exhibiting higher adhesion forces may be better adapted to colonize a new surface, especially during sudden changes in environmental conditions. Escherichia coli was characterized by a higher adhesion force, a stronger ability to form biofilm and larger heterogeneity index calculated in comparison with Bacillus subtilis. Higher adhesion forces are associated with a more efficient attachment of bacteria observed in an adhesion assay and might provide a basis for successful colonization, survival and multiplications in changing environment. The atomic force microscopy provides a platform for investigation of the adhesion heterogeneity of individual cells within a population, which may be expected to underpin further elucidation of the adaptive significance of phenotypic heterogeneity in a natural environment.

AFM Study of Nanoscale Membrane Perturbation Induced by Antimicrobial Lipopeptide C14 KYR

Lipopeptides have been extensively studied as potential antimicrobial agents. In this study, we focused on the C₁₄-KYR lipopeptide, a modified version of the KYR tripeptide with myristic acid at the N-terminus. Here, membrane perturbation of live E. coli treated with the parent KYR and C₁₄-KYR peptides was compared at the nanoscale level using AFM imaging. AFM analyses, including average cellular roughness and force spectroscopy, revealed the severe surface disruption mechanism of C₁₄-KYR. A loss of surface roughness and changes in topographic features included membrane shrinkage, periplasmic membrane separation from the cell wall, and cytosolic leakage. Additional evidence from synchrotron radiation FTIR microspectroscopy (SR-FTIR) revealed a marked structural change in the membrane component after lipopeptide attack. The average roughness of the E. coli cell before and after treatment with C₁₄-KYR was 129.2 ± 51.4 and 223.5 ± 14.1 nm, respectively. The average rupture force of the cell treated with C₁₄-KYR was 0.16 nN, four times higher than that of the untreated cell. Our study demonstrates that the mechanistic effect of the lipopeptide against bacterial cells can be quantified through surface imaging and adhesion force using AFM.

Binding Affinity and Driving Forces for the Interaction of Calixarene-Based Micellar Aggregates With Model Antibiotics in Neutral Aqueous Solution

The search for novel surfactants or drug delivery systems able to improve the performance of old-generation antibiotics is a topic of great interest. Self-assembling amphiphilic calix[4]arene derivatives provide well-defined nanostructured systems that exhibit promising features for antibiotics delivery. In this work, we investigated the capability of two micellar polycationic calix[4]arene derivatives to recognize and host ofloxacin, chloramphenicol, or tetracycline in neutral aqueous solution. The formation of the nanoaggregates and the host–guest equilibria were examined by nano-isothermal titration calorimetry, dynamic light scattering, and mono- and bi-dimensional NMR. The thermodynamic characterization revealed that the calix[4]arene-based micellar aggregates are able to effectively entrap the model antibiotics and enabled the determination of both the species and the driving forces for the molecular recognition process. Indeed, the formation of the chloramphenicol–micelle adduct was found to be enthalpy driven, whereas entropy drives the formation of the adducts with both ofloxacin and tetracycline. NMR spectra corroborated ITC data about the positioning of the antibiotics in the calixarene nanoaggregates.

Nanoscale Evidence Unravels Microalgae Flocculation Mechanism Induced by Chitosan

Microalgae are a promising resource for biofuel production, although their industrial use is limited by the lack of effective harvesting techniques. Flocculation consists in the aggregation and adhesion of cells into flocs that can be more easily removed from water than individual cells. Although it is an efficient harvesting technique, contamination is a major issue as chemical flocculants are often used. An alternative is to use natural biopolymers flocculants such as chitosan. Chitosan is a biobased nontoxic polymer that has been effectively used to harvest Chlorella vulgaris cells at a pH lower than its pK_a (6.5). While the reported flocculation mechanism is said to rely on electrostatic interactions between chitosan and the negative cell surface, no molecular evidence has yet confirmed this mechanism. In this study, we performed force spectroscopy atomic force microscopy (AFM) experiments to probe the interactions between C. vulgaris cells and chitosan at the molecular scale to decipher its flocculation mechanism. Our results showed that at pH 6, chitosan interacts with C. vulgaris cell wall through biological interactions rather than electrostatic interactions. These observations were confirmed by comparing the data with cationically modified cellulose nanocrystals, for which the flocculation mechanism, relying on an electrostatic patch mechanism, has already been described for C. vulgaris. Further AFM experiments also showed that a different mechanism was at play at higher pH, based on chitosan precipitation. Thus, this AFM-based approach highlights the complexity of chitosan-induced flocculation mechanisms for C. vulgaris.

Macrophage activation on "phagocytic synapse" arrays: Spacing of nanoclustered ligands directs TLR1/2 signaling with an intrinsic limit

The activation of Toll-like receptor heterodimer 1/2 (TLR1/2) by microbial components plays a critical role in host immune responses against pathogens. TLR1/2 signaling is sensitive to the chemical structure of ligands, but its dependence on the spatial distribution of ligands on microbial surfaces remains unexplored. Here, we reveal the quantitative relationship between TLR1/2-triggered immune responses and the spacing of ligand clusters by designing an artificial "phagocytic synapse" nanoarray platform to mimic the cell-microbe interface. The ligand spacing dictates the proximity of receptor clusters on the cell surface and consequently the pro-inflammatory responses of macrophages. However, cell responses reach their maximum at small ligand spacings when the receptor nanoclusters become adjacent to one another. Our study demonstrates the feasibility of using spatially patterned ligands to modulate innate immunity. It shows that the receptor clusters of TLR1/2 act as a driver in integrating the spatial cues of ligands into cell-level activation events.

Atomic Force Microscopy (AFM) As a Surface Mapping Tool in Microorganisms Resistant Toward Antimicrobials: A Mini-Review

The worldwide emergence of antimicrobial resistance (AMR) in pathogenic microorganisms, including bacteria and viruses due to a plethora of reasons, such as genetic mutation and indiscriminate use of antimicrobials, is a major challenge faced by the healthcare sector today. One of the issues at hand is to effectively screen and isolate resistant strains from sensitive ones. Utilizing the distinct nanomechanical properties (e.g., elasticity, intracellular turgor pressure, and Young’s modulus) of microbes can be an intriguing way to achieve this; while atomic force microscopy (AFM), with or without modification of the tips, presents an effective way to investigate such biophysical properties of microbial surfaces or an entire microbial cell. Additionally, advanced AFM instruments, apart from being compatible with aqueous environments—as often is the case for biological samples—can measure the adhesive forces acting between AFM tips/cantilevers (conjugated to bacterium/virion, substrates, and molecules) and target cells/surfaces to develop informative force-distance curves. Moreover, such force spectroscopies provide an idea of the nature of intercellular interactions (e.g., receptor-ligand) or propensity of microbes to aggregate into densely packed layers, that is, the formation of biofilms—a property of resistant strains (e.g., Staphylococcus aureus, Pseudomonas aeruginosa). This mini-review will revisit the use of single-cell force spectroscopy (SCFS) and single-molecule force spectroscopy (SMFS) that are emerging as powerful additions to the arsenal of researchers in the struggle against resistant microbes, identify their strengths and weakness and, finally, prioritize some future directions for research.

Microscopic Investigation of the Combined Use of Antibiotics and Biosurfactants on Methicillin Resistant Staphylococcus aureus

One current strategy to deal with the serious issue of antibiotic resistance is to use biosurfactants, weak antimicrobials in their own right, with antibiotics in order to extend the efficacy of antibiotics. Although an adjuvant effect has been observed, the underlying mechanisms are poorly understood. To investigate the nature of the antibiotic and biosurfactant interaction, we undertook a scanning electron microscopy (SEM) and atomic force microscopy (AFM) microscopic study of the effects of the tetracycline antibiotic, combined with sophorolipid and rhamnolipid biosurfactants, on Methicillin-resistant Staphylococcus aureus using tetracycline concentrations below and above the minimum inhibitory concentration (MIC). Control and treated bacterial samples were prepared with an immersion technique by adsorbing the bacteria onto glass substrates grafted with the poly-cationic polymer polyethyleneimine. Bacterial surface morphology, hydrophobic and hydrophilic surface characters as well as the local bacterial cell stiffness were measured following combined antibiotic and biosurfactant treatment. The sophorolipid biosurfactant stands alone insofar as, when used with the antibiotic at sub-MIC concentration, it resulted in bacterial morphological changes, larger diameters (from 758 ± 75 to 1276 ± 220 nm, p-value = 10^-4) as well as increased bacterial core stiffness (from 205 ± 46 to 396 ± 66 mN/m, p-value = 5 × 10^-5). This investigation demonstrates that such combination of microscopic analysis can give useful information which could complement biological assays to understand the mechanisms of synergy between antibiotics and bioactive molecules such as biosurfactants.

Variations in the Morphology, Mechanics and Adhesion of Persister and Resister E. coli Cells in Response to Ampicillin: AFM Study

Persister bacterial cells are great at surviving antibiotics. The phenotypic means by which they do that are underexplored. As such, atomic force microscope (AFM) was used to quantify the contributions of the surface properties of the outer membrane of multidrug resistance (MDR)-Escherichia coli Strains (A5 and A9) in the presence of ampicillin at minimum inhibitory concentration (MIC) (resistant cells) and at 20× MIC (persistent cells). The properties quantified were morphology, root mean square (RMS) roughness, adhesion, elasticity, and bacterial surface biopolymers' thickness and grafting density. Compared to untreated cells, persister cells of E. coli A5 increased their RMS, adhesion, apparent grafting density, and elasticity by 1.2, 3.4, 2.0, and 3.3 folds, respectively, and decreased their surface area and brush thickness by 1.3 and 1.2 folds, respectively. Similarly, compared to untreated cells, persister cells of E. coli A9 increased their RMS, adhesion and elasticity by 1.6, 4.4, and 4.5 folds, respectively; decreased their surface area and brush thickness by 1.4 and 1.6 folds, respectively; and did not change their grafting densities. Our results indicate that resistant and persistent E. coli A5 cells battled ampicillin by decreasing their size and going through dormancy. The resistant E. coli A9 cells resisted ampicillin through elongation, increased surface area, and adhesion. In contrast, the persistent E. coli A9 cells resisted ampicillin through increased roughness, increased surface biopolymers' grafting densities, increased cellular elasticities, and decreased surface areas. Mechanistic insights into how the resistant and persistent E. coli cells respond to ampicillin's treatment are instrumental to guide design efforts exploring the development of new antibiotics or renovating the existing antibiotics that may kill persistent bacteria by combining more than one mechanism of action.

Microbial adhesion and ultrastructure from the single-molecule to the single-cell levels by Atomic Force Microscopy

In the last decades, atomic force microscopy (AFM) has evolved towards an accurate and lasting tool to study the surface of living cells in physiological conditions. Through imaging, single-molecule force spectroscopy and single-cell force spectroscopy modes, AFM allows to decipher at multiple scales the morphology and the molecular interactions taking place at the cell surface. Applied to microbiology, these approaches have been used to elucidate biophysical properties of biomolecules and to directly link the molecular structures to their function. In this review, we describe the main methods developed for AFM-based microbial surface analysis that we illustrate with examples of molecular mechanisms unravelled with unprecedented resolution.

Deciphering multivalent glycocluster-lectin interactions through AFM characterization of the self-assembled nanostructures

Pseudomonas aeruginosa is a human opportunistic pathogen responsible for lung infections in cystic fibrosis patients. The emergence of resistant strains and its ability to form a biofilm seem to give a selective advantage to the bacterium and thus new therapeutic approaches are needed. To infect the lung, the bacterium uses several virulence factors, like LecA lectins. These proteins are involved in bacterial adhesion due to their specific interaction with carbohydrates of the host epithelial cells. The tetrameric LecA lectin specifically binds galactose residues. A new therapeutic approach is based on the development of highly affine synthetic glycoclusters able to selectively link with LecA to interfere with the natural carbohydrate-LecA interaction. In this study, we combined atomic force microscopy imaging and molecular dynamics simulations to visualize and understand the arrangements formed by LecA and five different glycoclusters. Our glycoclusters are small scaffolds characterized by a core and four branches, which terminate in a galactose residue. Depending on the nature of the core and the branches, the glycocluster-lectin interaction can be modulated and the affinity increased. We show that glycocluster-LecA arrangements highly depend on the glycocluster architecture: the core influences the rigidity of the geometry and the directionality of the branches, whereas the nature of the branch determines the compactness of the structure and the ease of binding.

Direct observation of the cell-wall remodeling in adhering Staphylococcus aureus 27217: An AFM study supported by SEM and TEM

We took benefit from Atomic Force Microscopy (AFM) in the force spectroscopy mode to describe the time evolution – over 24 h – of the surface nanotopography and mechanical properties of the strain Staphylococcus aureus 27217 from bacterial adhesion to the first stage of biofilm genesis. In addition, Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM) experiments allowed identifying two types of self-adhering subpopulations (the so-called “bald” and “hairy” cells) and revealed changes in their relative populations with the bacterial culture age and the protocol of preparation. We indeed observed a dramatic evanescing of the “hairy” subpopulation for samples that underwent centrifugation and resuspension processes. When examined by AFM, the “hairy” cell surface resembled to a herringbone structure characterized by upper structural units with lateral dimensions of ∼70 nm and a high Young modulus value (∼2.3 MPa), a mean depth of the trough between them of ∼15 nm and a resulting roughness of ∼5 nm. By contrast, the “bald” cells appeared much softer (∼0.35 MPa) with a roughness one order of magnitude lower. We observed too the gradual detachment of the herringbone patterns from the “hairy” bacterial envelope of cell harvested from a 16 h old culture and their progressive accumulation between the bacteria in the form of globular clusters. The secretion of a soft extracellular polymeric substance was also identified that, in addition to the globular clusters, may contribute to the initiation of the biofilm spatial organization.

Changes in nanomechanical properties and adhesion dynamics of algal cells during their growth

Nanomechanical and structural characterisations of algal cells are of key importance for understanding their adhesion behaviour at interfaces in the aquatic environment. We examine here the nanomechanical properties and adhesion dynamics of the algal cells during two phases of their growth using complementary surface methods and the mathematical modelling. Mechanical properties of motile cells are hard to assess while keeping cells viable, and studies to date have been limited. Immobilisation of negatively charged cells to a positively charged substrate enables high-resolution AFM imaging and nanomechanical measurements. Cells were stiffer and more hydrophobic in the exponential than in the stationary phase, suggesting molecular modification of the cell envelope during aging. The corresponding properties of algal cells were in agreement with the increase of critical interfacial tensions of adhesion, determined amperometrically. Cells in exponential phase possessed a larger cell volume, in agreement with the large amount of amperometrically measured displaced charge at the interface. Differences in the kinetics of adhesion and spreading of cells at the interface were attributed to their various volumes and nanomechanical properties that varied during cell aging. Our findings contribute to the present body of knowledge on the biophysics of algal cells on a fundamental level.

Changes in Cellular Elasticities and Conformational Properties of Bacterial Surface Biopolymers of Multidrug-Resistant Escherichia coli (MDR-E. coli) Strains in Response to Ampicillin

The roles of the thicknesses and grafting densities of the surface biopolymers of four multi-drug resistant (MDR) Escherichia coli bacterial strains that varied in their biofilm formation in controlling cellular elasticities after exposure to ampicillin were investigated using atomic force microscopy. Exposure to ampicillin was carried out at minimum inhibitory concentrations for different duration times. Our results indicated that the four strains resisted ampicillin through variable mechanisms. Strain A5 did not change its cellular properties upon exposure to ampicillin and as such resisted ampicillin through dormancy. Strain H5 increased its biopolymer brush thickness, adhesion and biofilm formation and kept its roughness, surface area and cell elasticity unchanged upon exposure to ampicillin. As such, this strain likely limits the diffusion of ampicillin by forming strong biofilms. At three hours’ exposure to ampicillin, strains D4 and A9 increased their roughness, surface areas, biofilm formation, and brush thicknesses and decreased their elasticities. Therefore, at short exposure times to ampicillin, these strains resisted ampicillin through forming strong biofilms that impede ampicillin diffusion. At eight hours’ exposure to ampicillin, strains D4 and A9 collapsed their biopolymers, increased their apparent grafting densities and increased their cellular elasticities. Therefore, at long exposure times to ampicillin, cells utilized their higher rigidity to reduce the diffusion of ampicillin into the cells. The findings of this study clearly point to the potential of using the nanoscale characterization of MDR bacterial properties as a means to monitor cell modifications that enhance “phenotypic antibiotic resistance”.

Localized incorporation of outer membrane components in the pathogen Brucella abortus

The zoonotic pathogen Brucella abortus is part of the Rhizobiales, which are alpha-proteobacteria displaying unipolar growth. Here, we show that this bacterium exhibits heterogeneity in its outer membrane composition, with clusters of rough lipopolysaccharide co-localizing with the essential outer membrane porin Omp2b, which is proposed to allow facilitated diffusion of solutes through the porin. We also show that the major outer membrane protein Omp25 and peptidoglycan are incorporated at the new pole and the division site, the expected growth sites. Interestingly, lipopolysaccharide is also inserted at the same growth sites. The absence of long-range diffusion of main components of the outer membrane could explain the apparent immobility of the Omp2b clusters, as well as unipolar and mid-cell localizations of newly incorporated outer membrane proteins and lipopolysaccharide. Unipolar growth and limited mobility of surface structures also suggest that new surface variants could arise in a few generations without the need of diluting pre-existing surface antigens.

Surface enhanced fluorescence and nanoscopic cell wall deformation in adhering Staphylococcus aureus upon exposure to cell wall active and non-active antibiotics

In infections, bacteria often adhere to surfaces and become deformed by the forces with which they adhere. Nanoscopic cell wall deformation defines bacterial responses to environmental conditions and is likely influenced by antibiotics. Here, staphylococcal cell wall deformation upon exposure to cell wall active and non-active antibiotics or their combinations is compared for two green-fluorescent (GFP) isogenic Staphylococcus aureus strains adhering to a gold surface, of which one lacks peptidoglycan cross-linking. Exposure to cell wall active antibiotics caused greater cell wall deformation than a buffer control in the GFP parent and in the Δpbp4GFP isogenic mutant, as measured by surface-enhanced-fluorescence. Cell wall non-active antibiotics only yielded greater deformation than a buffer control in the parent strain, while combinations of cell wall active and non-active antibiotics did not cause greater cell wall deformation. 3D-analysis of the impact of adhesion forces and Young's moduli of the cell wall, both measured using atomic force microscopy, led to the conclusion that increased deformation was mainly due to cell wall weakening and not due to the effects of antibiotics on adhesion forces. Interactions between bacteria and antibiotics are mostly studied using planktonic bacteria, while during infection, bacteria are in an adhering state that deforms their cell wall and therewith influences their adaptive responses. We anticipate that the demonstration of cell wall weakening in adhering bacteria under the influence of antibiotics and the role of peptidoglycan herein will aid in the development of new antibiotics. Surface-enhanced-fluorescence may accordingly develop into a new, highly-sensitive method for diagnosing antibiotic-resistant bacteria.

Detrimental impact of silica nanoparticles on the nanomechanical properties of Escherichia coli, studied by AFM

Despite great innovative and technological promises, nanoparticles (NPs) can ultimately exert an antibacterial activity by affecting the cell envelope integrity. This envelope, by conferring the cell its rigidity and protection, is intimately related to the mechanical behavior of the bacterial surface. Depending on their size, surface chemistry, shape, NPs can induce damages to the cell morphology and structure among others, and are therefore expected to alter the overall mechanical properties of bacteria. Although Atomic Force Microscopy (AFM) stands as a powerful tool to study biological systems, with high resolution and in near physiological environment, it has rarely been applied to investigate at the same time both morphological and mechanical degradations of bacteria upon NPs treatment. Consequently, this study aims at quantifying the impact of the silica NPs (SiO₂-NPs) on the mechanical properties of E. coli cells after their exposure, and relating it to their toxic activity under a critical diameter. Cell elasticity was calculated by fitting the force curves with the Hertz model, and was correlated with the morphological study. SiO₂-NPs of 100 nm diameter did not trigger any significant change in the Young modulus of E. coli, in agreement with the bacterial intact morphology and membrane structure. On the opposite, the 4 nm diameter SiO₂-NPs did induce a significant decrease in E. coli Young modulus, mainly associated with the disorganization of lipopolysaccharides in the outer membrane and the permeation of the underlying peptidoglycan layer. The subsequent toxic behavior of these NPs is finally confirmed by the presence of membrane residues, due to cell lysis, exhibiting typical adhesion features.

Design, synthesis and antibacterial evaluation of a polycationic calix[4]arene derivative alone and in combination with antibiotics

The growing antibiotic resistance phenomenon continues to stimulate the search for new compounds and strategies to combat bacterial infections. In this study, we designed and synthesized a new polycationic macrocyclic compound (2) bearing four N-methyldiethanol ammonium groups clustered and circularly organized by a calix[4]arene scaffold. The in vitro activity of compound 2, alone and in combination with known antibiotics (ofloxacin, chloramphenicol or tetracycline), was assessed against strains of Staphylococcus aureus (ATCC 6538 and methicillin-resistant isolate 15), S. epidermidis (ATCC 35984 and methicillin-resistant isolate 57), and Pseudomonas aeruginosa (ATCC 9027 and antibiotic-resistant isolate 1). Calix[4]arene derivative 2 showed significant antibacterial activity against ATCC and methicillin-resistant Gram positive Staphylococci, improved the stability of tetracycline in water, and in combination with antibiotics enhanced the antibiotic efficacy against Gram negative P. aeruginosa by an additive effect.

Methods of Micropatterning and Manipulation of Cells for Biomedical Applications

Micropatterning and manipulation of mammalian and bacterial cells are important in biomedical studies to perform in vitro assays and to evaluate biochemical processes accurately, establishing the basis for implementing biomedical microelectromechanical systems (bioMEMS), point-of-care (POC) devices, or organs-on-chips (OOC), which impact on neurological, oncological, dermatologic, or tissue engineering issues as part of personalized medicine. Cell patterning represents a crucial step in fundamental and applied biological studies in vitro, hence today there are a myriad of materials and techniques that allow one to immobilize and manipulate cells, imitating the 3D in vivo milieu. This review focuses on current physical cell patterning, plus chemical and a combination of them both that utilizes different materials and cutting-edge micro-nanofabrication methodologies.

Removal of Antibiotic-Resistant Bacteria and Antibiotic Resistance Genes Affected by Varying Degrees of Fouling on Anaerobic Microfiltration Membranes

An anaerobic membrane bioreactor was retrofitted with polyvinylidene fluoride (PVDF) microfiltration membrane units, each of which was fouled to a different extent. The membranes with different degrees of fouling were evaluated for their efficiencies in removing three antibiotic-resistant bacteria (ARB), namely, bla_NDM-1-positive Escherichia coli PI-7, bla_CTX-M-15-positive Klebsiella pneumoniae L7, and bla_OXA-48-positive E. coli UPEC-RIY-4, as well as their associated plasmid-borne antibiotic resistance genes (ARGs). The results showed that the log removal values (LRVs) of ARGs correlated positively with the extent of membrane fouling and ranged from 1.9 to 3.9. New membranes with a minimal foulant layer could remove more than 5 log units of ARB. However, as the membranes progressed to subcritical fouling, the LRVs of ARB decreased at increasing operating transmembrane pressures (TMPs). The LRV recovered back to 5 when the membrane was critically fouled, and the achieved LRV remained stable at different operating TMPs. Furthermore, characterization of the surface attributed the removal of both the ARB and ARGs to adsorption, which was facilitated by an increasing hydrophobicity and a decreasing surface ζ potential as the membranes fouled. Our results indicate that both the TMP and the foulant layer synergistically affected ARB removal, but the foulant layer was the main factor that contributed to ARG removal.

Cell biology of microbes and pharmacology of antimicrobial drugs explored by Atomic Force Microscopy

Antimicrobial molecules have been used for more than 50 years now and are the basis of modern medicine. No surgery can nowdays be imagined to be performed without antibiotics; dreadful diseases like tuberculosis, leprosis, siphilys, and more broadly all microbial induced diseases, can be cured only through the use of antimicrobial treatments. However, the situation is becoming more and more complex because of the ability of microbes to adapt, develop, acquire, and share mechanisms of resistance to antimicrobial agents. We choose to introduce this review by briefly drawing the panorama of antimicrobial discovery and development, but also of the emergence of microbial resistance. Then we describe how Atomic Force Microscopy (AFM) can be used to provide a better understanding of the mechanisms of action of these drugs at the nanoscale level on microbial interfaces. In this section, we will address these questions: (1) how does drug treatment affect the morphology of single microbes?; (2) do antimicrobial molecules modify the nanomechanical properties of microbes, or do the nanomechanical properties of microbes play a role in antimicrobial activity and efficiency?; and (3) how are the adhesive abilitites of microbes affected by antimicrobial drugs treatment? Finally, in a second part of this review we focus on recent studies aimed at changing the paradigm of the single molecule/cell technology that AFM typically represents. Recent work dealing with the creation of a microbe array which can be explored by AFM will be presented, as these developments constitute the first steps toward transforming AFM into a higher throughput technology. We also discuss papers using AFM as NanoMechnanicalSensors (NEMS), and demonstrate the interest of such approaches in clinical microbiology to detect quickly and with high accuracy microbial resistance.

Biophysical properties of cardiomyocyte surface explored by multiparametric AFM

PeakForce Quantitative Nanomechanical Mapping (PeakForce QNM) multiparametric AFM mode was adapted to qualitative and quantitative study of the lateral membrane of cardiomyocytes (CMs), extending this powerful mode to the study of soft cells. On living CM, PeakForce QNM depicted the crests and hollows periodic alternation of cell surface architecture previously described using AFM Force Volume (FV) mode. PeakForce QNM analysis provided better resolution in terms of pixel number compared to FV mode and reduced acquisition time, thus limiting the consequences of spontaneous living adult CM dedifferentiation once isolated from the cardiac tissue. PeakForce QNM mode on fixed CMs clearly visualized subsarcolemmal mitochondria (SSM) and their loss following formamide treatment, concomitant with the interfibrillar mitochondria climbing up and forming heaps at the cell surface. Interestingly, formamide-promoted SSM loss allowed visualization of the sarcomeric apparatus ultrastructure below the plasma membrane. High PeakForce QNM resolution led to better contrasted mechanical maps than FV mode and provided correlation between adhesion, dissipation, mechanical and topographical maps. Modified hydrophobic AFM tip enhanced contrast on adhesion and dissipation maps and suggested that CM surface crests and hollows exhibit distinct chemical properties. Finally, two-dimensional Fast Fourier Transform to objectively quantify AFM maps allowed characterization of periodicity of both sarcomeric Z-line and M-band. Overall, this study validated PeakForce QNM as a valuable and innovative mode for the exploration of living and fixed CMs. In the future, it could be applied to depict cell membrane architectural, mechanical and chemical defects as well as sarcomeric abnormalities associated with cardiac diseases.

Atomic Force Microscopy Studies of the Interaction of Antimicrobial Peptides with Bacterial Cells

Antimicrobial peptides (AMPs) are promising therapeutic alternatives to conventional antibiotics. Many AMPs are membrane-active but their mode of action in killing bacteria or in inhibiting their growth remains elusive. Recent studies indicate the mechanism of action depends on peptide structure and lipid components of the bacterial cell membrane. Owing to the complexity of working with living cells, most of these studies have been conducted with synthetic membrane systems, which neglect the possible role of bacterial surface structures in these interactions. In recent years, atomic force microscopy has been utilized to study a diverse range of biological systems under non-destructive, physiologically relevant conditions that yield in situ biophysical measurements of living cells. This approach has been applied to the study of AMP interaction with bacterial cells, generating data that describe how the peptides modulate various biophysical behaviours of individual bacteria, including the turgor pressure, cell wall elasticity, bacterial capsule thickness, and organization of bacterial adhesins.

Morphological and ultrastructural changes in bacterial cells as an indicator of antibacterial mechanism of action

Efforts to reduce the global burden of bacterial disease and contend with escalating bacterial resistance are spurring innovation in antibacterial drug and biocide development and related technologies such as photodynamic therapy and photochemical disinfection. Elucidation of the mechanism of action of these new agents and processes can greatly facilitate their development, but it is a complex endeavour. One strategy that has been popular for many years, and which is garnering increasing interest due to recent technological advances in microscopy and a deeper understanding of the molecular events involved, is the examination of treated bacteria for changes to their morphology and ultrastructure. In this review, we take a critical look at this approach. Variables affecting antibacterial-induced alterations are discussed first. These include characteristics of the test organism (e.g. cell wall structure) and incubation conditions (e.g. growth medium osmolarity). The main body of the review then describes the different alterations that can occur. Micrographs depicting these alterations are presented, together with information on agents that induce the change, and the sequence of molecular events that lead to the change. We close by highlighting those morphological and ultrastructural changes which are consistently induced by agents sharing the same mechanism (e.g. spheroplast formation by peptidoglycan synthesis inhibitors) and explaining how changes that are induced by multiple antibacterial classes (e.g. filamentation by DNA synthesis inhibitors, FtsZ disruptors, and other types of agent) can still yield useful mechanistic information. Lastly, recommendations are made regarding future study design and execution.

Cell wall as a target for bacteria inactivation by pulsed electric fields

The integrity and morphology of bacteria is sustained by the cell wall, the target of the main microbial inactivation processes. One promising approach to inactivation is based on the use of pulsed electric fields (PEF). The current dogma is that irreversible cell membrane electro-permeabilisation causes the death of the bacteria. However, the actual effect on the cell-wall architecture has been poorly explored. Here we combine atomic force microscopy and electron microscopy to study the cell-wall organization of living Bacillus pumilus bacteria at the nanoscale. For vegetative bacteria, exposure to PEF led to structural disorganization correlated with morphological and mechanical alterations of the cell wall. For spores, PEF exposure led to the partial destruction of coat protein nanostructures, associated with internal alterations of cortex and core. Our findings reveal for the first time that the cell wall and coat architecture are directly involved in the electro-eradication of bacteria.

The selective interactions of cationic tetra-p-guanidinoethylcalix[4]arene with lipid membranes: theoretical and experimental model studies

Behavior of cationic tetra-p-guanidinoethylcalix[4]arene (CX1) and its building block, p-guanidinoethylphenol (mCX1) in model monolayer lipid membranes was investigated using all atom molecular dynamics simulations and surface pressure measurements. Members of two classes of lipids were taken into account: zwitterionic 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and anionic 1,2-dimyristoyl-sn-glycero-3-phospho-l-serine sodium salt (DMPS) as models of eukaryotic and bacterial cell membranes, respectively. It was demonstrated that CX1 and mCX1 accumulate near the negatively charged DMPS monolayers. The adsorption to neutral monolayers was negligible. In contrast to mCX1, CX1 penetrated into the hydrophobic part of the monolayer. The latter effect, which is possible due to a flip-flop inversion of the CX1 orientation in the lipid layer compared to the aqueous phase, may be responsible for its antibacterial activity.

Bacteriophilic tetra-p-guanidinoethyl-calix[4]arene derived polymers. Syntheses and E. coli sequestration studies

New resins functionalized by the antibacterial tetra-p-guanidinoethylcalix[4]arene were synthesized, and their bacteriophilic properties were evaluated (E. coli) by capillary electrophoresis.

Influence of biomaterial nanotopography on the adhesive and elastic properties of Staphylococcus aureus cells

Despite the well-known beneficial effects of biomaterial nanopatterning on host tissue integration, the influence of controlled nanoscale topography on bacterial colonisation and infection remains unknown.

Nanotechnology in dentistry: prevention, diagnosis, and therapy

Nanotechnology has rapidly expanded into all areas of science; it offers significant alternative ways to solve scientific and medical questions and problems. In dentistry, nanotechnology has been exploited in the development of restorative materials with some significant success. This review discusses nanointerfaces that could compromise the longevity of dental restorations, and how nanotechnolgy has been employed to modify them for providing long-term successful restorations. It also focuses on some challenging areas in dentistry, eg, oral biofilm and cancers, and how nanotechnology overcomes these challenges. The recent advances in nanodentistry and innovations in oral health-related diagnostic, preventive, and therapeutic methods required to maintain and obtain perfect oral health, have been discussed. The recent advances in nanotechnology could hold promise in bringing a paradigm shift in dental field. Although there are numerous complex therapies being developed to treat many diseases, their clinical use requires careful consideration of the expense of synthesis and implementation.

Single-bacterium nanomechanics in biomedicine: unravelling the dynamics of bacterial cells

The use of the atomic force microscope (AFM) in microbiology has progressed significantly throughout the years since its first application as a high-resolution imaging instrument. Modern AFM setups are capable of characterizing the nanomechanical behaviour of bacterial cells at both the cellular and molecular levels, where elastic properties and adhesion forces of single bacterium cells can be examined under different experimental conditions. Considering that bacterial and biofilm-mediated infections continue to challenge the biomedical field, it is important to understand the biophysical events leading towards bacterial adhesion and colonization on both biological and non-biological substrates. The purpose of this review is to present the latest findings concerning the field of single-bacterium nanomechanics, and discuss future trends and applications of nanoindentation and single-cell force spectroscopy techniques in biomedicine.

Directed assembly of living Pseudomonas aeruginosa bacteria on PEI patterns generated by nanoxerography for statistical AFM bioexperiments

Immobilization of living micro-organisms on predefined areas of substrates is a prerequisite for their characterizations by atomic force microscopy (AFM) in culture media. It remains challenging since micro-organisms should not be denatured but attached strongly enough to be scanned with an AFM tip, in a liquid phase. In this work, a novel approach is proposed to electrostatically assemble biological objects of interest on 2 nm thick polyethylenimine (PEI) patterns fabricated by nanoxerography. This nanoxerography process involves electrostatic trapping of PEI chains on negatively charged patterns written on electret thin films by AFM or electrical microcontact printing. The capability of this approach is demonstrated using a common biological system, Pseudomonas aeruginosa bacteria. These negatively charged bacteria are selectively assembled on large scale arrays of PEI patterns. In contrast to other PEI continuous films commonly used for cell anchoring, these ultrathin PEI patterns strongly attached on the surface do not cause any denaturation of the assembled Pseudomonas aeruginosa bacteria. AFM characterizations of large populations of individual living bacteria in culture media can thus be easily performed through this approach, providing the opportunity to perform representative statistical data analysis. Interestingly, this process may be extended to any negatively charged micro-organism in solution.