Effects of antibacterial agents and drugs monitored by atomic force microscopy

Biochemical Interactions through Microscopic Techniques: Structural and Molecular Characterization

Many researchers and scientists have contributed significantly to provide structural and molecular characterizations of biochemical interactions using microscopic techniques in the recent decade, as these biochemical interactions play a crucial role in the production of diverse biomaterials and the organization of biological systems. The properties, activities, and functionalities of the biomaterials and biological systems need to be identified and modified for different purposes in both the material and life sciences. The present study aimed to review the advantages and disadvantages of three main branches of microscopy techniques (optical microscopy, electron microscopy, and scanning probe microscopy) developed for the characterization of these interactions. First, we explain the basic concepts of microscopy and then the breadth of their applicability to different fields of research. This work could be useful for future research works on biochemical self-assembly, biochemical aggregation and localization, biological functionalities, cell viability, live-cell imaging, material stability, and membrane permeability, among others. This understanding is of high importance in rapid, inexpensive, and accurate analysis of biochemical interactions.

Nanomotion Detection-Based Rapid Antibiotic Susceptibility Testing

Rapid antibiotic susceptibility testing (AST) could play a major role in fighting multidrug-resistant bacteria. Recently, it was discovered that all living organisms oscillate in the range of nanometers and that these oscillations, referred to as nanomotion, stop as soon the organism dies. This finding led to the development of rapid AST techniques based on the monitoring of these oscillations upon exposure to antibiotics. In this review, we explain the working principle of this novel technique, compare the method with current ASTs, explore its application and give some advice about its implementation. As an illustrative example, we present the application of the technique to the slowly growing and pathogenic Bordetella pertussis bacteria.

Nanostructured TiC Layer is Highly Suitable Surface for Adhesion, Proliferation and Spreading of Cells

Cell culture is usually performed in 2D polymer surfaces; however, several studies are conducted with the aim to screen functional coating molecules to find substrates more suitable for cell adhesion and proliferation. The aim of this manuscript is to compare the cell adhesion and cytoskeleton organization of different cell types on different surfaces. Human primary fibroblasts, chondrocytes and osteoblasts isolated from patients undergoing surgery were seeded on polystyrene, poly-d-lysine-coated glass and titanium carbide slides and left to grow for several days. Then their cytoskeleton was analyzed, both by staining cells with phalloidin, which highlights actin fibers, and using Atomic Force Microscopy. We also monitored the production of Fibroblast Growth Factor-2, Bone Morphogenetic Protein-2 and Osteocalcin, using ELISA, and we highlighted production of Collagen type I in fibroblasts and osteoblasts and Collagen type II in chondrocytes by immunofluorescences. Fibroblasts, chondrocytes and osteoblasts showed both an improved proliferative activity and a good adhesion ability when cultured on titanium carbide slides, compared to polystyrene and poly-d-lysine-coated glass. In conclusion, we propose titanium carbide as a suitable surface to cultivate cells such as fibroblasts, chondrocytes and osteoblasts, allowing the preservation of their differentiated state and good adhesion properties.

A perspective view on the nanomotion detection of living organisms and its features

The insurgence of newly arising, rapidly developing health threats, such as drug-resistant bacteria and cancers, is one of the most urgent public-health issues of modern times. This menace calls for the development of sensitive and reliable diagnostic tools to monitor the response of single cells to chemical or pharmaceutical stimuli. Recently, it has been demonstrated that all living organisms oscillate at a nanometric scale and that these oscillations stop as soon as the organisms die. These nanometric scale oscillations can be detected by depositing living cells onto a micro-fabricated cantilever and by monitoring its displacements with an atomic force microscope-based electronics. Such devices, named nanomotion sensors, have been employed to determine the resistance profiles of life-threatening bacteria within minutes, to evaluate, among others, the effect of chemicals on yeast, neurons, and cancer cells. The data obtained so far demonstrate the advantages of nanomotion sensing devices in rapidly characterizing microorganism susceptibility to pharmaceutical agents. Here, we review the key aspects of this technique, presenting its major applications. and detailing its working protocols.

Fengycins From Bacillus amyloliquefaciens MEP218 Exhibit Antibacterial Activity by Producing Alterations on the Cell Surface of the Pathogens Xanthomonas axonopodis pv. vesicatoria and Pseudomonas aeruginosa PA01

Bacillus amyloliquefaciens MEP₂18 is an autochthonous bacterial isolate with antibacterial and antifungal activities against a wide range of phytopathogenic microorganisms. Cyclic lipopeptides (CLP), particularly fengycins, produced by this bacterium; are the main antimicrobial compounds responsible for the growth inhibition of phytopathogens. In this work, the CLP fraction containing fengycins with antibacterial activity was characterized by LC-ESI-MS/MS. In addition, the antibacterial activity of these fengycins was evaluated on the pathogens Xanthomonas axonopodis pv. vesicatoria (Xav), a plant pathogen causing the bacterial spot disease, and Pseudomonas aeruginosa PA01, an opportunistic human pathogen. In vitro inhibition assays showed bactericidal effects on Xav and PA01. Atomic force microscopy images revealed dramatic alterations in the bacterial surface topography in response to fengycins exposure. Cell damage was evidenced by a decrease in bacterial cell heights and the loss of intracellular content measured by potassium efflux assays. Furthermore, the viability of MRC-5 human normal lung fibroblasts was not affected by the treatment with fengycins. This study shows in vivo evidence on the less-known properties of fengycins as antibacterial molecules and leaves open the possibility of using this CLP as a novel antibiotic.

Emerging technologies for antibiotic susceptibility testing

Superbugs such as infectious bacteria pose a great threat to humanity due to an increase in bacterial mortality leading to clinical treatment failure, lengthy hospital stay, intravenous therapy and accretion of bacteraemia. These disease-causing bacteria gain resistance to drugs over time which further complicates the treatment. Monitoring of antibiotic resistance is therefore necessary so that bacterial infectious diseases can be diagnosed rapidly. Antimicrobial susceptibility testing (AST) provides valuable information on the efficacy of antibiotic agents and their dosages for treatment against bacterial infections. In clinical laboratories, most widely used AST methods are disk diffusion, gradient diffusion, broth dilution, or commercially available semi-automated systems. Though these methods are cost-effective and accurate, they are time-consuming, labour-intensive, and require skilled manpower. Recently much attention has been on developing rapid AST techniques to avoid misuse of antibiotics and provide effective treatment. In this review, we have discussed emerging engineering AST techniques with special emphasis on phenotypic AST. These techniques include fluorescence imaging along with computational image processing, surface plasmon resonance, Raman spectra, and laser tweezer as well as micro/nanotechnology-based device such as microfluidics, microdroplets, and microchamber. The mechanical and electrical behaviour of single bacterial cell and bacterial suspension for the study of AST is also discussed.

Emerging Analytical Techniques for Rapid Pathogen Identification and Susceptibility Testing

In the face of looming threats from multi-drug resistant microorganisms, there is a growing need for technologies that will enable rapid identification and drug susceptibility profiling of these pathogens in health care settings. In particular, recent progress in microfluidics and nucleic acid amplification is pushing the boundaries of timescale for diagnosing bacterial infections. With a diverse range of techniques and parallel developments in the field of analytical chemistry, an integrative perspective is needed to understand the significance of these developments. This review examines the scope of new developments in assay technologies grouped by key enabling domains of research. First, we examine recent development in nucleic acid amplification assays for rapid identification and drug susceptibility testing in bacterial infections. Next, we examine advances in microfluidics that facilitate acceleration of diagnostic assays via integration and scale. Lastly, recentdevelopments in biosensor technologies are reviewed. We conclude this review with perspectives on the use of emerging concepts to develop paradigm-changing assays.

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 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”.

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.

Methods for Atomic Force Microscopy of Biological and Living Specimens

Two main precautions must be taken into account to obtain high-resolution morphological and nanomechanical characterization of biological specimens with an atomic force microscope: the tip-sample interaction and the sample-substrate adhesion. In this chapter we discuss the necessary steps for a correct preparation of three types of biological samples: erythrocytes, bacteria, and osteoblasts. The main goal is to deliver reproducible protocols to produce good cellular adhesion and minimizing the morphological alterations of the specimens.

Inhibiting P. fluorescens biofilms with fluoropolymer-embedded silver nanoparticles: an in-situ spectroscopic study

Surface colonization by microorganisms leads to the formation of biofilms, i.e. aggregates of bacteria embedded within a matrix of extracellular polymeric substance. This promotes adhesion to the surface and protects bacterial community, providing an antimicrobial-resistant environment. The inhibition of biofilm growth is a crucial issue for preventing bacterial infections. Inorganic nanoparticle/Teflon-like (CF_x) composites deposited via ion beam sputtering demonstrated very efficient antimicrobial activity. In this study, we developed Ag-CF_x thin films with tuneable metal loadings and exceptional in-plane morphological and chemical homogeneity. Ag-CF_x antimicrobial activity was studied via mid-infrared attenuated total reflection spectroscopy utilizing specifically adapted multi-reflection waveguides. Biofilm was sampled by carefully depositing the Ag-CF_x film on IR inactive regions of the waveguide. Real-time infrared spectroscopy was used to monitor Pseudomonas fluorescens biofilm growth inhibition induced by the bioactive silver ions released from the nanoantimicrobial coating. Few hours of Ag-CF_x action were sufficient to affect significantly biofilm growth. These findings were corroborated by atomic force microscopy (AFM) studies on living bacteria exposed to the same nanoantimicrobial. Morphological analyses showed a severe bacterial stress, leading to membrane leakage/collapse or to extended cell lysis as a function of incubation time.

An approach to study ultrastructural changes and adaptive strategies displayed by Acinetobacter guillouiae SFC 500-1A under simultaneous Cr(VI) and phenol treatment

Acinetobacter guillouiae SFC 500-1A, a native bacterial strain isolated from tannery sediments, is able to simultaneously remove high concentrations of Cr(VI) and phenol. In this complementary study, high-resolution microscopy techniques, such as atomic force microscopy (AFM) and transmission electron microscopy (TEM), were used to improve our understanding of some bacterial adaptive mechanisms that enhance their ability to survive. AFM contributed in gaining insight into changes in bacterial size and morphology. It allowed the unambiguous identification of pollutant-induced cellular disturbances and the visualization of bacterial cells with depth sensitivity. TEM analysis revealed that Cr(VI) produced changes mainly at the intracellular level, whereas phenol produced alterations at the membrane level. This strain tended to form more extensive biofilms after phenol treatment, which was consistent with microscopy images and the production of exopolysaccharides (EPSs). In addition, other exopolymeric substances (DNA, proteins) significantly increased under Cr(VI) and phenol treatment. These exopolymers are important for biofilm formation playing a key role in bacterial aggregate stability, being especially useful for bioremediation of environmental pollutants. This study yields the first direct evidences of a range of different changes in A. guillouiae SFC 500-1A which seems to be adaptive strategies to survive in stressful conditions.

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.

Nanotools and molecular techniques to rapidly identify and fight bacterial infections

Reducing the emergence and spread of antibiotic-resistant bacteria is one of the major healthcare issues of our century. In addition to the increased mortality, infections caused by multi-resistant bacteria drastically enhance the healthcare costs, mainly because of the longer duration of illness and treatment. While in the last 20years, bacterial identification has been revolutionized by the introduction of new molecular techniques, the current phenotypic techniques to determine the susceptibilities of common Gram-positive and Gram-negative bacteria require at least two days from collection of clinical samples. Therefore, there is an urgent need for the development of new technologies to determine rapidly drug susceptibility in bacteria and to achieve faster diagnoses. These techniques would also lead to a better understanding of the mechanisms that lead to the insurgence of the resistance, greatly helping the quest for new antibacterial systems and drugs. In this review, we describe some of the tools most currently used in clinical and microbiological research to study bacteria and to address the challenge of infections. We discuss the most interesting advancements in the molecular susceptibility testing systems, with a particular focus on the many applications of the MALDI-TOF MS system. In the field of the phenotypic characterization protocols, we detail some of the most promising semi-automated commercial systems and we focus on some emerging developments in the field of nanomechanical sensors, which constitute a step towards the development of rapid and affordable point-of-care testing devices and techniques. While there is still no innovative technique that is capable of completely substituting for the conventional protocols and clinical practices, many exciting new experimental setups and tools could constitute the basis of the standard testing package of future microbiological tests.

Effects of membrane lipid composition and antibacterial drugs on the rigidity of Escherichia coli: Different contributions of various bacterial substructures

The rigidity/stiffness is an important biomechanical property of bacteria and potentially correlated with many bacterial activities. While the rigidity or fluidity of the bacterial membrane has been extensively studied, the contributions of different bacterial substructures to the bacterial rigidity are less investigated. Here, we utilized four Escherichia coli (E. coli) strains with different membrane lipid compositions and three antibacterial drugs (EDTA, lysozyme, and streptomycin) to specifically alter bacterial substructures. By using atomic force microscopy (AFM), we found that the average height and Young's modulus of phosphatidylethanolamine (PE)-deficient E. coli strains were larger than those of PE(+) strains and that EDTA, EDTA plus lysozyme instead of lysozyme alone, and streptomycin all caused significant decreases in height and Young's modulus of the four E. coli strains. Our data imply that membrane lipid composition, the integrated outer membrane, the cell wall, and the cytoplasmic content are all responsible for bacterial rigidity but to different extents.

Morphofunctional reaction of bacteria treated with antimicrobial peptides derived from farm animal platelets

Classical microbiological approach and atomic force microscopy were used to evaluate the mechanisms of biological activity of antimicrobial peptides (AMPs) derived from platelets of farm animals. It is established that AMPs inhibit both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) microorganisms. Differences revealed in the biological activity of AMP preparations obtained from the organisms of various species can be reduced to quantitative differences. While qualitative changes of bacterial cells were substantially similar, changes in the integrity of cell walls resulted in disintegration of the bacterial outer and/or cytoplasmic membranes.

Nanomechanical motion of Escherichia coli adhered to a surface

Nanomechanical motion of bacteria adhered to a chemically functionalized silicon surface is studied by means of a microcantilever. A non-specific binding agent is used to attach Escherichia coli (E. coli) to the surface of a silicon microcantilever. The microcantilever is kept in a liquid medium, and its nanomechanical fluctuations are monitored using an optical displacement transducer. The motion of the bacteria couples efficiently to the microcantilever well below its resonance frequency, causing a measurable increase in the microcantilever fluctuations. In the time domain, the fluctuations exhibit large-amplitude low-frequency oscillations. In corresponding frequency-domain measurements, it is observed that the mechanical energy is focused at low frequencies with a 1/f^α -type power law. A basic physical model is used for explaining the observed spectral distribution of the mechanical energy. These results lay the groundwork for understanding the motion of microorganisms adhered to surfaces and for developing micromechanical sensors for bacteria.

Real-time monitoring of protein conformational changes using a nano-mechanical sensor

Proteins can switch between different conformations in response to stimuli, such as pH or temperature variations, or to the binding of ligands. Such plasticity and its kinetics can have a crucial functional role, and their characterization has taken center stage in protein research. As an example, Topoisomerases are particularly interesting enzymes capable of managing tangled and supercoiled double-stranded DNA, thus facilitating many physiological processes. In this work, we describe the use of a cantilever-based nanomotion sensor to characterize the dynamics of human topoisomerase II (Topo II) enzymes and their response to different kinds of ligands, such as ATP, which enhance the conformational dynamics. The sensitivity and time resolution of this sensor allow determining quantitatively the correlation between the ATP concentration and the rate of Topo II conformational changes. Furthermore, we show how to rationalize the experimental results in a comprehensive model that takes into account both the physics of the cantilever and the dynamics of the ATPase cycle of the enzyme, shedding light on the kinetics of the process. Finally, we study the effect of aclarubicin, an anticancer drug, demonstrating that it affects directly the Topo II molecule inhibiting its conformational changes. These results pave the way to a new way of studying the intrinsic dynamics of proteins and of protein complexes allowing new applications ranging from fundamental proteomics to drug discovery and development and possibly to clinical practice.

Atomic force microscopy in microbiology: new structural and functional insights into the microbial cell surface

Microbial cells sense and respond to their environment using their surface constituents. Therefore, understanding the assembly and biophysical properties of cell surface molecules is an important research topic. With its ability to observe living microbial cells at nanometer resolution and to manipulate single-cell surface molecules, atomic force microscopy (AFM) has emerged as a powerful tool in microbiology. Here, we survey major breakthroughs made in cell surface microbiology using AFM techniques, emphasizing the most recent structural and functional insights.