Mechanical robustness of Pseudomonas aeruginosa biofilms

Recent advances in studying single bacteria and biofilm mechanics

Bacterial biofilms correspond to surface-associated bacterial communities embedded in hydrogel-like matrix, in which high cell density, reduced diffusion and physico-chemical heterogeneity play a protective role and induce novel behaviors. In this review, we present recent advances on the understanding of how bacterial mechanical properties, from single cell to high-cell density community, determine biofilm tri-dimensional growth and eventual dispersion and we attempt to draw a parallel between these properties and the mechanical properties of other well-studied hydrogels and living systems.

Mechanistic action of weak acid drugs on biofilms

Selective permeability of a biofilm matrix to some drugs has resulted in the development of drug tolerant bacteria. Here we studied the efficacy of a weak organic acid drug, N-acetyl-L-cysteine (NAC), on the eradication of biofilms formed by the mucoid strain of Pseudomonas aeruginosa and investigated the commonality of this drug with that of acetic acid. We showed that NAC and acetic acid at pH < pKa can penetrate the matrix and eventually kill 100% of the bacteria embedded in the biofilm. Once the bacteria are killed, the microcolonies swell in size and passively shed bacteria, suggesting that the bacteria act as crosslinkers within the extracellular matrix. Despite shedding of the bacteria, the remnant matrix remains intact and behaves as a pH-responsive hydrogel. These studies not only have implications for drug design but also offer a route to generate robust soft matter materials.

In Vitro Studies on a Microfluidic Sensor with Embedded Obstacles Using New Antibacterial Synthetic Compounds (1-TDPPO) Mixed Prop-2-en-1-one with Difluoro Phenyl

This paper describes the use of an analytical microfluidic sensor for accelerating chemo-repellent response and strong anti-bacterial 1-(Thien-2-yl)-3-(2, 6-difluoro phenyl) prop-2-en-1-one (1-TDPPO). The chemically-synthesized antimicrobial agent, which included prop-2-en-1-one and difluoro phenyl groups, was moving through an optically transparent polydimethylsiloxane (PDMS) microfluidic sensor with circular obstacles arranged evenly. The response, growth and distribution of fluorescent labeling Pseudomonas aeruginosa PAO1 against the antimicrobial agent were monitored by confocal laser scanning microscope (CLSM). The microfluidic sensor along with 1-TDPPOin this study exhibits the following advantages: (i) Real-time chemo-repellent responses of cell dynamics; (ii) Rapid eradication of biofilm by embedded obstacles and powerful antibacterial agents, which significantly reduce the response time compared to classical methods; (iii) Minimal consumption of cells and antimicrobial agents; and (iv) Simplifying the process of the normalization of the fluorescence intensity and monitoring of biofilm by captured images and datasets.

Evolutionary adaptations of biofilms infecting cystic fibrosis lungs promote mechanical toughness by adjusting polysaccharide production

Biofilms are communities of microbes embedded in a matrix of extracellular polymeric substances, largely polysaccharides. Multiple types of extracellular polymeric substances can be produced by a single bacterial strain. The distinct polymer components of biofilms are known to provide chemical protection, but little is known about how distinct extracellular polysaccharides may also protect biofilms against mechanical stresses such as shear or phagocytic engulfment. Decades-long infections of Pseudomonas. aeruginosa biofilms in the lungs of cystic fibrosis patients are natural models for studies of biofilm fitness under pressure from antibiotics and the immune system. In cystic fibrosis infections, production of the extracellular polysaccharide alginate has long been known to increase with time and to chemically protect biofilms. More recently, it is being recognized that chronic cystic fibrosis infections also evolve to increase production of another extracellular polysaccharide, Psl; much less is known about Psl’s protective benefits to biofilms. We use oscillatory bulk rheology, on biofilms grown from longitudinal clinical isolates and from genetically-manipulated lab strains, to show that increased Psl stiffens biofilms and increases biofilm toughness, which is the energy cost to cause the biofilm to yield mechanically. Further, atomic force microscopy measurements reveal greater intercellular cohesion for higher Psl expression. Of the three types of extracellular polysaccharides produced by P. aeruginosa, only Psl increases the stiffness. Stiffening by Psl requires CdrA, a protein that binds to mannose groups on Psl and is a likely cross-linker for the Psl components of the biofilm matrix. We compare the elastic moduli of biofilms to the estimated stresses exerted by neutrophils during phagocytosis, and infer that increased Psl could confer a mechanical protection against phagocytic clearance.

Bacteria in lungs of people with cystic fibrosis can evolve through decades to build a tough biofilm that resists the body’s defences. Vernita Gordon and colleagues at the University of Texas, with co-workers in Europe, examined biofilms cultured from lung samples taken from patients at intervals over many years. The infecting bacterial populations had steadily evolved to increase production of specific carbohydrate components of the biofilms. The researchers found that increasing production of one carbohydrate component strengthens the biofilms, most likely due to the carbohydrate being crosslinked by protein molecules. The investigation suggests that the mechanics of the carbohydrate-protein network protects the biofilms from being broken into smaller pieces that can be engulfed by defensive cells called phagocytes. This new insight into the evolution of mechanical toughness complements the previously observed evolution of increasing chemical protection. Understanding these processes will assist efforts to combat them.

Modulation of the mechanical properties of bacterial biofilms in response to environmental challenges

In this review, we highlight recent research on the relationship between biofilm matrix composition, biofilm mechanics and environmental stimuli.

Through thick and thin: a microfluidic approach for continuous measurements of biofilm viscosity and the effect of ionic strength

Continuous, non-intrusive measurements of time-varying viscosity of Pseudomonas sp. biofilms are made using a microfluidic method that combines video tracking with a semi-empirical viscous flow model. The approach uses measured velocity and height of tracked biofilm segments, which move under the constant laminar flow of a nutrient solution. Following a low viscosity growth stage, rapid thickening was observed. During this stage, viscosity increased by over an order of magnitude in less than ten hours. The technique was also demonstrated as a promising platform for parallel experiments by subjecting multiple biofilm-laden microchannels to nutrient solutions containing NaCl in the range of 0 to 34 mM. Preliminary data suggest a strong relationship between ionic strength and biofilm properties, such as average viscosity and rapid thickening onset time. The technique opens the way for a combinatorial approach to study the response of biofilm viscosity under well-controlled physical, chemical and biological growth conditions.

A microfluidic method and custom model for continuous, non-intrusive biofilm viscosity measurements under different nutrient conditions

Straight, low-aspect ratio micro flow cells are used to support biofilm attachment and preferential accumulation at the short side-wall, which progressively reduces the effective channel width. The biofilm shifts downstream at measurable velocities under the imposed force from the constant laminar co-flowing nutrient stream. The dynamic behaviour of the biofilm viscosity is modeled semi-analytically, based on experimental measurements of biofilm dimensions and velocity as inputs. The technique advances the study of biofilm mechanical properties by strongly limiting biases related to non-Newtonian biofilm properties (e.g., shear dependent viscosity) with excellent time resolution. To demonstrate the proof of principle, young Pseudomonas sp. biofilms were analyzed under different nutrient concentrations and constant micro-flow conditions. The striking results show that large initial differences in biofilm viscosities grown under different nutrient concentrations become nearly identical in less than one day, followed by a continuous thickening process. The technique verifies that in 50 h from inoculation to early maturation stages, biofilm viscosity could grow by over 2 orders of magnitude. The approach opens the way for detailed studies of mechanical properties under a wide variety of physiochemical conditions, such as ionic strength, temperature, and shear stress.

Use of organic acids for prevention and removal of Bacillus subtilis biofilms on food contact surfaces

The efficacies of organic acid (citric, malic, and gallic acids) treatments at 1% and 2% concentrations on prevention and removal of Bacillus subtilis biofilms were investigated in this study. The analyses were conducted on microtitration plates and stainless steel coupons. The biofilm removal activities of these organic acids were compared with chlorine on both surfaces. The results showed that citric acid treatments were as powerful as chlorine treatments for prevention and removal of biofilms. The antibiofilm effects of malic acid treatments were higher than gallic acid and less than citric acid treatment. When the antibiofilm effects of these acids and chlorine on the two surfaces were compared, the prevention and removal of biofilms were measured higher on microtitration plates than those on stainless steel coupons. Higher reductions were obtained by increasing concentrations of sanitizers on 24-hour biofilm with 20-minute sanitizer treatments for removal of biofilms.

Advances in the microrheology of complex fluids

New developments in the microrheology of complex fluids are considered. Firstly the requirements for a simple modern particle tracking microrheology experiment are introduced, the error analysis methods associated with it and the mathematical techniques required to calculate the linear viscoelasticity. Progress in microrheology instrumentation is then described with respect to detectors, light sources, colloidal probes, magnetic tweezers, optical tweezers, diffusing wave spectroscopy, optical coherence tomography, fluorescence correlation spectroscopy, elastic- and quasi-elastic scattering techniques, 3D tracking, single molecule methods, modern microscopy methods and microfluidics. New theoretical techniques are also reviewed such as Bayesian analysis, oversampling, inversion techniques, alternative statistical tools for tracks (angular correlations, first passage probabilities, the kurtosis, motor protein step segmentation etc), issues in micro/macro rheological agreement and two particle methodologies. Applications where microrheology has begun to make some impact are also considered including semi-flexible polymers, gels, microorganism biofilms, intracellular methods, high frequency viscoelasticity, comb polymers, active motile fluids, blood clots, colloids, granular materials, polymers, liquid crystals and foods. Two large emergent areas of microrheology, non-linear microrheology and surface microrheology are also discussed.

Direct Comparison of Physical Properties of Bacillus subtilis NCIB 3610 and B-1 Biofilms

Many bacteria form surface-attached communities known as biofilms. Due to the extreme resistance of these bacterial biofilms to antibiotics and mechanical stresses, biofilms are of growing interest not only in microbiology but also in medicine and industry. Previous studies have determined the extracellular polymeric substances present in the matrix of biofilms formed by Bacillus subtilis NCIB 3610. However, studies on the physical properties of biofilms formed by this strain are just emerging. In particular, quantitative data on the contributions of biofilm matrix biopolymers to these physical properties are lacking. Here, we quantitatively investigated three physical properties of B. subtilis NCIB 3610 biofilms: the surface roughness and stiffness and the bulk viscoelasticity of these biofilms. We show how specific biomolecules constituting the biofilm matrix formed by this strain contribute to those biofilm properties. In particular, we demonstrate that the surface roughness and surface elasticity of 1-day-old NCIB 3610 biofilms are strongly affected by the surface layer protein BslA. For a second strain,B. subtilis B-1, which forms biofilms containing mainly γ-polyglutamate, we found significantly different physical biofilm properties that are also differently affected by the commonly used antibacterial agent ethanol. We show that B-1 biofilms are protected from ethanol-induced changes in the biofilm's stiffness and that this protective effect can be transferred to NCIB 3610 biofilms by the sole addition of γ-polyglutamate to growing NCIB 3610 biofilms. Together, our results demonstrate the importance of specific biofilm matrix components for the distinct physical properties of B. subtilis biofilms.

Multicomponent model of deformation and detachment of a biofilm under fluid flow

A novel biofilm model is described which systemically couples bacteria, extracellular polymeric substances (EPS) and solvent phases in biofilm. This enables the study of contributions of rheology of individual phases to deformation of biofilm in response to fluid flow as well as interactions between different phases. The model, which is based on first and second laws of thermodynamics, is derived using an energetic variational approach and phase-field method. Phase-field coupling is used to model structural changes of a biofilm. A newly developed unconditionally energy-stable numerical splitting scheme is implemented for computing the numerical solution of the model efficiently. Model simulations predict biofilm cohesive failure for the flow velocity between [Formula: see text] and [Formula: see text] m s(-1) which is consistent with experiments. Simulations predict biofilm deformation resulting in the formation of streamers for EPS exhibiting a viscous-dominated mechanical response and the viscosity of EPS being less than [Formula: see text]. Higher EPS viscosity provides biofilm with greater resistance to deformation and to removal by the flow. Moreover, simulations show that higher EPS elasticity yields the formation of streamers with complex geometries that are more prone to detachment. These model predictions are shown to be in qualitative agreement with experimental observations.

Biomechanical Analysis of Infectious Biofilms

The removal of infectious biofilms from tissues or implanted devices and their transmission through fluid transport systems depends in part of the mechanical properties of their polymeric matrix. Linking the various physical and chemical microscopic interactions to macroscopic deformation and failure modes promises to unveil design principles for novel therapeutic strategies targeting biofilm eradication, and provide a predictive capability to accelerate the development of devices, water lines, etc, that minimise microbial dispersal. Here, our current understanding of biofilm mechanics is appraised from the perspective of biophysics , with an emphasis on constitutive modelling that has been highly successful in soft matter. Fitting rheometric data to viscoelastic models has quantified linear and nonlinear stress relaxation mechanisms, how they vary between species and environments, and how candidate chemical treatments alter the mechanical response. The rich interplay between growth, mechanics and hydrodynamics is just becoming amenable to computational modelling and promises to provide unprecedented characterisation of infectious biofilms in their native state.

Functional bacterial amyloid increases Pseudomonas biofilm hydrophobicity and stiffness

The success of Pseudomonas species as opportunistic pathogens derives in great part from their ability to form stable biofilms that offer protection against chemical and mechanical attack. The extracellular matrix of biofilms contains numerous biomolecules, and it has recently been discovered that in Pseudomonas one of the components includes β-sheet rich amyloid fibrils (functional amyloid) produced by the fap operon. However, the role of the functional amyloid within the biofilm has not yet been investigated in detail. Here we investigate how the fap-based amyloid produced by Pseudomonas affects biofilm hydrophobicity and mechanical properties. Using atomic force microscopy imaging and force spectroscopy, we show that the amyloid renders individual cells more resistant to drying and alters their interactions with hydrophobic probes. Importantly, amyloid makes Pseudomonas more hydrophobic and increases biofilm stiffness 20-fold. Deletion of any one of the individual members of in the fap operon (except the putative chaperone FapA) abolishes this ability to increase biofilm stiffness and correlates with the loss of amyloid. We conclude that amyloid makes major contributions to biofilm mechanical robustness.

Molecular determinants of mechanical properties of V. cholerae biofilms at the air-liquid interface

Biofilm formation increases both the survival and infectivity of Vibrio cholerae, the causative agent of cholera. V. cholerae is capable of forming biofilms on solid surfaces and at the air-liquid interface, termed pellicles. Known components of the extracellular matrix include the matrix proteins Bap1, RbmA, and RbmC, an exopolysaccharide termed Vibrio polysaccharide, and DNA. In this work, we examined a rugose strain of V. cholerae and its mutants unable to produce matrix proteins by interfacial rheology to compare the evolution of pellicle elasticity in real time to understand the molecular basis of matrix protein contributions to pellicle integrity and elasticity. Together with electron micrographs, visual inspection, and contact angle measurements of the pellicles, we defined distinct contributions of the matrix proteins to pellicle morphology, microscale architecture, and mechanical properties. Furthermore, we discovered that Bap1 is uniquely required for the maintenance of the mechanical strength of the pellicle over time and contributes to the hydrophobicity of the pellicle. Thus, Bap1 presents an important matrix component to target in the prevention and dispersal of V. cholerae biofilms.

Microbial colonization of pancreatic duct stents: a prospective analysis

OBJECTIVE

The aim of the study was to analyze the microbial colonization rate as well as the spectrum and number of microorganisms in relation to the indwelling time of pancreatic stents.

METHODS

Forty pancreatic stents were prepared according to a standardized protocol and subsequently sonicated to optimize bacterial release from the biofilm on the stents.

RESULTS

Two hundred forty-six microorganisms were identified. Thirty-nine of 40 stents were colonized with microorganisms. Aerobic gram-positive microorganisms (106/246 [43%]) accounted for the greatest proportion. The predominant microorganisms were Streptococcus species (46/246 [19%]), which were isolated from 27 (68%) of 40 stents. Stents with a short indwelling time (3-13 days) were mainly colonized with aerobic gram-positive bacteria (82%) and Candida species (63%). In contrast, anaerobes (P < 0.01, 69% vs 18%) and aerobic gram-negative microorganisms (P < 0.01, 93% vs 45%) such as Enterobacteriaceae (P < 0.01, 86% vs 27%) were significantly more present on stents with a long indwelling time (29-93 days), compared with stents with a short indwelling time.

CONCLUSIONS

Microbial analysis of pancreatic duct stents revealed a very high colonization rate. Furthermore, the spectrum and number of microorganisms altered with the indwelling time of the stent. However, clinical relevance of our findings remains unclear.

Selected metal ions protect Bacillus subtilis biofilms from erosion

Many problems caused by bacterial biofilms can be traced back to their high resilience towards chemical perturbations and their extraordinary sturdiness towards mechanical forces. However, the molecular mechanisms that link the mechanical properties of a biofilm with the ability of bacteria to survive in different chemical environments remain enigmatic. Here, we study the erosion stability of Bacillus subtilis (B. subtilis) biofilms in the presence of different chemical environments. We find that these biofilms can utilize the absorption of certain metal ions such as Cu(2+), Zn(2+), Fe(2+), Fe(3+) and Al(3+) into the biofilm matrix to avoid erosion by shear forces. Interestingly, many of these metal ions are toxic for planktonic B. subtilis bacteria. However, their toxic activity is suppressed when the ions are absorbed into the biofilm matrix. Our experiments clearly demonstrate that the biofilm matrix has to fulfill a dual function, i.e. regulating both the mechanical properties of the biofilm and providing a selective barrier towards toxic chemicals.

An experimental and computational study of the hydrodynamics of high-velocity water microdrops for interproximal tooth cleaning

The flow field and local hydrodynamics of high-velocity water microdrops impacting the interproximal (IP) space of typodont teeth were studied experimentally and computationally. Fourteen-day old Streptococcus mutans biofilms in the IP space were treated by a prototype AirFloss delivering 115 µL of water at a maximum exit-velocity of 60 ms(-1) in a 33-ms burst. Using high-speed imaging, footage was generated showing the details of the burst, and demonstrating the removal mechanism of the biofilms. Footage was also generated to characterize the viscoelastic behavior of the biofilms when impacted by an air-only burst, which was compared to the water burst. Image analysis demonstrated the importance of fluid forces on the removal pattern of interdental biofilms. X-ray micro-Computed Tomography (µ-CT) was used to obtain 3D images of the typodont and the IP spaces. Computational Fluid Dynamics (CFD) simulations were performed to study the effect of changing the nozzle position and design on the hydrodynamics within the IP space. Results confirmed our previous data regarding the wall shear stress generated by high-velocity water drops which dictated the efficacy of biofilm detachment. Finally, we showed how CFD models could be used to optimize water drop or burst design towards a more effective biofilm removal performance.

Viscoelasticity of biofilms and their recalcitrance to mechanical and chemical challenges

We summarize different studies describing mechanisms through which bacteria in a biofilm mode of growth resist mechanical and chemical challenges. Acknowledging previous microscopic work describing voids and channels in biofilms that govern a biofilms response to such challenges, we advocate a more quantitative approach that builds on the relation between structure and composition of materials with their viscoelastic properties. Biofilms possess features of both viscoelastic solids and liquids, like skin or blood, and stress relaxation of biofilms has been found to be a corollary of their structure and composition, including the EPS matrix and bacterial interactions. Review of the literature on viscoelastic properties of biofilms in ancient and modern environments as well as of infectious biofilms reveals that the viscoelastic properties of a biofilm relate with antimicrobial penetration in a biofilm. In addition, also the removal of biofilm from surfaces appears governed by the viscoelasticity of a biofilm. Herewith, it is established that the viscoelasticity of biofilms, as a corollary of structure and composition, performs a role in their protection against mechanical and chemical challenges. Pathways are discussed to make biofilms more susceptible to antimicrobials by intervening with their viscoelasticity, as a quantifiable expression of their structure and composition.

Recalcitrance of biofilms against mechanical and chemical challenges has been looked at for ages from a microbiological perspective, but an approach based on viscoelastic properties of biofilms yields new insights in this recalcitrance.

Material properties of biofilms-a review of methods for understanding permeability and mechanics

Microorganisms can form biofilms, which are multicellular communities surrounded by a hydrated extracellular matrix of polymers. Central properties of the biofilm are governed by this extracellular matrix, which provides mechanical stability to the 3D biofilm structure, regulates the ability of the biofilm to adhere to surfaces, and determines the ability of the biofilm to adsorb gases, solutes, and foreign cells. Despite their critical relevance for understanding and eliminating of biofilms, the materials properties of the extracellular matrix are understudied. Here, we offer the reader a guide to current technologies that can be utilized to specifically assess the permeability and mechanical properties of the biofilm matrix and its interacting components. In particular, we highlight technological advances in instrumentation and interactions between multiple disciplines that have broadened the spectrum of methods available to conduct these studies. We review pioneering work that furthers our understanding of the material properties of biofilms.

Interplay of physical mechanisms and biofilm processes: review of microfluidic methods

Bacteria in natural and artificial environments often reside in self-organized, integrated communities known as biofilms. Biofilms are highly structured entities consisting of bacterial cells embedded in a matrix of self-produced extracellular polymeric substances (EPS). The EPS matrix acts like a biological 'glue' enabling microbes to adhere to and colonize a wide range of surfaces. Once integrated into biofilms, bacterial cells can withstand various forms of stress such as antibiotics, hydrodynamic shear and other environmental challenges. Because of this, biofilms of pathogenic bacteria can be a significant health hazard often leading to recurrent infections. Biofilms can also lead to clogging and material degradation; on the other hand they are an integral part of various environmental processes such as carbon sequestration and nitrogen cycles. There are several determinants of biofilm morphology and dynamics, including the genotypic and phenotypic states of constituent cells and various environmental conditions. Here, we present an overview of the role of relevant physical processes in biofilm formation, including propulsion mechanisms, hydrodynamic effects, and transport of quorum sensing signals. We also provide a survey of microfluidic techniques utilized to unravel the associated physical mechanisms. Further, we discuss the future research areas for exploring new ways to extend the scope of the microfluidic approach in biofilm studies.

Disruption and eradication of P. aeruginosa biofilms using nitric oxide-releasing chitosan oligosaccharides

Biofilm disruption and eradication were investigated as a function of nitric oxide- (NO) releasing chitosan oligosaccharide dose and the results compared with control (i.e., non-NO-releasing) chitosan oligosaccharides and tobramycin. Quantification of biofilm expansion/contraction and multiple-particle tracking microrheology were used to assess the structural integrity of the biofilm before and after antibacterial treatment. While tobramycin had no effect on the physical properties of the biofilm, NO-releasing chitosan oligosaccharides exhibited dose-dependent behavior with biofilm degradation. Control chitosan oligosaccharides increased biofilm elasticity, indicating that the scaffold may mitigate the biofilm disrupting power of nitric oxide somewhat. The results from this study indicate that nitric oxide-releasing chitosan oligosaccharides act as dual-action therapeutics capable of eradicating and physically disrupting P. aeruginosa biofilms.

Soft robotic concepts in catheter design: an on-demand fouling-release urinary catheter

Infectious biofilms are problematic in many healthcare-related devices and are especially challenging and ubiquitous in urinary catheters. This report presents an on-demand fouling-release methodology to mechanically disrupt and remove biofilms, and proposes this method for the active removal of infectious biofilms from the previously inaccessible main drainage lumen of urinary catheters. Mature Proteus mirabilis crystalline biofilms detach from silicone elastomer substrates upon application of strain to the substrate, and increasing the strain rate increases biofilm detachment. The study presents a quantitative relationship between applied strain rate and biofilm debonding through an analysis of biofilm segment length and the driving force for debonding. Based on this mechanism, hydraulic and pneumatic elastomer actuation is used to achieve surface strain selectively within the lumen of prototypes of sections of a fouling-release urinary catheter. Proof-of-concept prototypes of sections of active, fouling-release catheters are constructed using techniques typical to soft robotics including 3D printing and replica molding, and those prototypes demonstrate release of mature P. mirabilis crystalline biofilms (e.g., ≈90%) from strained surfaces. These results provide a basis for the development of a new urinary catheter technology in which infectious biofilms are effectively managed through new methods that are entirely complementary to existing approaches.

Modelling and analysis of a gene-regulatory feed-forward loop with basal expression of the second regulator

Efficient adaptation strategies to changing environmental conditions are essential for bacteria to survive and grow. Fundamental restructuring of their metabolism is usually mediated by corresponding gene regulation. Here, often several different environmental stimuli have to be integrated into a reasonable, energy-efficient response. Fast fluctuations and overshooting have to be filtered out. The gene regulatory network for the anaerobic adaptation of the pathogenic bacterium Pseudomonas aeruginosa is organized as a feed-forward loop (FFL), which is a three-gene network motif composed of two transcription factors (Anr for oxygen, NarxL for nitrate) and one target (Nar for nitrate reductase). The upstream transcription factor (Anr) induces the downstream transcription factor (NarXL). Both regulators act together positively by inducing the target (Nar) via a direct and indirect regulation path (coherent type-1 FFL). Since full promoter activity is only achieved when both transcription factors are present the target operon is expressed with a delay. Thus, in response to environmental stimuli (oxygen, nitrate), signals are mediated and processed in a way that short pulses are filtered out. In this study we analyze a special kind of FFL called FFLk by means of a family of ordinary differential equation models. The secondary FFL regulator (NarXL) is expressed constitutively but further induced in the presence of the upstream stimuli. This FFL modification has substantial influence on the response time and cost-benefit ratio mediated by environmental fluctuations. In order to find conditions where this regulatory network motif might be beneficial, we analyzed various models and environments. We describe the observed evolutional advantage of FFLk and its role in environmental adaptation and pathogenicity.

Single particle tracking reveals spatial and dynamic organization of the E. coli biofilm matrix

Biofilms are communities of surface-adherent bacteria surrounded by secreted polymers known as the extracellular polymeric substance (EPS). Biofilms are harmful in many industries, and thus it is of great interest to understand their mechanical properties and structure to determine ways to destabilize them. By performing single particle tracking with beads of varying surface functionalization it was found that charge interactions play a key role in mediating mobility within biofilms. With a combination of single particle tracking and microrheological concepts, it was found that Escherichia coli biofilms display height dependent charge density that evolves over time. Statistical analyses of bead trajectories and confocal microscopy showed inter-connecting micron scale channels that penetrate throughout the biofilm, which may be important for nutrient transfer through the system. This methodology provides significant insight into a particular biofilm system and can be applied to many others to provide comparisons of biofilm structure. The elucidation of structure provides evidence for the permeability of biofilms to microscale objects, and the ability of a biofilm to mature and change properties over time.

Visualization of microbiological processes underlying stress relaxation in Pseudomonas aeruginosa biofilms

Bacterial biofilms relieve themselves from external stresses through internal rearrangement, as mathematically modeled in many studies, but never microscopically visualized for their underlying microbiological processes. The aim of this study was to visualize rearrangement processes occurring in mechanically deformed biofilms using confocal-laser-scanning-microscopy after SYTO9 (green-fluorescent) and calcofluor-white (blue-fluorescent) staining to visualize bacteria and extracellular-polymeric matrix substances, respectively. We apply 20% uniaxial deformation to Pseudomonas aeruginosa biofilms and fix deformed biofilms prior to staining, after allowing different time-periods for relaxation. Two isogenic P. aeruginosa strains with different abilities to produce extracellular polymeric substances (EPS) were used. By confocal-laser-scanning-microscopy all biofilms showed intensity distributions for fluorescence from which rearrangement of EPS and bacteria in deformed biofilms were derived. For the P. aeruginosa strain producing EPS, bacteria could not find new, stable positions within 100 s after deformation, while EPS moved toward deeper layers within 20 s. Bacterial rearrangement was not seen in P. aeruginosa biofilms deficient in production of EPS. Thus, EPS is required to stimulate bacterial rearrangement in mechanically deformed biofilms within the time-scale of our experiments, and the mere presence of water is insufficient to induce bacterial movement, likely due to its looser association with the bacteria.

Drinking water biofilm cohesiveness changes under chlorination or hydrodynamic stress

Attempts at removal of drinking water biofilms rely on various preventive and curative strategies such as nutrient reduction in drinking water, disinfection or water flushing, which have demonstrated limited efficiency. The main reason for these failures is the cohesiveness of the biofilm driven by the physico-chemical properties of its exopolymeric matrix (EPS). Effective cleaning procedures should break up the matrix and/or change the elastic properties of bacterial biofilms. The aim of this study was to evaluate the change in the cohesive strength of two-month-old drinking water biofilms under increasing hydrodynamic shear stress τw (from ∼0.2 to ∼10 Pa) and shock chlorination (applied concentration at T0: 10 mg Cl2/L; 60 min contact time). Biofilm erosion (cell loss per unit surface area) and cohesiveness (changes in the detachment shear stress and cluster volumes measured by atomic force microscopy (AFM)) were studied. When rapidly increasing the hydrodynamic constraint, biofilm removal was found to be dependent on a dual process of erosion and coalescence of the biofilm clusters. Indeed, 56% of the biofilm cells were removed with, concomitantly, a decrease in the number of the 50-300 μm(3) clusters and an increase in the number of the smaller (i.e., <50 μm(3)) and larger (i.e., >600 μm(3)) ones. Moreover, AFM evidenced the strengthening of the biofilm structure along with the doubling of the number of contact points, NC, per cluster volume unit following the hydrodynamic disturbance. This suggests that the compactness of the biofilm exopolymers increases with hydrodynamic stress. Shock chlorination removed cells (-75%) from the biofilm while reducing the volume of biofilm clusters. Oxidation stress resulted in a decrease in the cohesive strength profile of the remaining drinking water biofilms linked to a reduction in the number of contact points within the biofilm network structure in particular for the largest biofilm cluster volumes (>200 μm(3)). Changes in the cohesive strength of drinking water biofilms subsequent to cleaning/disinfection operations call into question the effectiveness of cleaning-in-place procedures. The combined alternating use of oxidation and shear stress sequences needs to be investigated as it could be an important adjunct to improving biofilm removal/reduction procedures.

Pseudomonas biofilms: possibilities of their control

Genus Pseudomonas includes a large number of species that can be encountered in biotechnological processes as well as in the role of serious human or plant pathogens. Pseudomonads easily form biofilms on various types of surfaces. The biofilm phenotype is characterized by an increased resistance to environmental influences including resistance to antibiotics and other disinfectants, causing a number of problems in health care, food industry, and other areas. Considerable attention is therefore paid to the possibilities of eradication/destruction of pseudomonads biofilms both in terms of understanding the mechanisms of biofilm formation and at the level of finding suitable antibiofilm tools applicable in practice. The first part of this review is devoted to an overview of the regulatory mechanisms that are directly or indirectly involved in the formation of biofilm. The most effective approaches to suppressing the formation of biofilm that do not cause the development of resistance are based on the application of substances that interfere with the regulatory molecules or block the appropriate regulatory mechanisms involved in biofilm development by the cells. Pseudomonads biofilm formation is, similar to other microorganisms, a sophisticated process with many regulatory elements. The suppression of this process therefore also requires multiple antibiofilm tools.

Biophysics of biofilm infection

This article examines a likely basis of the tenacity of biofilm infections that has received relatively little attention: the resistance of biofilms to mechanical clearance. One way that a biofilm infection persists is by withstanding the flow of fluid or other mechanical forces that work to wash or sweep microorganisms out of the body. The fundamental criterion for mechanical persistence is that the biofilm failure strength exceeds the external applied stress. Mechanical failure of the biofilm and release of planktonic microbial cells is also important in vivo because it can result in dissemination of infection. The fundamental criterion for detachment and dissemination is that the applied stress exceeds the biofilm failure strength. The apparent contradiction for a biofilm to both persist and disseminate is resolved by recognizing that biofilm material properties are inherently heterogeneous. There are also mechanical aspects to the ways that infectious biofilms evade leukocyte phagocytosis. The possibility of alternative therapies for treating biofilm infections that work by reducing biofilm cohesion could (1) allow prevailing hydrodynamic shear to remove biofilm, (2) increase the efficacy of designed interventions for removing biofilms, (3) enable phagocytic engulfment of softened biofilm aggregates, and (4) improve phagocyte mobility and access to biofilm.

Microstructure and mechanical properties of in situ Streptococcus mutans biofilms

Insight into live microbial biofilm microstructure and mechanical properties and their interactions with the underlying substrate can lead to the development of new remedial strategies and/or materials. Here we report mechanical properties of dental pathogenic Streptococcus mutans biofilms, grown on a polystyrene-coated plate of a shear rheometer in physiologically relevant conditions, precisely controlled in a custom built bioreactor. In situ measurements demonstrated the importance of microstructure and composition of extracellular polymeric substances on the biofilm modulus. The biofilms behave like a weak gel with storage moduli higher than loss moduli. The simple but robust experimental technique presented here can easily be extended to other biofilm-material systems.

Disruption of putrescine biosynthesis in Shewanella oneidensis enhances biofilm cohesiveness and performance in Cr(VI) immobilization

Although biofilm-based bioprocesses have been increasingly used in various applications, the long-term robust and efficient biofilm performance remains one of the main bottlenecks. In this study, we demonstrated that biofilm cohesiveness and performance of Shewanella oneidensis can be enhanced through disrupting putrescine biosynthesis. Through random transposon mutagenesis library screening, one hyperadherent mutant strain, CP2-1-S1, exhibiting an enhanced capability in biofilm formation, was obtained. Comparative analysis of the performance of biofilms formed by S. oneidensis MR-1 wild type (WT) and CP2-1-S1 in removing dichromate (Cr2O7(2-)), i.e., Cr(VI), from the aqueous phase showed that, compared with the WT biofilms, CP2-1-S1 biofilms displayed a substantially lower rate of cell detachment upon exposure to Cr(VI), suggesting a higher cohesiveness of the mutant biofilms. In addition, the amount of Cr(III) immobilized by CP2-1-S1 biofilms was much larger, indicating an enhanced performance in Cr(VI) bioremediation. We further showed that speF, a putrescine biosynthesis gene, was disrupted in CP2-1-S1 and that the biofilm phenotypes could be restored by both genetic and chemical complementations. Our results also demonstrated an important role of putrescine in mediating matrix disassembly in S. oneidensis biofilms.

Formation of Kinneyia via shear-induced instabilities in microbial mats

Kinneyia are a class of microbially mediated sedimentary fossils. Characterized by clearly defined ripple structures, Kinneyia are generally found in areas that were formally littoral habitats and covered by microbial mats. To date, there has been no conclusive explanation of the processes involved in the formation of these fossils. Microbial mats behave like viscoelastic fluids. We propose that the key mechanism involved in the formation of Kinneyia is a Kelvin-Helmholtz-type instability induced in a viscoelastic film under flowing water. A ripple corrugation is spontaneously induced in the film and grows in amplitude over time. Theoretical predictions show that the ripple instability has a wavelength proportional to the thickness of the film. Experiments carried out using viscoelastic films confirm this prediction. The ripple pattern that forms has a wavelength roughly three times the thickness of the film. This behaviour is independent of the viscosity of the film and the flow conditions. Laboratory-analogue Kinneyia were formed via the sedimentation of glass beads, which preferentially deposit in the troughs of the ripples. Well-ordered patterns form, with both honeycomb-like and parallel ridges being observed, depending on the flow speed. These patterns correspond well with those found in Kinneyia, with similar morphologies, wavelengths and amplitudes being observed.

Role of environmental and antibiotic stress on Staphylococcus epidermidis biofilm microstructure

Cellular clustering and separation of Staphylococcus epidermidis surface adherent biofilms were found to depend significantly on both antibiotic and environmental stress present during growth under steady flow. Image analysis techniques common to colloidal science were applied to image volumes acquired with high-resolution confocal laser scanning microscopy to extract spatial positions of individual bacteria in volumes of size ~30 × 30 × 15 μm(3). The local number density, cluster distribution, and radial distribution function were determined at each condition by analyzing the statistics of the bacterial spatial positions. Environmental stressors of high osmotic pressure (776 mM NaCl) and sublethal antibiotic dose (1.9 μg/mL vancomycin) decreased the average bacterial local number density 10-fold. Device-associated bacterial biofilms are frequently exposed to these environmental and antibiotic stressors while undergoing flow in the bloodstream. Characteristic density phenotypes associated with low, medium, and high local number densities were identified in unstressed S. epidermidis biofilms, while stressed biofilms contained medium- and low-density phenotypes. All biofilms exhibited clustering at length scales commensurate with cell division (~1.0 μm). However, density phenotypes differed in cellular connectivity at the scale of ~6 μm. On this scale, nearly all cells in the high- and medium-density phenotypes were connected into a single cluster with a structure characteristic of a densely packed disordered fluid. However, in the low-density phenotype, the number of clusters was greater, equal to 4% of the total number of cells, and structures were fractal in nature with d(f) =1.7 ± 0.1. The work advances the understanding of biofilm growth, informs the development of predictive models of transport and mechanical properties of biofilms, and provides a method for quantifying the kinetics of bacterial surface colonization as well as biofilm fracture and fragmentation.

Spectrum of pathogens in acute cholangitis in patients with and without biliary endoprosthesis

BACKGROUND

Knowledge of bacterial spectrum for acute cholangitis is essential for adequate empiric antibiotic treatment. Main focus of the study was to analyse the spectrum of pathogens in acute cholangitis with and without biliary endoprosthesis.

METHODS

Retrospective cohort study of 1024 patients with acute cholangitis treated at a German tertiary center.

RESULTS

447 cholangitis episodes with positive bile and/or blood cultures obtained from 388 patients were studied. In total, 1088 pathogen were isolated. The predominant strains were Enterococcus species (25%), followed by Escherichia coli (18%) and Klebsiella species (14%). Bacteraemia was mainly caused by E. coli (91/282; 32%) and Enterococcus species (550/282; 18%). The incidences of Enterococcus species [121(74%) vs. 89(60%); p = 0.011] and non-fermenters [41(25%) vs. 16(11%); p = 0.001] were significantly higher in cholangitis episodes with biliary endoprosthesis compared to cholangitis episodes without biliary endoprosthesis. In particular, more Pseudomonas aeruginosa [27(16%) vs. 12(8%); p = 0.027] and Enterococcus faecium [59(36%) vs. 34(23%); p = 0.013] were isolated from patients with a biliary endoprosthesis.

CONCLUSIONS

Unlike cholangitis without stent, the presence of biliary endoprosthesis in patients with cholangitis can serve as a surrogate indicator of nosocomial pathogens and therefore should be considered, when selecting empiric antimicrobial therapy.

Quantitative analysis of amyloid-integrated biofilms formed by uropathogenic Escherichia coli at the air-liquid interface

Bacterial biofilms are complex multicellular assemblies, characterized by a heterogeneous extracellular polymeric matrix, that have emerged as hallmarks of persistent infectious diseases. New approaches and quantitative data are needed to elucidate the composition and architecture of biofilms, and such data need to be correlated with mechanical and physicochemical properties that relate to function. We performed a panel of interfacial rheological measurements during biofilm formation at the air-liquid interface by the Escherichia coli strain UTI89, which is noted for its importance in studies of urinary tract infection and for its assembly of functional amyloid fibers termed curli. Brewster-angle microscopy and measurements of the surface elasticity (G(s)') and stress-strain response provided sensitive and quantitative parameters that revealed distinct stages during bacterial colonization, aggregation, and eventual formation of a pellicle at the air-liquid interface. Pellicles that formed under conditions that upregulate curli production exhibited an increase in strength and viscoelastic properties as well as a greater ability to recover from stress-strain perturbation. The results suggest that curli, as hydrophobic extracellular amyloid fibers, enhance the strength, viscoelasticity, and resistance to strain of E. coli biofilms formed at the air-liquid interface.

Molecular architecture and assembly principles of Vibrio cholerae biofilms

In their natural environment, microbes organize into communities held together by an extracellular matrix composed of polysaccharides and proteins. We developed an in vivo labeling strategy to allow the extracellular matrix of developing biofilms to be visualized with conventional and superresolution light microscopy. Vibrio cholerae biofilms displayed three distinct levels of spatial organization: cells, clusters of cells, and collections of clusters. Multiresolution imaging of living V. cholerae biofilms revealed the complementary architectural roles of the four essential matrix constituents: RbmA provided cell-cell adhesion; Bap1 allowed the developing biofilm to adhere to surfaces; and heterogeneous mixtures of Vibrio polysaccharide, RbmC, and Bap1 formed dynamic, flexible, and ordered envelopes that encased the cell clusters.

Hydrodynamic deformation and removal of Staphylococcus epidermidis biofilms treated with urea, chlorhexidine, iron chloride, or DispersinB

The force-deflection and removal characteristics of bacterial biofilm were measured by two different techniques before and after chemical, or enzymatic, treatment. The first technique involved time lapse imaging of a biofilm grown in a capillary flow cell and subjected to a brief shear stress challenge imparted through increased fluid flow. Biofilm removal was determined by calculating the reduction in biofilm area from quantitative analysis of transmission images. The second technique was based on micro-indentation using an atomic force microscope. In both cases, biofilms formed by Staphylococcus epidermidis were exposed to buffer (untreated control), urea, chlorhexidine, iron chloride, or DispersinB. In control experiments, the biofilm exhibited force-deflection responses that were similar before and after the same treatment. The biofilm structure was stable during the post-treatment shear challenge (1% loss). Biofilms treated with chlorhexidine became less deformable after treatment and no increase in biomass removal was seen during the post-treatment shear challenge (2% loss). In contrast, biofilms treated with urea or DispersinB became more deformable and exhibited significant biofilm loss during the post-treatment flow challenge (71% and 40%, respectively). During the treatment soak phase, biofilms exposed to urea swelled. Biofilms exposed to iron chloride showed little difference from the control other than slight contraction during the treatment soak. These observations suggest the following interpretations: (1) chemical or enzymatic treatments, including those that are not frankly antimicrobial, can alter the cohesion of bacterial biofilm; (2) biocidal treatments (e.g., chlorhexidine) do not necessarily weaken the biofilm; and (3) biofilm removal following treatment with agents that make the biofilm more deformable (e.g., urea, DispersinB) depend on interaction between the moving fluid and the biofilm structure. Measurements such as those reported here open the door to development of new technologies for controlling detrimental biofilms by targeting biofilm cohesion rather than killing microorganisms.