Luminescent Nanosensors for Ratiometric Monitoring of Three-Dimensional Oxygen Gradients in Laboratory and Clinical Pseudomonas aeruginosa Biofilms

Persistent Luminescence Nanosensors: A Generalized Optode-Based Platform for Autofluorescence-Free Sensing in Biological Systems

Fluorescent nanosensors have revolutionized diagnostics and our ability to monitor cellular dynamics. Yet, distinguishing sensor signals from autofluorescence remains a challenge. Here, we merged optode-based sensing with near-infrared-emitting ZnGa2O4:Cr3+ persistent luminescence nanoparticles (PLNPs) to create nanocomposites for autofluorescence-free "glow-in-the-dark" sensing. Hydrophobic modification and incorporation of the persistent luminescence nanoparticles into an optode-based nanoparticle core yielded persistent luminescence nanosensors (PLNs) for five analytes (K+, Na+, Ca2+, pH, and O2) via two distinct mechanisms. We demonstrated the viability of the PLNs by quantifying K+ in fetal bovine serum, calibrating the pH PLNs in the same, and ratiometrically monitoring O2 metabolism in cultures of Saccharomyces cerevisiae, all the while overcoming their respective autofluorescence signatures. This highly modular platform allows for facile tuning of the sensing functionality, optical properties, and surface chemistry and promises high signal-to-noise ratios in complex optical environments.

Organosilica Nanosensors for Monitoring Spatiotemporal Changes in Oxygen Levels in Bacterial Cultures

Oxygen plays a central role in aerobic metabolism, and while many approaches have been developed to measure oxygen concentration in biological environments over time, monitoring spatiotemporal changes in dissolved oxygen levels remains challenging. To address this, we developed a ratiometric core-shell organosilica nanosensor for continuous, real-time optical monitoring of oxygen levels in biological environments. The nanosensors demonstrate good steady state characteristics (KpSV = 0.40 L/mg, R2 = 0.95) and respond reversibly to changes in oxygen concentration in buffered solutions and report similar oxygen level changes in response to bacterial cell growth (Escherichia coli) in comparison to a commercial bulk optode-based sensing film. We further demonstrated that the oxygen nanosensors could be distributed within a growing culture of E. coli and used to record oxygen levels over time and in different locations within a static culture, opening the possibility of spatiotemporal monitoring in complex biological systems.

Sensor system for analysis of biofilm sensitivity to ampicillin

The resistance of biofilms to antibiotics is a key factor that makes bacterial infections unsusceptible to antimicrobial therapy. The results of classical tests of cell sensitivity to antibiotics cannot be used to predict therapeutic success in infections associated with biofilm formation. We describe a simple and rapid method for the real-time evaluation of bacterial biofilm sensitivity to antibiotics, with Pseudomonas putida and ampicillin as examples. The method uses an electric biosensor to detect the difference between changes in the biofilm electric polarizability, thereby evaluating antibiotic sensitivity. The electric signals showed that P. putida biofilms were susceptible to ampicillin and that at high antibiotic concentrations, the biofilms differed markedly in their susceptibility (dose-dependent effect). The sensor also detected differences between biofilms before and after ampicillin treatment. The electric-signal changes enabled us to describe the physical picture of the processes occurring in bacterial biofilms in the presence of ampicillin. The approach used in this study is promising for evaluating the activity of various compounds against biofilms, because it permits a conclusion about the antibiotic sensitivity of biofilm bacteria to be made in real time and in a short period (analysis time, not longer than 20 min). An added strong point is that analysis can be done directly in liquid, without preliminary sample preparation. KEY POINTS: • Sensor system to analyze biofilm antimicrobial susceptibility is described. • The signal change depended on the ampicillin concentration (dose-dependent effect). • The sensor allows real-time determination of the antibiofilm effect of ampicillin.

Triplet-Triplet Annihilation Upconversion-Based Oxygen Sensors to Overcome the Limitation of Autofluorescence

Autofluorescence is one of the many challenges in bioimaging as it can mask the emission from fluorescent probes or markers, a limitation that can be overcome via upconversion. Herein, we have developed a nanosensor that uses triplet-triplet annihilation upconversion to optically report changes in the dissolved oxygen concentration. Using a sensitizer-annihilator dye pairing of platinum(II) octaethylporphyrin and 9,10-diphenylanthracene, we monitored the oxygen consumption (as a proxy for metabolic activity) over time in a biological system─Saccharomyces cerevisiae (brewing yeast). The nanosensor demonstrated good reversibility over multiple cycles and showed good signal and colloidal stability when tested over the course of 7 days, and it was sensitive to dissolved oxygen from 0.00 to 3.17 mg/L O2. Additionally, there was no signal overlap between the nanosensor emission and S. cerevisiae autofluorescence, thus underscoring the utility of upconversion as a facile and economical means of overcoming autofluorescence.

The role of nanocomposites against biofilm infections in humans

The use of nanomaterials in several fields of science has undergone a revolution in the last few decades. It has been reported by the National Institutes of Health (NIH) that 65% and 80% of infections are accountable for at least 65% of human bacterial infections. One of their important applications in healthcare is the use of nanoparticles (NPs) to eradicate free-floating bacteria and those that form biofilms. A nanocomposite (NC) is a multiphase stable fabric with one or three dimensions that are much smaller than 100 nm, or systems with nanoscale repeat distances between the unique phases that make up the material. Using NC materials to get rid of germs is a more sophisticated and effective technique to destroy bacterial biofilms. These biofilms are refractory to standard antibiotics, mainly to chronic infections and non-healing wounds. Materials like graphene and chitosan can be utilized to make several forms of NCs, in addition to different metal oxides. The ability of NCs to address the issue of bacterial resistance is its main advantage over antibiotics. This review highlights the synthesis, characterization, and mechanism through which NCs disrupt Gram-positive and Gram-negative bacterial biofilms, and their relative benefits and drawbacks. There is an urgent need to develop materials like NCs with a larger spectrum of action due to the rising prevalence of human bacterial diseases that are multidrug-resistant and form biofilms.

Optical O2 Sensors Also Respond to Redox Active Molecules Commonly Secreted by Bacteria

From a metabolic perspective, molecular oxygen (O2) is arguably the most significant constituent of Earth's atmosphere. Nearly every facet of microbial physiology is sensitive to the presence and concentration of O2, which is the most favorable terminal electron acceptor used by organisms and also a dangerously reactive oxidant. As O2 has such sweeping implications for physiology, researchers have developed diverse approaches to measure O2 concentrations in natural and laboratory settings. Recent improvements to phosphorescent O2 sensors piqued our interest due to the promise of optical measurement of spatiotemporal O2 dynamics. However, we found that our preferred bacterial model, Pseudomonas aeruginosa PA14, secretes more than one molecule that quenches such sensors, complicating O2 measurements in PA14 cultures and biofilms. Assaying supernatants from cultures of 9 bacterial species demonstrated that this phenotype is common: all supernatants quenched a soluble O2 probe substantially. Phosphorescent O2 probes are often embedded in solid support for protection, but an embedded probe called O2NS was quenched by most supernatants as well. Measurements using pure compounds indicated that quenching is due to interactions with redox-active small molecules, including phenazines and flavins. Uncharged and weakly polar molecules like pyocyanin were especially potent quenchers of O2NS. These findings underscore that optical O2 measurements made in the presence of bacteria should be carefully controlled to ensure that O2, and not bacterial secretions, is measured, and motivate the design of custom O2 probes for specific organisms to circumvent sensitivity to redox-active metabolites. IMPORTANCE When they are closely packed, as in biofilms, colonies, and soils, microbes can consume O2 faster than it diffuses. As such, O2 concentrations in natural environments can vary greatly over time and space, even on the micrometer scale. Wetting soil, for example, slows O2 diffusion higher in the soil column, which, in concert with microbial respiration, greatly diminishes [O2] at depth. Given that variation in [O2] has outsized implications for microbial physiology, there is great interest in measuring the dynamics of [O2] in microbial cultures and biofilms. We demonstrate that certain classes of bacterial metabolites frustrate optical measurement of [O2] with phosphorescent sensors, but also that some species (e.g., E. coli) do not produce problematic secretions under the conditions tested. Our work therefore offers a strategy for identifying organisms and culture conditions in which optical quantification of spatiotemporal [O2] dynamics with current sensors is feasible.

Sensors in a Flash! Oxygen Nanosensors for Microbial Metabolic Monitoring Synthesized by Flash Nanoprecipitation

Flash nanoprecipitation (FNP) is an efficient and scalable nanoparticle synthesis method that has not previously been applied to nanosensor fabrication. Current nanosensor fabrication methods have traditionally exhibited poor replicability and consistency resulting in high batch-to-batch variability, highlighting the need for a more tunable and efficient method such as FNP. We used FNP to fabricate nanosensors to sense oxygen based on an oxygen-sensitive dye and a reference dye, as a tool for measuring microbial metabolism. We used fluorescence spectroscopy to optimize nanosensor formulations, calibrate the nanosensors for oxygen concentration determination, and measure oxygen concentrations through oxygen-sensitive dye luminescence. FNP provides an effective platform for making sensors capable of responding to oxygen concentration in gas-bubbled solutions as well as in microbial environments. The environments we tested the sensors in arePseudomonas aeruginosa biofilms andSaccharomyces cerevisiae liquid cultures─both settings where oxygen concentration is highly dependent on microbial activity. With FNP now applied to nanosensor fabrication, future nanosensor applications can take advantage of improved product quality through better replicability and consistency while maintaining the original function of the nanosensor.

Detection and Characterization of Bacterial Biofilms and Biofilm-Based Sensors

Microbial biofilms have caused serious concerns in healthcare, medical, and food industries because of their intrinsic resistance against conventional antibiotics and cleaning procedures and their capability to firmly adhere on surfaces for persistent contamination. These global issues strongly motivate researchers to develop novel methodologies to investigate the kinetics underlying biofilm formation, to understand the response of the biofilm with different chemical and physical treatments, and to identify biofilm-specific drugs with high-throughput screenings. Meanwhile microbial biofilms can also be utilized positively as sensing elements in cell-based sensors due to their strong adhesion on surfaces. In this perspective, we provide an overview on the connections between sensing and microbial biofilms, focusing on tools used to investigate biofilm properties, kinetics, and their response to chemicals or physical agents, and biofilm-based sensors, a type of biosensor using the bacterial biofilm as a biorecognition element to capture the presence of the target of interest by measuring the metabolic activity of the immobilized microbial cells. Finally we discuss possible new research directions for the development of robust and rapid biofilm related sensors with high temporal and spatial resolutions, pertinent to a wide range of applications.

Nanoparticle-Based Liquid-Liquid Extraction for the Determination of Metal Ions

Traditional liquid phase extraction techniques that use optically responsive ligands provide benefits that enable cost-efficient and rapid measurements. However, these approaches have limitations in their excessive use of organic solvents and multistep procedures. Here, we developed a simple, nanoscale extraction approach by replacing the macroscopic organic phase with hydrophobic polymeric nanoparticles that are dispersed in an aqueous feed. The concentration of analytes in polymeric nanoparticle suspensions is governed by similar partition principles to liquid-liquid phase extraction techniques. By encasing optically responsive metal ligands inside polymeric nanoparticles, we introduce a one-step metal quantification assay based on traditional two-phase extraction methodologies. As an initial proof of concept, we encapsulated bathophenanthroline (BP) inside the particles to extract then quantify Fe2+ with colorimetry in a dissolved supplement tablet and creek water. These Fe2+ nanosensors are sensitive and selective and report out with fluorescence by adding a fluorophore (DiO) into the particle core. To show that this new rapid extraction assay is not exclusive to measuring Fe2+, we replaced BP with either 8-hydroxyquinoline or bathocuproine to measure Al3+ or Cu+, respectively, in water samples. Utilizing this nanoscale extraction approach will allow users to rapidly quantify metals of interest without the drawbacks of larger-scale phase extraction approaches while also allowing for the expansion of phase extraction methodologies into areas of biological research.

A near-infrared optical nanosensor for measuring aerobic respiration in microbial systems

We developed a ratiometric oxygen-sensitive nanosensor and demonstrated application in monitoring metabolic oxygen consumption in microbial samples over time. Based on a near-infrared (NIR) emitting oxygen-quenched luminophore, platinum(II) octaethylporphine ketone (PtOEPK), along with a stable dioctadecyl dicarbocyanine reference dye (DiD), this nanosensor system provides an advantageous approach for overcoming imaging issues in biological systems, such as autofluorescence and optical scattering in the visible wavelength region. The dyes are encapsulated within a polymer-based nanoparticle matrix to maintain them at a constant ratio in biological samples, precluding the need for complex synthetic approaches. With this constant ratio of the two dyes, the nanosensor response can be measured as a ratio of their two signals, accounting for nanosensor concentration artifacts in measurements. The nanosensors are reversible, which enabled us to temporally monitor systems in which dissolved oxygen concentrations both increase and decrease. These sensors were applied for the monitoring of oxygen in samples of Saccharomyces cerevisiae (brewing yeast) in a 96-well optical fluorescence plate reader format over 60 h. By mixing the nanosensors directly into the sample well with the yeast, we were able to dynamically track metabolic activity changes over time due to varying cell concentration and exposure to an antimicrobial agent. This system could be a potential platform for high-throughput screening of various species or variants of microbes with unknown metabolic rates in response to external stimuli (antimicrobials, metabolites, etc.).

LipiSensors: Exploiting Lipid Nanoemulsions to Fabricate Ionophore-Based Nanosensors

Ionophore-based nanosensors (IBNS) are tools that enable quantification of analytes in complex chemical and biological systems. IBNS methodology is adopted from that of bulk optodes where an ion exchange event is converted to a change in optical output. While valuable, an important aspect for application is the ability to intentionally tune their size with simple approaches, and ensure that they contain compounds safe for application. Lipidots are a platform of size tunable lipid nanoemulsions with a hydrophobic lipid core typically used for imaging and drug delivery. Here, we present LipiSensors as size tunable IBNS by exploiting the Lipidot model as a hydrophobic structural support for the sensing moieties that are traditionally encased in plasticized PVC nanoparticles. The LipiSensors we demonstrate here are sensitive and selective for calcium, reversible, and have a lifetime of approximately one week. By changing the calcium sensing components inside the hydrophobic core of the LipiSensors to those sensitive for oxygen, they are also able to be used as ratiometric O₂ sensitive nanosensors via a quenching-based mechanism. LipiSensors provide a versatile, general platform nanosensing with the ability to directly tune the size of the sensors while including biocompatible materials as the structural support by merging sensing approaches with the Lipidot platform.

Triplet-Triplet Annihilation Upconversion Based Nanosensors for Fluorescence Detection of Potassium

Typical ionophore-based nanosensors use Nile blue derived indicators called chromoionophores, which must contend with strong background absorption, autofluorescence, and scattering in biological samples that limit their usefulness. Here, we demonstrate potassium-selective nanosensors that utilize triplet-triplet annihilation upconversion to minimize potential optical interference in biological media and a pH-sensitive quencher molecule to modulate the upconversion intensity in response to changes in analyte concentration. A triplet-triplet annihilation dye pair (platinum(II) octaethylporphyrin and 9,10-diphenylanthracene) was integrated into nanosensors containing an analyte binding ligand (ionophore), charge-balancing additive, and a pH indicator quencher. The nanosensor response to potassium was shown to be reversible and stable for 3 days. In addition, the nanosensors are selective against sodium, calcium, and magnesium (selectivity coefficients in log₁₀ units of -2.2 for calcium, -2.0 for sodium, and -2.4 for magnesium), three interfering ions found in biological samples. The lack of signal overlap between the upconversion nanosensors and GFP, a common biological fluorescent indicator, is demonstrated in confocal microscope images of sensors embedded in a bacterial biofilm.

Nanodiagnostics to monitor biofilm oxygen metabolism for antibiotic susceptibility testing

A method utilizing oxygen-sensitive nanosensor technology to monitor the oxygen consumption dynamics of living biofilms as they are exposed to antibiotics. This method provides information on the MBIC as well as kinetic response.