Optical Biosensing of Bacteria and Bacterial Communities

Electrochemical and spectroelectrochemical characterization of bacteria and bacterial systems

Microbes, such as bacteria, can be described, at one level, as small, self-sustaining chemical factories. Based on the species, strain, and even the environment, bacteria can be useful, neutral or pathogenic to human life, so it is increasingly important that we be able to characterize them at the molecular level with chemical specificity and spatial and temporal resolution in order to understand their behavior. Bacterial metabolism involves a large number of internal and external electron transfer processes, so it is logical that electrochemical techniques have been employed to investigate these bacterial metabolites. In this mini-review, we focus on electrochemical and spectroelectrochemical methods that have been developed and used specifically to chemically characterize bacteria and their behavior. First, we discuss the latest mechanistic insights and current understanding of microbial electron transfer, including both direct and mediated electron transfer. Second, we summarize progress on approaches to spatiotemporal characterization of secreted factors, including both metabolites and signaling molecules, which can be used to discern how natural or external factors can alter metabolic states of bacterial cells and change either their individual or collective behavior. Finally, we address in situ methods of single-cell characterization, which can uncover how heterogeneity in cell behavior is reflected in the behavior and properties of collections of bacteria, e.g. bacterial communities. Recent advances in (spectro)electrochemical characterization of bacteria have yielded important new insights both at the ensemble and the single-entity levels, which are furthering our understanding of bacterial behavior. These insights, in turn, promise to benefit applications ranging from biosensors to the use of bacteria in bacteria-based bioenergy generation and storage.

Hygroscopicity and mass transfer limit of mixed glutaric acid/MgSO4/water particles

Tropospheric aerosols are usually complex mixtures of inorganic and organic components, which show non-ideal behavior in hygroscopicity, mass transfer, and partitioning between gas and aerosols. In this study, we applied a novel approach based on a combination of a pulse RH controlling system and a rapid scan vacuum FTIR spectrometer to investigate the mass transfer limit of magnesium sulfate/glutaric acid (GA) mixture aerosol particles. The liquid water band area of the aerosols is used to reveal the mass transfer limit during the rapid pulse RH downward and upward processes. Partitioning equilibrium between the aerosol particles and water gas phase is observed at the higher RH range (73-50%). When the RH is lower than 40%, there is a hysteresis for the liquid water content changing with the RH, indicating the limited water mass transfer in the aerosols.

Rapid and multiplex detection of nosocomial pathogens on a phage-based magnetoresistive lab-on-chip platform

Nosocomial or hospital-acquired infections (HAIs) have a major impact on mortality worldwide. Enterococcus and Staphylococcus are among the leading causes of HAIs and thus are important pathogens to control mainly due to their increased antibiotic resistance. The gold-standard diagnostic methods for HAIs are time-consuming, which hinders timely and adequate treatment. Therefore, the development of fast and accurate diagnostic tools is an urgent demand. In this study, we combined the sensitivity of magnetoresistive (MR) sensors, the portability of a lab-on-chip platform, and the specificity of phage receptor binding proteins (RBPs) as probes for the rapid and multiplex detection of Enterococcus and Staphylococcus. For this, bacterial cells were firstly labelled with magnetic nanoparticles (MNPs) functionalized with RBPs and then measured on the MR sensors. The results indicate that the RBP-MNPS provided a specific individual and simultaneous capture of more than 70% of Enterococcus and Staphylococcus cells. Moreover, high signals from the MR sensors were obtained for these samples, providing the detection of both pathogens at low concentrations (10 CFU/ml) in less than 2 h. Overall, the lab-on-chip MR platform herein presented holds great potential to be used as a point-of-care for the rapid, sensitive and specific multiplex diagnosis of bacterial infections.

Imaging, Identification and Inhibition of Microorganisms Using AIEgens

Microorganisms, including bacteria, viruses and fungi, are ubiquitous in nature. Some are extremely beneficial to life on Earth, whereas some cause diseases and disrupt normal human physiology. Pathogenic microorganisms can also undergo mutations and develop resistance to antimicrobial agents, which complicates diagnostic and therapeutic regimens. This calls for continuing efforts to develop new strategies and tools that can provide fast, sensitive and accurate diagnosis, as well as effective treatment of ever-evolving infectious diseases. Aggregation-induced emission luminogens (AIEgens) have shown promise in imaging, identification and inhibition of various microbial species. Compared to conventional organic fluorophores, AIEgens can offer improved photostability, and have found utilities in imaging microorganisms. AIEgens have been shown to detect microbial viability and differentiate among different microbial strains. Theranostic AIEgens that integrate imaging and killing of microbes have also been developed. This review highlights examples in the literature where AIEgens have been employed as molecular probes in the imaging, discrimination and killing of bacteria, viruses and fungi.

Advances in Optical Detection of Human-Associated Pathogenic Bacteria

Bacterial infection is a global burden that results in numerous hospital visits and deaths annually. The rise of multi-drug resistant bacteria has dramatically increased this burden. Therefore, there is a clinical need to detect and identify bacteria rapidly and accurately in their native state or a culture-free environment. Current diagnostic techniques lack speed and effectiveness in detecting bacteria that are culture-negative, as well as options for in vivo detection. The optical detection of bacteria offers the potential to overcome these obstacles by providing various platforms that can detect bacteria rapidly, with minimum sample preparation, and, in some cases, culture-free directly from patient fluids or even in vivo. These modalities include infrared, Raman, and fluorescence spectroscopy, along with optical coherence tomography, interference, polarization, and laser speckle. However, these techniques are not without their own set of limitations. This review summarizes the strengths and weaknesses of utilizing each of these optical tools for rapid bacteria detection and identification.

On the application of multi-parametric optical phenotyping of bacterial colonies for multipurpose microbiological diagnostics

The development of new diagnostics techniques and modalities is critical for early detection of microbial contamination. In this study, the novel integrated system for multi-parametric optical phenotyping and characterization of bacterial colonies, is presented. The system combines Mach-Zehnder interferometer with a spectral imaging system for capturing multispectral diffraction patterns and multispectral two-dimensional transmission maps of bacterial colonies, along with the simultaneous interferometric profilometry. The herein presented investigation was carried out on five representative bacteria species and nearly 3000 registered multispectral optical signatures. The interferograms were analyzed by four-step phase shift algorithm to reconstruct the colony profile to enable the obtaining of the comparable optical signatures. The dedicated image processing algorithms were used for extraction of quantitative features of these signatures. The random forest algorithm was applied for selection of the most predictive set of features, which were used in classification model based on Support-Vector Machine. Obtained results have shown that the use of multiple multispectral optical signatures provide a multi-parametric bacteria identification at an exceptionally high accuracy (99.4-100%), significantly better than in case of classification based on each of these signatures (multispectral diffraction patterns, two-dimensional transmission coefficient maps), separately. Obtained results revealed that analysis of multispectral signatures can also be applied for characterisation of physical, physicochemical and chemical properties of the bacterial colonies in the presence of the antimicrobial factors. Therefore, the proposed label-free, non-destructive optical technique has perspectives to be exploited in the multipurpose diagnostics and it can be used as a pre-screening tool in microbiological laboratories.

'Mixing-and-measuring' surface-enhanced Raman scattering (SERS) detection of Bacillus cereus for potentially aiding gold mine field exploration

Bacillus cereus, a common soil bacterium, has been shown to act as a biogeochemical indicator for concealed mineralisations, e.g., vein-type Au deposits. Field and cultivation-free detection of Bacillus cereus in the presence of Au³⁺ and other metal ions is significantly important but still almost blank in current biogeochemical prospecting of gold mine system. Herein, a self-established simple approach was slightly improved to make silver nanoparticles (Ag NPs) rapidly concentrated on every bacterial cell, and highly strong and distinct surface-enhanced Raman scattering (SERS) signals of Bacillus cereus free from any native fluorescence have been obtained in a so called 'mixing-and-measuring' manner. Furthermore, SERS was used for the first time to our knowledge to investigate the impacts of different concentrations of metal ions on Bacillus cereus, and successfully utilized for distinguishing Au³⁺ ions from other species. A more convincing multi-Raman criterion based on Raman bands, and further the entire Raman spectrum in combination with statistical analysis (e.g., principal component analysis (PCA)) were found capable of detecting spectral differences of Bacillus cereus in the presence of metal ions (Au³⁺, Ag⁺, Cu²⁺ and Zn²⁺) with different concentrations. An interesting phenomenon has been found that except for Au³⁺ ions, the highest permissive concentration of other metal ions for the detected Bacillus cereus is up to 10 μg/mL possibly due to their resistance to Au. The results also indicate that an effective biogeochemical exploration technique of SERS spectral response may be developed, where Bacillus cereus spore counts are measured in the field and used as a pre-screening method to target areas useful for further sampling and complete geochemical analysis.

Microscale and Nanoscale Electrophotonic Diagnostic Devices

Detecting and identifying infectious agents and potential pathogens in complex environments and characterizing their mode of action is a critical need. Traditional diagnostics have targeted a single characteristic (e.g., spectral response, surface receptor, mass, intrinsic conductivity, etc.). However, advances in detection technologies have identified emerging approaches in which multiple modes of action are combined to obtain enhanced performance characteristics. Particularly appealing in this regard, electrophotonic devices capable of coupling light to electron translocation have experienced rapid recent growth and offer significant advantages for diagnostics. In this review, we explore three specific promising approaches that combine electronics and photonics: (1) assays based on closed bipolar electrochemistry coupling electron transfer to color or fluorescence, (2) sensors based on localized surface plasmon resonances, and (3) emerging nanophotonics approaches, such as those based on zero-mode waveguides and metamaterials.

Hygroscopic behavior and fractional crystallization of mixed (NH4)2SO4/glutaric acid aerosols by vacuum FTIR

The hygroscopicity and phase transition of the mixed aerosol particles are significantly dependent upon relative humidity (RH) and interactions between particle components. Although the efflorescence behavior of particles has been studied widely, the crystallization behavior of each component in the particles is still poorly understood. Here, we study the hygroscopicity and crystallization behaviors of internally mixed ammonium sulfate (AS)/glutaric acid (GA) aerosols by a vacuum FTIR spectrometer coupled with a RH-controlling system. The mixed AS/GA aerosols in two different RH control processes (equilibrium and RH pulsed processes) show the fractional crystallization upon dehydration with AS crystallizing prior to GA in mixed particles with varying organic to inorganic molar ratios (OIRs). The initial efflorescence relative humidity (ERH) of AS decreased from ~43% for pure AS particles to ~41%, ~36% and ~34% for mixed AS/GA particles with OIRs of 2:1, 1:1 and 1:2, respectively. Compared to the ERH of 35% for pure GA, the initial ERHs of GA in mixed AS/GA particles were determined to be 31%, 30% and 28% for OIRs of 2:1, 1:1 and 1:2, respectively, indicating that the presence of AS decreased the crystallization RH of GA instead of inducing the heterogeneous nucleation of GA. When the AS fractions first crystallized at around 36% RH in the 1:1 mixed particles, GA remained noncrystalline until 30% RH. For the first time, the crystallization ratios of AS and GA are obtained for the internally mixed particles during the rapid downward RH pulsed process. The crystallization ratio of AS can reach around 100% at around 24% RH for both pure AS and the 1:1 mixed particles, consistent with the equilibrium RH process. It is clear that the RH downward rate did not influence efflorescence behavior of AS in pure AS and AS in mixed particles. In contrast, the crystallization ratio of GA can reach about 90% at 15.4% RH for pure GA particles in excellent agreement with the equilibrium RH process, whereas it is only up to 50% at 16.0% RH in the 1:1 mixed particles during the rapid downward pulsed process lower than that of the equilibrium RH process. Our results reveal that the rapid RH downward rate could inhibit the efflorescence of GA in the mixed droplets.

Spatiotemporal Dynamics of Molecular Messaging in Bacterial Co-Cultures Studied by Multimodal Chemical Imaging

Microbial community behavior is coupled to a set of genetically-regulated chemical signals that correlate with cell density - the quorum sensing (QS) system - and there is growing appreciation that the QS-regulated behavior of bacteria is chemically, spatially, and temporally complex. In addition, while it has been known for some time that different species use different QS networks, we are beginning to appreciate that different strains of the same bacterial species also differ in their QS networks. Here we combine mass spectrometric imaging (MSI) and confocal Raman microscopy (CRM) approaches to investigate co-cultures involving different strains (FRD1 and PAO1C) of the same species (Pseudomonas aeruginosa) as well as those involving different species (P. aeruginosa and E. coli). Combining MSI and CRM makes it possible to supersede the limits imposed by individual imaging approaches and enables the spatial mapping of individual bacterial species and their microbial products within a mixed bacterial community growing in situ on surfaces. MSI is used to delineate the secretion of a specific rhamnolipid surfactant as well as alkyl quinolone (AQ) messengers between FRD1 and PAO1C strains of P. aeruginosa, showing that the spatial distribution and production rate of AQ messengers in PAO1C far outstrips that of FRD1. In the case of multiple species, CRM is used to show that the prolific secretion of AQs by the PAO1C strain of P. aeruginosa is used to mediate its interaction with co-cultured E. coli.

Whole-cell biosensing by siderophore-based molecular recognition and localized surface plasmon resonance

A siderophore-based active bacterial pull-down strategy was integrated in a localized surface plasmon resonance (LSPR) sensing platform and subsequently tested by detecting whole-cell Acinetobacter baumannii. The LSPR-based whole-cell sensing approach was previously demonstrated with aptamer-based molecular recognition motifs, and here it is extended to the powerful siderophore system, which exploits the natural bacterial need to sequester Fe(III). Specifically, a biscatecholate-monohydroxamate mixed ligand siderophore linked to a biotin via three polyethylene glycol repeating units was synthesized and immobilized on Au trigonal nanoprisms of an LSPR sensor. The resulting surface-confined biotinylated siderophore subsequently chelated Fe(III), forming a siderophore-Fe(III) complex which was shown to be competent to recognize A. baumannii. Target bacteria were captured and then detected by measuring wavelength shifts in the LSPR extinction spectrum. This siderophore pull-down LSPR biosensor approach is rapid (≤3 h detection) and sensitive - with a limit of detection (LOD) of 80 bacterial cells and a linear wavelength shift over the range 4 × 10² to 4 × 10⁶ cfu mL^-1. As intended by design, the siderophore-based biosensor was selective for A. baumannii over Pseudomonas aeruginosa, Escherichia coli, and Bacillus cereus, and was stable in ambient conditions for up to 2 weeks.

Observing HNO3 release dependent upon metal complexes in malonic acid/nitrate droplets

Although the dicarboxylic acid has been reported to react with nitrate for aged internally mixed aerosols in atmosphere, the quantitative nitrate depletion dependent upon composition in particles is still not well constrained. The chemical composition evolutions for malonic acid/sodium nitrate (MA/SN), malonic acid/magnesium nitrate (MA/MN) and malonic acid/calcium nitrate (MA/CN) particles with the organic to inorganic molar ratio (OIR) of 1:1 are investigated by vacuum Fourier transform infrared spectroscopy (FTIR). Upon dehydration, the intensity of the asymmetric stretching mode of COO^- group (ν_as-COO^-) increases, accompanying the decrease in OH feather band and COOH band and NO₃^- band. These band changes suggest malonate salts formation and HNO₃ release. The quantitative NO₃^- depletion data shows that the reactivity of MA-MN is most and that of MA-SN is least. Analysis of the stretching mode of COO^- indicates the different bond type between metal cation and carboxylate anion. In addition, water content in particles decreases at the constant RH, implying water loss with the chemical reaction. When the RH changes very quickly, water uptake delay during the humidification process reveals that water mass transport is limited below 37% RH.

Whole-Cell Pseudomonas aeruginosa Localized Surface Plasmon Resonance Aptasensor

The detection of whole-cell Pseudomonas aeruginosa presents an intriguing challenge with direct applications in health care and the prevention of nosocomial infection. To address this problem, a localized surface plasmon resonance (LSPR) based sensing platform was developed to detect whole-cell Pseudomonas aeruginosa strain PAO1 using a surface-confined aptamer as an affinity reagent. Nanosphere lithography (NSL) was used to fabricate a sensor surface containing a hexagonal array of Au nanotriangles. The sensor surface was subsequently modified with biotinylated polyethylene glycol (Bt-PEG) thiol/PEG thiol (1:3), neutravidin, and biotinylated aptamer in a sandwich format. The 1:3 (v/v) ratio of Bt-PEG thiol/PEG thiol was specifically chosen to maximize PAO1 binding while minimizing nonspecific adsorption and steric hindrance. In contrast to prior whole-cell LSPR work, the LSPR wavelength shift was shown to be linearly related to bacterial concentration over the range of 10-103 cfu mL-1. This LSPR sensing platform is rapid (∼3 h for detection), sensitive (down to the level of a single bacterium), selective for detection of Pseudomonas strain PAO1 over other strains, and exhibits a clinically relevant dynamic range and excellent shelf life (≥2 months) when stored at ambient conditions. This versatile LSPR sensing platform should be extendable to a wide range of supermolecular analytes, including both bacteria and viruses, by switching affinity reagents, and it has potential to be used in point-of-care and field-based applications.

Photonic monitoring of treatment during infection and sepsis: development of new detection strategies and potential clinical applications

Despite the strong decline in the infection-associated mortality since the development of the first antibiotics, infectious diseases are still a major cause of death in the world. With the rising number of antibiotic-resistant pathogens, the incidence of deaths caused by infections may increase strongly in the future. Survival rates in sepsis, which occurs when body response to infections becomes uncontrolled, are still very poor if an adequate therapy is not initiated immediately. Therefore, approaches to monitor the treatment efficacy are crucially needed to adapt therapeutic strategies according to the patient's response. An increasing number of photonic technologies are being considered for diagnostic purpose and monitoring of therapeutic response; however many of these strategies have not been introduced into clinical routine, yet. Here, we review photonic strategies to monitor response to treatment in patients with infectious disease, sepsis, and septic shock. We also include some selected approaches for the development of new drugs in animal models as well as new monitoring strategies which might be applicable to evaluate treatment response in humans in the future. Figure Label-free probing of blood properties using photonics.