Rapid Identification of Pseudomonas spp. via Raman Spectroscopy Using Pyoverdine as Capture Probe

Bacterial siderophores: diversity, uptake pathways and applications

Iron is an essential nutrient for the growth, survival and virulence of almost all bacteria. To access iron, many bacteria produce siderophores, molecules with a high affinity for iron. Research has highlighted substantial diversity in the chemical structure of siderophores produced by bacteria, as well as remarkable variety in the molecular mechanisms involved in strategies for acquiring iron through these molecules. The metal-chelating properties of siderophores, characterized by their high affinity for iron and ability to chelate numerous other metals (albeit with lower affinity compared with iron), have also generated interest in diverse fields. Siderophores find applications in the environment, such as in bioremediation and agriculture, in which emerging and innovative strategies are being developed to address pollution and enhance nutrient availability for plants. Moreover, in medicine, siderophores could be used as a tool for novel antimicrobial therapies and medical imaging, as well as in haemochromatosis, thalassemia or cancer treatments. This Review offers insights into the diversity of siderophores, highlighting their potential applications in environmental and medical contexts.

Detection of Microorganisms Using Artificial Siderophore-FeIII Complex-Modified Substrates

Four FeIII complexes of typical artificial siderophore ligands containing catecholate and/or hydroxamate groups of tricatecholate, biscatecholate-monohydroxamate, monocatecholate-bishydroxamate, and trihydroxamate type artificial siderophores (K3[FeIIILC3], K2[FeIIILC2H1], K[FeIIILC1H2], and [FeIIILH3]) were modified on Au substrate surfaces. Their abilities to adsorb microorganisms were investigated using scanning electron microscopy, quartz crystal microbalance, and AC impedance methods. The artificial siderophore-iron complexes modified on Au substrates (FeLC3/Au, FeLC2H1/Au, FeLC1H2/Au, and FeLH3/Au) showed the selective immobilization behavior for various microorganisms, depending on the structural features of the artificial siderophores (the number of catecholate and hydroxamate arms). Their specificities corresponded well with the structural characteristics of natural siderophores released by microorganisms and used for FeIII ion uptake. These findings suggest that they were generated via specific interactions between the artificial siderophore-FeIII complexes and the receptors on microorganism surfaces. Our observations revealed that the FeL/Au systems may be potentially used as effective microbe-capturing probes that can enable rapid and simple detection and identification of various microorganisms.

A zero-sum game or an interactive frame? Iron competition between bacteria and humans in infection war

ABSTRACT

Iron is an essential trace element for both humans and bacteria. It plays a vital role in life, such as in redox reactions and electron transport. Strict regulatory mechanisms are necessary to maintain iron homeostasis because both excess and insufficient iron are harmful to life. Competition for iron is a war between humans and bacteria. To grow, reproduce, colonize, and successfully cause infection, pathogens have evolved various mechanisms for iron uptake from humans, principally Fe 3+ -siderophore and Fe 2+ -heme transport systems. Humans have many innate immune mechanisms that regulate the distribution of iron and inhibit bacterial iron uptake to help resist bacterial invasion and colonization. Meanwhile, researchers have invented detection test strips and coupled antibiotics with siderophores to create tools that take advantage of this battle for iron, to help eliminate pathogens. In this review, we summarize bacterial and human iron metabolism, competition for iron between humans and bacteria, siderophore sensors, antibiotics coupled with siderophores, and related phenomena. We also discuss how competition for iron can be used for diagnosis and treatment of infection in the future.

Detection of multi-resistant clinical strains of E. coli with Raman spectroscopy

In recent years, we have seen a steady rise in the prevalence of antibiotic-resistant bacteria. This creates many challenges in treating patients who carry these infections, as well as stopping and preventing outbreaks. Identifying these resistant bacteria is critical for treatment decisions and epidemiological studies. However, current methods for identification of resistance either require long cultivation steps or expensive reagents. Raman spectroscopy has been shown in the past to enable the rapid identification of bacterial strains from single cells and cultures. In this study, Raman spectroscopy was applied for the differentiation of resistant and sensitive strains of Escherichia coli. Our focus was on clinical multi-resistant (extended-spectrum β-lactam and carbapenem-resistant) bacteria from hospital patients. The spectra were collected using both UV resonance Raman spectroscopy in bulk and single-cell Raman microspectroscopy, without exposure to antibiotics. We found resistant strains have a higher nucleic acid/protein ratio, and used the spectra to train a machine learning model that differentiates resistant and sensitive strains. In addition, we applied a majority of voting system to both improve the accuracy of our models and make them more applicable for a clinical setting. This method could allow rapid and accurate identification of antibiotic resistant bacteria, and thus improve public health.

Advanced detection and sensing strategies of Pseudomonas aeruginosa and quorum sensing biomarkers: A review

Pseudomonas aeruginosa (P. aeruginosa), a ubiquitous opportunistic pathogen, can frequently cause chronic obstructive pulmonary disease, cystic fibrosis and chronic wounds, and potentially lead to severe morbidity and mortality. Timely and adequate treatment of nosocomial infection in clinic depends on rapid detection and accurate identification of P. aeruginosa and its early-stage antibiotic susceptibility test. Traditional methods like plating culture, polymerase chain reaction, and enzyme-linked immune sorbent assays are time-consuming and require expensive equipment, limiting the rapid diagnostic application. Advanced sensing strategy capable of fast, sensitive and simple detection with low cost has therefore become highly desired in point of care testing (POCT) of nosocomial pathogens. Within this review, advanced detection and sensing strategies for P. aeruginosa cells along with associated quorum sensing (QS) molecules over the last ten years are discussed and summarized. Firstly, the principles of four commonly used sensing strategies including localized surface plasmon resonance (LSPR), surface-enhanced Raman spectroscopy (SERS), electrochemistry, and fluorescence are briefly overviewed. Then, the advancement of the above sensing techniques for P. aeruginosa cells and its QS biomarkers detection are introduced, respectively. In addition, the integration with novel compatible platforms towards clinical application is highlighted in each section. Finally, the current achievements are summarized along with proposed challenges and prospects.

Siderophores for medical applications: Imaging, sensors, and therapeutics

Siderophores are low-molecular-weight chelators produced by microorganisms to scavenge iron from the environment and deliver it to cells via specific receptors. Tremendous researches on the molecular basis of siderophore regulation, synthesis, secretion, and uptake have inspired their diverse applications in the medical field. Replacing iron with radionuclides in siderophores, such as the most prominent Ga-68 for positron emission tomography (PET), carves out ways for targeted imaging of infectious diseases and cancers. Additionally, the high affinity of siderophores for metal ions or microorganisms makes them a potent detecting moiety in sensors that can be used for diagnosis. As for therapeutics, the notable Trojan horse-inspired siderophore-antibiotic conjugates demonstrate enhanced toxicity against multi-drug resistant (MDR) pathogens. Besides, siderophores can tackle iron overload diseases and, when combined with moieties such as hydrogels and nanoparticles, a wide spectrum of iron-induced diseases and even cancers. In this review, we briefly outline the related mechanisms, before summarizing the siderophore-based applications in imaging, sensors, and therapeutics.

Biochemical characterization of pathogenic bacterial species using Raman spectroscopy and discrimination model based on selected spectral features

This study aimed to evaluate the differences in the Raman spectra of nine clinical species of bacteria isolated from infections (three Gram-positive and six Gram-negative species), correlating the spectra with the chemical composition of each species and to develop a classification model through discriminant analysis to categorize each bacterial strain using the peaks with the most significant differences. Bacteria were cultured in Mueller Hinton agar and a sample of biomass was harvested and placed in an aluminum sample holder. A total of 475 spectra from 115 different strains were obtained through a dispersive Raman spectrometer (830 nm) with exposure time of 50 s. The intensities of the peaks were evaluated by one-way analysis of variance (ANOVA) and the peaks with significant differences were related to the differences in the biochemical composition of the strains. Discriminant analysis based on quadratic distance applied to the peaks with the most significant differences and partial least squares applied to the whole spectrum showed 89.5% and 90.1% of global accuracy, respectively, for classification of the spectra in all the groups. Raman spectroscopy could be a promising technique to identify spectral differences related to the biochemical content of pathogenic microorganisms and to provide a faster diagnosis of infectious diseases.

Modulation of Siderophore Production by Pseudomonas fluorescens Through the Manipulation of the Culture Medium Composition

Pseudomonas fluorescens has the ability to produce the siderophore pyoverdine, a biotechnologically significant iron chelator, which has a wide range of potential applications, such as in agriculture (iron fertilizers) and medicine (development of antibiotics). The present work aimed to evaluate the influence of culture medium composition on the production of siderophores by P. fluorescens DSM 50090, an industrial relevant strain. It was found that the bacterium grown in minimal medium succinate (MMS) had a higher siderophore production than in King B medium. The replacement of succinate by glycerol or dextrose, in minimal medium, originated lower siderophore production. The increase of succinate concentration, the addition of amino acids or the reduction of phosphate in the culture medium did not improve siderophore production by P. fluorescens. The results obtained strongly suggest that (i) MMS is more appropriate than King B for large-scale production of siderophores; (ii) the modification of the culture medium composition, particularly the type of carbon source, influences the level of siderophore secreted; (iii) the production of siderophore by P. fluorescens seems to be a tightly regulated process; once a maximum siderophore concentration has been reached in the culture medium, the bacterium seems to be unable to produce more compound.

Optical Identification of Middle Ear Infection

Ear infection is one of the most commonly occurring inflammation diseases in the world, especially for children. Almost every child encounters at least one episode of ear infection before he/she reaches the age of seven. The typical treatment currently followed by physicians is visual inspection and antibiotic prescription. In most cases, a lack of improper treatment results in severe bacterial infection. Therefore, it is necessary to design and explore advanced practices for effective diagnosis. In this review paper, we present the various types of ear infection and the related pathogens responsible for middle ear infection. We outline the conventional techniques along with clinical trials using those techniques to detect ear infections. Further, we highlight the need for emerging techniques to reduce ear infection complications. Finally, we emphasize the utility of Raman spectroscopy as a prospective non-invasive technique for the identification of middle ear infection.

Sample preparation for Raman microspectroscopy

Raman spectroscopy and its variants allow for the investigation of a wide range of biological and biomedical samples, i. e. tissue sections, single cells and small molecules. The obtained information is on a molecular level. By making use of databases and chemometrical approaches, the chemical composition of complex samples can also be defined. The measurement procedure is straight forward, however most often sample preparation protocols must be implemented. While pure samples, such as high purity powders or highly concentrated chemicals in aqueous solutions, can be directly measured without any prior sample purification step, samples of biological origin, such as tissue sections, pathogens in suspension or biofluids, food and beverages often require pre-processing steps prior to Raman measurements. In this book chapter, different strategies for handling and processing various sample matrices for a subsequent Raman microspectroscopic analysis were introduced illustrating the high potential of this promising technique for life science and medical applications. The presented methods range from standalone techniques, such as filtration, centrifugation or immunocapture to innovative platform approaches which will be exemplary addressed. Therefore, the reader will be introduced to methods that will simplify the complexity of the matrix in which the targeted molecular species are present allowing direct Raman measurements with bench top or portable setups.

Synergistic effect between silver nanoparticles and antifungal agents on Candida albicans revealed by dynamic surface-enhanced Raman spectroscopy

Identifying the mechanisms of action of new potential antibiotics is a necessary but time-consuming and costly process. We have developed an ultra-rapid, highly sensitive, and reproducible dynamic surface-enhanced Raman spectroscopy (D-SERS) method to discriminate and evaluate the sensitivity of Candida albicans to antifungal agents with different mechanisms by using silver nanoparticles (Ag NPs). Although Ag NPs have been used conventionally for the enhancement of Raman signals, the accompanying influence of Ag NPs on the microbes has not been investigated. Herein, surface charge and concentration of Ag NPs are likely to be the main influencing factors. Then different concentrations of Ag NPs with the same surface charge as C. albicans were prepared to find the optimal conditions for enhancement of Raman signals while minimally affecting tested fungi. Spectral variations were observed with increasing concentrations of Ag NPs, as well as those of antifungal agents, including echinocandin and azole drugs. The results indicated that the combination of sub-lethal Ag NPs and echinocandin drugs revealed potent synergistic effects against fungi. This could be explained by the metabolism of fungi, the result of which has also been verified by transmission electron microscopy (TEM). Lastly, the combination of sub-lethal Ag NPs and echinocandin drugs was used for a mammalian cell toxicity assay to demonstrate whether the optimal combination could cause lower cytotoxicity to mammalian cells. This work opens a window not only for the evaluation of antifungal agents with different mechanisms, but also for the clinical treatment of fungal infections or even new drug development.

Interference-Enhanced Raman Spectroscopy as a Promising Tool for the Detection of Biomolecules on Raman-Compatible Surfaces

Raman spectroscopy in combination with appropriate sample preparation strategies, for example, enrichment of bacteria on metal surfaces, has been proven to be a promising approach for rapidly diagnosing infectious diseases. Unfortunately, the fabrication of the required chip substrates is usually very challenging due to the lack of feasible instruments that can be used for quality control in the surface modification process. The intrinsically weak Raman signal of the biomolecules, employed for the enrichment of the micro-organisms on the chip surface, does not allow for monitoring of the successful immobilization by means of a Raman spectroscopic approach. Within this contribution, we demonstrate how a simple modification of a plain aluminum surface enables enhancement (or a decrease, if desired) of the Raman signal of molecules deposited on that surface. The manipulation of the Raman signal strength is achieved via exploiting interference effects that occur, if the highly reflective aluminum surface is modified with thin layers of transparent dielectrics like aluminum oxide. The thicknesses of these layers were determined by theoretical considerations and calculations. For the first time, it is shown that the interference effects can be used for the detection of biomolecules as well by investigating the siderophore ferrioxamine B. The observed degree of enhancement was approximately 1 order of magnitude. Moreover, the employed aluminum/aluminum oxide layers have been thoroughly characterized using atomic force and scanning electron microscopy as well as X-ray reflectometry and UV-Vis measurements.

Immobilized FhuD2 Siderophore-Binding Protein Enables Purification of Salmycin Sideromycins from Streptomyces violaceus DSM 8286

Siderophores are a structurally diverse class of natural products common to most bacteria and fungi as iron(III)-chelating ligands. Siderophores, including trihydroxamate ferrioxamines, are used clinically to treat iron overload diseases and show promising activity against many other iron-related human diseases. Here, we present a new method for the isolation of ferrioxamine siderophores from complex mixtures using affinity chromatography based on resin-immobilized FhuD2, a siderophore-binding protein (SBP) from Staphylococcus aureus. The SBP-resin enabled purification of charge positive, charge negative, and neutral ferrioxamine siderophores. Treatment of culture supernatants from Streptomyces violaceus DSM 8286 with SBP-resin provided an analytically pure sample of the salmycins, a mixture of structurally complex glycosylated sideromycins (siderophore-antibiotic conjugates) with potent antibacterial activity toward human pathogenic Staphylococcus aureus (minimum inhibitory concentration (MIC) = 7 nM). Siderophore affinity chromatography could enable the rapid discovery of new siderophore and sideromycin natural products from complex mixtures to aid drug discovery and metabolite identification efforts in a broad range of therapeutic areas.

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.

A Critical Review on Ultrasensitive, Spectroscopic-based Methods for High-throughput Monitoring of Bacteria during Infection Treatment

The world is in the midst of a pre-emptive public health emergency, one that is just as dramatic as the global aggressive viruses-related crises (Ebola, Zika, or SARS), but not as visible. The "superbugs" and their antimicrobial resistance do not cause much public alarm or awareness, but provoke financial losses of $100 trillion annually (WHO, http://www.who.int/mediacentre/commentaries/superbugs-action-now/en/ ). This status quo review offers an overview of ultrasensitive methods for high-throughput monitoring of bacteria during infection treatment, the effects of antibiotics on bacteria at single-cell level and the challenges we will face in their detection due to the extraordinary capability of these "superbugs" to gain and constantly improve multiresistance to antibiotics. A special emphasis is put on the ultrasensitive spectroscopic-based analysis techniques, using nanotechnology or not necessarily, that are more and more promising alternatives to conventional culture-based ones. The particular case of Mycobacteria detection is discussed based on recent reported work.

Culture-Free Detection of Crop Pathogens at the Single-Cell Level by Micro-Raman Spectroscopy

The rapid and sensitive identification of invasive plant pathogens has important applications in biotechnology, plant quarantine, and food security. Current methods are far too time-consuming and need a pre-enrichment period ranging from hours to days. Here, a micro-Raman spectroscopy-based bioassay for culture-free pathogen quarantine inspection at the single cell level within 40 min is presented. The application of this approach can readily and specifically detect plant pathogens Burkholderia gladioli pv. alliicola and Erwinia chrysanthemi that are closely related pathogenically. Furthermore, the single-bacterium detection was able to discriminate them from a reference Raman spectral library including multiple quarantine-relevant pathogens with broad host ranges and an array of pathogenic variants. To show the usefulness of this assay, Burkholderia gladioli pv. alliicola and Erwinia chrysanthemi are detected at single-bacterium level in plant tissue lesions without pre-enrichment. The results are confirmed by the plate-counting method and a genetic molecular approach, which display comparable recognition ratios to the Raman spectroscopy-based bioassay. The results represent a critical step toward the use of micro-Raman spectroscopy in rapid and culture-free discrimination of quarantine relevant plant pathogens.

Optical Biosensing of Bacteria and Bacterial Communities

Bacterial sensing is important for understanding the numerous roles bacteria play in nature and in technology, understanding and managing bacterial populations, detecting pathogenic bacterial infections, and preventing the outbreak of illness. Current analytical challenges in bacterial sensing center on the dilemma of rapidly acquiring quantitative information about bacteria with high detection efficiency, sensitivity, and specificity, while operating within a reasonable budget and optimizing the use of ancillary tools, such as multivariate statistics. This review starts from a general description of bacterial sensing methods and challenges, and then focuses on bacterial characterization using optical methods including Raman spectroscopy and imaging, infrared spectroscopy, fluorescence spectroscopy and imaging, and plasmonics, including both extended and localized surface plasmon resonance spectroscopy. The advantages and drawbacks of each method in relation to the others are discussed, as are their applications. A particularly promising direction in bacterial sensing lies in combining multiple approaches to achieve multiplex analysis, and examples where this has been achieved are highlighted.

Highly Specific Bacteriophage-Affinity Strategy for Rapid Separation and Sensitive Detection of Viable Pseudomonas aeruginosa

A virulent bacteriophage highly specific to Pseudomonas aeruginosa (P. aeruginosa) was isolated from hospital sewage using a lambda bacteriophage isolation protocol. The bacteriophage, named as PAP1, was used to functionalize tosyl-activated magnetic beads to establish a bacteriophage-affinity strategy for separation and detection of viable P. aeruginosa. Recognition of the target bacteria by tail fibers and baseplate of the bacteriophage led to capture of P. aeruginosa onto the magnetic beads. After a replication cycle of about 100 min, the progenies lysed the target bacteria and released the intracellular adenosine triphosphate. Subsequently, firefly luciferase-adenosine triphosphate bioluminescence system was used to quantitate the amount of P. aeruginosa. This bacteriophage-affinity strategy for viable P. aeruginosa detection showed a linear range of 6.0 × 10² to 3.0 × 10⁵ CFU mL^-1, with a detection limit of 2.0 × 10² CFU mL^-1. The whole process for separation and detection could be completed after bacteria capture, bacteriophage replication, and bacteria lysis within 2 h. Since the isolated bacteriophage recognized the target bacteria with very high specificity, the proposed strategy did not show any signal response to all of the tested interfering bacteria. Furthermore, it excluded the interference from inactivated P. aeruginosa because the bacteriophage could replicate only in viable cells. The proposed strategy had been applied for detection of P. aeruginosa in glucose injection, human urine, and rat plasma. In the further work, this facile bacteriophage-affinity strategy could be extended for detection of other pathogens by utilizing virulent bacteriophage specific to other targets.