In Vitro Fiber-Probe-Based Identification of Pathogens in Biofilms by Raman Spectroscopy

Fiber array-based large spot confocal Raman system for rapid in situ detection of pathogenic bacterial colonies

Pathogenic bacteria infections are a major public health problem in current society. Rapid and reliable identification of these pathogens can help avoid the misuse of antibiotics and enable precision therapy. In this study, we present a large-spot confocal Raman system based on fiber array (LSCR-FA) for the in situ detection of microbial colonies on agar plates. This method can alleviate the problem of spatial heterogeneity of colonies to a certain extent and is fast and high-throughput. Additionally, we also applied machine learning algorithms with 5-fold cross-validation to analyze colony Raman spectral data and classify seven different pathogenic bacteria. Among them, the Support Vector Machine (SVM) achieved a high accuracy of 98.74 %. The results of the study demonstrate that the mentioned LSCR-FA system combined with machine learning algorithms provides a new, fast, and effective strategy for the identification of pathogenic bacteria and precise clinical treatment.

In situ monitoring of quorum sensing signalling molecules using a SERS chip with a micro -chamber array

The in situ monitoring of quorum sensing (QS) signal molecules in bacterial biofilms is crucial for the diagnosis and treatment of bacterial biofilms. In this work, a surface-enhanced Raman scattering (SERS) chip integrated with functional units of bacterial biofilms and in situ SERS detection is proposed for the monitoring of pyocyanine, an important signal molecule and biomarker secreted by Pseudomonas aeruginosa. The SERS chip was composed of a top self-assembled nano-silver SERS substrate layer, a PDMS layer containing a micro-chamber array and bottom quartz layer. The nano-silver SERS substrate showed good homogeneity and stability with an enhancement factor of up to 1.84 × 108 for pyocyanine, and the design of the SERS substrate located at the top layer of the chip could effectively attenuate interference from complex matrices. Using the SERS chip, a detection limit of as low as 1 nM for pyocyanine with a wide detection range of 1 nM-100 μM was observed. The proposed SERS chip could achieve the monitoring of pyocyanine during the growth of Pseudomonas aeruginosa biofilms with and without the treatment of different types of antibacterial drugs. Furthermore, pyocyanine secreted by Pseudomonas aeruginosa was confirmed using mass spectrometry (MS), and the concentration relationship obtained via MS/MS was consistent with that obtained via SERS detection. The proposed method based on the SERS chip for monitoring QS in bacterial biofilms offers the advantages of in situ detection, flexibility and efficiency.

Lighting the Path: Raman Spectroscopy's Journey Through the Microbial Maze

The rapid and precise identification of microorganisms is essential in environmental science, pharmaceuticals, food safety, and medical diagnostics. Raman spectroscopy, valued for its ability to provide detailed chemical and structural information, has gained significant traction in these fields, especially with the adoption of various excitation wavelengths and tailored optical setups. The choice of wavelength and setup in Raman spectroscopy is influenced by factors such as applicability, cost, and whether bulk or single-cell analysis is performed, each impacting sensitivity and specificity in bacterial detection. In this study, we investigate the potential of different excitation wavelengths for bacterial identification, utilizing a mock culture composed of six bacterial species: three Gram-positive (S. warneri, S. cohnii, and E. malodoratus) and three Gram-negative (P. stutzeri, K. terrigena, and E. coli). To improve bacterial classification, we applied machine learning models to analyze and extract unique spectral features from Raman data. The results indicate that the choice of excitation wavelength significantly influences the bacterial spectra obtained, thereby impacting the accuracy and effectiveness of the subsequent classification results.

Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms

Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.

Evaluation of poly(lactic acid) and ECOVIO based biocomposites loaded with antimicrobial sodium phosphate microparticles

Herein, biobased composite materials based on poly(lactic acid) (PLA) and poly(butylene adipate-co-terephthalate) (PBAT) as matrices, sodium hexametaphosphate microparticles (E452i, food additive microparticles, 1 and 5 wt%) as antimicrobial filler and acetyl tributyl citrate (ATBC, 15 wt%) as plasticizer, were developed for potential food packaging applications. Two set of composite films were obtained by melt-extrusion and compression molding, i) based on PLA matrix and ii) based on Ecovio® matrix (PLA/PBAT blend). Thermal characterization by thermogravimetric analysis and differential scanning calorimetry demonstrated that the incorporation of E452i particles improved thermal stability and crystallinity, while the mechanical test showed an increase in the Young's modulus. E452i particles also provide antimicrobial properties to the films against food-borne bacteria Listeria innocua and Staphylococcus aureus, with bacterial reduction percentages higher than 50 % in films with 5 wt% of particles. The films also preserved their disintegradability as demonstrated by an exhaustive characterization of the films under industrial composting conditions. Therefore, the results obtained in this work reveal the potential of these biocomposites as appropriated materials for antibacterial and compostable food packaging films.

Simultaneous Dual-Wavelength Source Raman Spectroscopy with a Handheld Confocal Probe for Analysis of the Chemical Composition of In Vivo Human Skin

Confocal Raman spectroscopy (CRS) is a powerful tool that has been widely used for biological tissue analysis because of its noninvasive nature, high specificity, and rich biochemical information. However, current commercial CRS systems suffer from limited detection regions (450-1750 cm-1), bulky sizes, nonflexibilities, slow acquisitions by consecutive excitations, and high costs if using a Fourier transform (FT) Raman spectroscopy with an InGaAs detector, which impede their adoption in clinics. In this study, we developed a portable CRS system with a simultaneous dual-wavelength source and a miniaturized handheld probe (120 mm × 60 mm × 50 mm) that can acquire spectra in both fingerprint (FP, 450-1750 cm-1) and high wavenumber (HW, 2800-3800 cm-1) regions simultaneously. An innovative design combining 671 and 785 nm lasers for simultaneous excitation through a compact and high-efficiency (>90%) wavelength combiner was implemented. Moreover, to decouple the fused FP and HW spectra, a first-of-its-kind precise Raman spectra separation algorithm (PRSSA) was developed based on the maximum a posteriori probability (MAP) estimate. The accuracy of spectra separation was greater than 99%, demonstrated in both phantom experiments and in vivo human skin measurements. The total data acquisition time was reduced by greater than 50% compared to other CRS systems. The results proved our proposed CRS system and PRSSA's superior capability in fast and ultrawideband spectra acquisition will significantly improve the integration of CRS in the clinical workflow.

Recent Progress in Spectroscopic Methods for the Detection of Foodborne Pathogenic Bacteria

Detection of foodborne pathogens at an early stage is very important to control food quality and improve medical response. Rapid detection of foodborne pathogens with high sensitivity and specificity is becoming an urgent requirement in health safety, medical diagnostics, environmental safety, and controlling food quality. Despite the existing bacterial detection methods being reliable and widely used, these methods are time-consuming, expensive, and cumbersome. Therefore, researchers are trying to find new methods by integrating spectroscopy techniques with artificial intelligence and advanced materials. Within this progress report, advances in the detection of foodborne pathogens using spectroscopy techniques are discussed. This paper presents an overview of the progress and application of spectroscopy techniques for the detection of foodborne pathogens, particularly new trends in the past few years, including surface-enhanced Raman spectroscopy, surface plasmon resonance, fluorescence spectroscopy, multiangle laser light scattering, and imaging analysis. In addition, the applications of artificial intelligence, microfluidics, smartphone-based techniques, and advanced materials related to spectroscopy for the detection of bacterial pathogens are discussed. Finally, we conclude and discuss possible research prospects in aspects of spectroscopy techniques for the identification and classification of pathogens.

Construction of an Ultrasensitive Molecularly Imprinted Virus Sensor Based on an "Explosive" Secondary Amplification Strategy for the Visual Detection of Viruses

Viral outbreaks have caused great disruptions to the economy and public health in recent years. The accurate detection of viruses is a key factor in controlling and overcoming epidemics. In this study, an ultrasensitive molecularly imprinted virus sensor was developed based on an "explosive" secondary amplification strategy. Magnetic particles coated with carbon quantum dots (Fe₃O₄@CDs) were used as carriers and fluorescent probes, while aptamers were introduced into the imprinting layer to enhance the specific recognition of the target virus enterovirus 71 (EV71). When EV71 was captured by the imprinted particles, the fluorescence of the CDs was quenched, especially after binding to the aptamer-modified ZIF-8 loaded with a large amount of phenolphthalein, thereby resulting in signal amplification. Then, when adjusting the pH of the solution to 12, the decomposition of ZIF-8 released phenolphthalein, which turned the solution red, leading to the second "explosive" amplification of the signal. Therefore, the detection of EV71 with ultrasensitivity was achieved, which allows for visual detection by the naked eye in the absence of any instruments. The detection limits for fluorescence and visualization detection were 8.33 fM and 2.08 pM, respectively. In addition, a satisfactory imprinting factor of 5.4 was achieved, and the detection time only needed 20 min. It is expected that this fluorescence-colorimetric dual-mode virus molecularly imprinted sensor will show excellent prospects in epidemic prevention and rapid clinical diagnosis.

Multimodal Handheld Probe for Characterizing Otitis Media - Integrating Raman Spectroscopy and Optical Coherence Tomography

Otitis media (OM) is a common disease of the middle ear, affecting 80% of children before the age of three. The otoscope, a simple illuminated magnifier, is the standard clinical diagnostic tool to observe the middle ear. However, it has limited contrast to detect signs of infection, such as clearly identifying and characterizing middle ear fluid or biofilms that accumulate within the middle ear. Likewise, invasive sampling of every subject is not clinically indicated nor practical. Thus, collecting accurate noninvasive diagnostic factors is vital for clinicians to deliver a precise diagnosis and effective treatment regimen. To address this need, a combined benchtop Raman spectroscopy (RS) and optical coherence tomography (OCT) system was developed. Together, RS-OCT can non-invasively interrogate the structural and biochemical signatures of the middle ear under normal and infected conditions.In this paper, in vivo RS scans from pediatric clinical human subjects presenting with OM were evaluated in parallel with RS-OCT data of physiologically relevant in vitro ear models. Component-level characterization of a healthy tympanic membrane and malleus bone, as well as OM-related middle ear fluid, identified the optimal position within the ear for RS-OCT data collection. To address the design challenges in developing a system specific to clinical use, a prototype non-contact multimodal handheld probe was built and successfully tested in vitro. Design criteria have been developed to successfully address imaging constraints imposed by physiological characteristics of the ear and optical safety limits. Here, we present the pathway for translation of RS-OCT for non-invasive detection of OM.

Raman spectroscopy for the differentiation of Enterobacteriaceae: a comparison of two methods

A comprehensive dataset of bacteria of the family Enterobacteriaceae was collected and measured with Raman spectroscopy. Fiber-probe based Raman spectroscopy enabled classification with 100% accuracy and remained robust with a validation dataset.