A novel method for identifying and distinguishing Cryptococcus neoformans and Cryptococcus gattii by surface-enhanced Raman scattering using positively charged silver nanoparticles

Recent Advances in Bacterial Detection Using Surface-Enhanced Raman Scattering

Rapid identification of microorganisms with a high sensitivity and selectivity is of great interest in many fields, primarily in clinical diagnosis, environmental monitoring, and the food industry. For over the past decades, a surface-enhanced Raman scattering (SERS)-based detection platform has been extensively used for bacterial detection, and the effort has been extended to clinical, environmental, and food samples. In contrast to other approaches, such as enzyme-linked immunosorbent assays and polymerase chain reaction, SERS exhibits outstanding advantages of rapid detection, being culture-free, low cost, high sensitivity, and lack of water interference. This review aims to cover the development of SERS-based methods for bacterial detection with an emphasis on the source of the signal, techniques used to improve the limit of detection and specificity, and the application of SERS in high-throughput settings and complex samples. The challenges and advancements with the implementation of artificial intelligence (AI) are also discussed.

Nanotechnology-based fungal detection and treatment: current status and future perspective

Fungal infections impose a significant impact on global health and encompass major expenditures in medical treatments. Human mycoses, a fungal co-infection associated with SARS-CoV-2, is caused by opportunistic fungal pathogens and is often overlooked or misdiagnosed. Recently, there is increasing threat about spread of antimicrobial resistance in fungus, mostly in hospitals and other healthcare facilities. The diagnosis and treatment of fungal infections are associated with several issues, including tedious and non-selective detection methods, the growth of drug-resistant bacteria, severe side effects, and ineffective drug delivery. Thus, a rapid and sensitive diagnostic method and a high-efficacy and low-toxicity therapeutic approach are needed. Nanomedicine has emerged as a viable option for overcoming these limitations. Due to the unique physicochemical and optical properties of nanomaterials and newer biosensing techniques, nanodiagnostics play an important role in the accurate and prompt differentiation and detection of fungal diseases. Additionally, nano-based drug delivery techniques can increase drug permeability, reduce adverse effects, and extend systemic circulation time and drug half-life. This review paper is aimed at highlighting recent, promising, and unique trends in nanotechnology to design and develop diagnostics and treatment methods for fungal diseases.

Determining Potential Link between Environmental and Clinical Isolates of Cryptococcus neoformans/Cryptococcus gattii Species Complexes Using Phenotypic and Genotypic Characterisation

Opportunistic infections due to Cryptococcus neoformans and C. gattii species complexes continue to rise unabated among HIV/AIDS patients, despite improved antifungal therapies. Here, we collected a total of 20 environmental and 25 presumptive clinical cryptococcal isolates from cerebrospinal fluid (CSF) samples of 175 patients enrolled in an ongoing clinical trial Ambition 1 Project (Botswana-Harvard Partnership). Identity confirmation of the isolates was done using MALDI-TOF MS and PCR. We describe the diversity of the isolates by PCR fingerprinting and sequencing (Oxford Nanopore Technology) of the intergenic spacer region. Mating types of the isolates were determined by amplification of the MAT locus. We report an unusual prevalence of 42.1% of C. neoformans x C. deneoformans hybrids Serotype AD (n = 16), followed by 39.5% of C. neoformans Serotype A (n = 15), 5.3% of C. deneoformans, Serotype D (n = 2), 7.9% of C. gattii (n = 3), and 5.3% of C. tetragattii (n = 2) in 38 representative isolates that have been characterized. Mating type-specific PCR performed on 38 representative environmental and clinical isolates revealed that 16 (42.1%) were MATa/MATα hybrids, 17 (44.7%) were MATα, and five (13.2%) possessed MATa mating type. We used conventional and NGS platforms to demonstrate a potential link between environmental and clinical isolates and lay a foundation to further describe mating patterns/history in Botswana.

A Systematic Review of Curtisia dentata Endemic to South Africa: Phytochemistry, Pharmacology, and Toxicology

The use of traditional medicine in treating a variety of both human and animal infections is ancient and still relevant. This is due to the resistance exhibited by most pathogenic microbial stains to currently-used antibiotics. The current work reports the phytochemistry, ethno-medicinal uses, toxicology, and most important pharmacological activities that validate the use of the plant species in African traditional medicine. Curtisia dendata is used in the treatment of many human and animal infections, including diarrhea, skin and related conditions, sexually transmitted infections, cancer, and a variety of ethno-veterinary infections. Pharmacologically, the plant species exhibited potent antimicrobial activity against a variety of pathogens. Further, both extracts and compounds isolated from the plant species exhibited potent antioxidant, anticancer, anti-parasitic, anti-inflammatory, and other important biological activities. Phytochemically, the plant species possess a variety of compounds, particularly triterpenes, that may well explain the various pharmacological activities of the plant species. The toxicological parameters, antimicrobial activities against microorganisms related to sexually transmitted infections, anti-diabetic effects, and inflammatory properties of the plant species are not well studied and still need to be explored. The biological activities observed validate the use of the plant species in African traditional medicine, particularly in the treatment of pulmonary infections associated with Mycobacterium species, and may well be due to the presence of triterpenes prevalent in the leaves.

Design, Fabrication, and Applications of SERS Substrates for Food Safety Detection: Review

Sustainable and safe food is an important issue worldwide, and it depends on cost-effective analysis tools with good sensitivity and reality. However, traditional standard chemical methods of food safety detection, such as high-performance liquid chromatography (HPLC), gas chromatography (GC), and tandem mass spectrometry (MS), have the disadvantages of high cost and long testing time. Those disadvantages have prevented people from obtaining sufficient risk information to confirm the safety of their products. In addition, food safety testing, such as the bioassay method, often results in false positives or false negatives due to little rigor preprocessing of samples. So far, food safety analysis currently relies on the enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR), HPLC, GC, UV-visible spectrophotometry, and MS, all of which require significant time to train qualified food safety testing laboratory operators. These factors have hindered the development of rapid food safety monitoring systems, especially in remote areas or areas with a relative lack of testing resources. Surface-enhanced Raman spectroscopy (SERS) has emerged as one of the tools of choice for food safety testing that can overcome these dilemmas over the past decades. SERS offers advantages over chromatographic mass spectrometry analysis due to its portability, non-destructive nature, and lower cost implications. However, as it currently stands, Raman spectroscopy is a supplemental tool in chemical analysis, reinforcing and enhancing the completeness and coverage of the food safety analysis system. SERS combines portability with non-destructive and cheaper detection costs to gain an advantage over chromatographic mass spectrometry analysis. SERS has encountered many challenges in moving toward regulatory applications in food safety, such as quantitative accuracy, poor reproducibility, and instability of large molecule detection. As a result, the reality of SERS, as a screening tool for regulatory announcements worldwide, is still uncommon. In this review article, we have compiled the current designs and fabrications of SERS substrates for food safety detection to unify all the requirements and the opportunities to overcome these challenges. This review is expected to improve the interest in the sensing field of SERS and facilitate the SERS applications in food safety detection in the future.

Leveraging single-cell Raman spectroscopy and single-cell sorting for the detection and identification of yeast infections

Invasive fungal infection serves as a great threat to human health. Discrimination between fungal and bacterial infections at the earliest stage is vital for effective clinic practice; however, traditional culture-dependent microscopic diagnosis of fungal infection usually requires several days, meanwhile, culture-independent immunological and molecular methods are limited by the detectable type of pathogens and the issues with high false-positive rates. In this study, we proposed a novel culture-independent phenotyping method based on single-cell Raman spectroscopy for the rapid discrimination between fungal and bacterial infections. Three Raman biomarkers, including cytochrome c, peptidoglycan, and nucleic acid, were identified through hierarchical clustering analysis of Raman spectra across 12 types of most common yeast and bacterial pathogens. Compared to those of bacterial pathogens, the single cells of yeast pathogens demonstrated significantly stronger Raman peaks for cytochrome c, but weaker signals for peptidoglycan and nucleic acid. A two-step protocol combining the three biomarkers was established and able to differentiate fungal infections from bacterial infections with an overall accuracy of 94.9%. Our approach was also used to detect ten raw urinary tract infection samples. Successful identification of fungi was achieved within half an hour after sample obtainment. We further demonstrated the accurate fungal species taxonomy achieved with Raman-assisted cell ejection. Our findings demonstrate that Raman-based fungal identification is a novel, facile, reliable, and with a breadth of coverage approach, that has a great potential to be adopted in routine clinical practice to reduce the turn-around time of invasive fungal disease (IFD) diagnostics.

What's New in Cryptococcus gattii: From Bench to Bedside and Beyond

Cryptococcus species are a major cause of life-threatening infections in immunocompromised and immunocompetent hosts. While most disease is caused by Cryptococcus neoformans, Cryptococcus gattii, a genotypically and phenotypically distinct species, is responsible for 11-33% of global cases of cryptococcosis. Despite best treatment, C. gattii infections are associated with early mortality rates of 10-25%. The World Health Organization's recently released Fungal Priority Pathogen List classified C. gattii as a medium-priority pathogen due to the lack of effective therapies and robust clinical and epidemiological data. This narrative review summarizes the latest research on the taxonomy, epidemiology, pathogenesis, laboratory testing, and management of C. gattii infections.

A SERS Platform for Rapid Detection of Drug Resistance of Non-Candida albicans Using Fe3O4@PEI and Triangular Silver Nanoplates

Purpose

Candida infection has a high mortality rate, and the increasing prevalence of non-Candida albicans drug resistance in recent years poses a potential threat to human health. Non-Candida albicans has long culture cycles, and its firm cell walls making it difficult to isolate DNA for sequencing.

Materials and Methods

Fe₃O₄@PEI (PEI, polyvinyl imine) was mixed with clinical samples to form Fe₃O₄@PEI@non-Candida albicans and enriched them with magnets. Triangular silver nanoplates enhanced the surface-enhanced Raman scattering (SERS) signal. SERS was used to detect the fingerprint spectrum of non-Candida albicans. Then, orthogonal partial least squares discriminant analysis (OPLS-DA) was used to analyze the drug resistance of non-Candida albicans.

Results

SERS combined with OPLS-DA could well analyze the drug resistance of non-Candida albicans. Through 10-fold-cross validation, the accuracy of training and test data is greater than 99%, indicating that the model has good classification ability. We used SERS for the first time to detect the drug resistance of non-Candida albicans directly.

Conclusion

This approach can be utilized without causing damage to the cell wall and can be accomplished in as little as 90 minutes. It can provide timely guidance for the treatment of patients with good clinical application potential.

Positively-charged plasmonic nanostructures for SERS sensing applications

Surface-enhanced Raman (SERS) spectroscopy has been establishing itself as an ultrasensitive analytical technique with a cross-disciplinary range of applications, which scientific growth is triggered by the continuous improvement in the design of advanced plasmonic materials with enhanced multifunctional abilities and tailorable surface chemistry. In this regard, conventional synthetic procedures yield negatively-charged plasmonic materials which can hamper the adhesion of negatively-charged species. To tackle this issue, metallic surfaces have been modified via diverse procedures with a broad array of surface ligands to impart positive charges. Cationic amines have been preferred because of their ability to retain a positive zeta potential even at alkaline pH as well as due to their wide accessibility in terms of structural features and cost. In this review, we will describe and discuss the different approaches for generating positively-charged plasmonic platforms and their applications in SERS sensing.

Nanomedicine as a promising strategy for the theranostics of infectious diseases

Infectious diseases caused by bacteria, viruses, and fungi and their global spread pose a great threat to human health. The 2019 World Health Organization report predicted that infection-related mortality will be similar to cancer mortality by 2050. Particularly, the global cumulative numbers of the recent outbreak of coronavirus disease (COVID-19) have reached 110.7 million cases and over 2.4 million deaths as of February 23, 2021. Moreover, the crisis of these infectious diseases exposes the many problems of traditional diagnosis, treatment, and prevention, such as time-consuming and unselective detection methods, the emergence of drug-resistant bacteria, serious side effects, and poor drug delivery. There is an urgent need for rapid and sensitive diagnosis as well as high efficacy and low toxicity treatments. The emergence of nanomedicine has provided a promising strategy to greatly enhance detection methods and drug treatment efficacy. Owing to their unique optical, magnetic, and electrical properties, nanoparticles (NPs) have great potential for the fast and selective detection of bacteria, viruses, and fungi. NPs exhibit remarkable antibacterial activity by releasing reactive oxygen species and metal ions, exerting photothermal effects, and causing destruction of the cell membrane. Nano-based delivery systems can further improve drug permeability, reduce the side effects of drugs, and prolong systemic circulation time and drug half-life. Moreover, effective drugs against COVID-19 are still lacking. Recently, nanomedicine has shown great potential to accelerate the development of safe and novel anti-COVID-19 drugs. This article reviews the fundamental mechanisms and the latest developments in the treatment and diagnosis of bacteria, viruses, and fungi and discusses the challenges and perspectives in the application of nanomedicine.

Striking Back against Fungal Infections: The Utilization of Nanosystems for Antifungal Strategies

Fungal infections have become a major health concern, given that invasive infections by Candida, Cryptococcus, and Aspergillus species have led to millions of mortalities. Conventional antifungal drugs including polyenes, echinocandins, azoles, allylamins, and antimetabolites have been used for decades, but their limitations include off-target toxicity, drug-resistance, poor water solubility, low bioavailability, and weak tissue penetration, which cannot be ignored. These drawbacks have led to the emergence of novel antifungal therapies. In this review, we discuss the nanosystems that are currently utilized for drug delivery and the application of antifungal therapies.

Fast label-free identification of bacteria by synchronous fluorescence of amino acids

Fast identification of pathogenic bacteria is an essential need for patient's diagnostic in hospitals and environmental monitoring of water and air quality. Bacterial cells consist of a very high amount of biological molecules whose content changes in response to different environmental conditions. The similarity between the molecular compositions of different bacterial cells limits the possibility to find unique markers to enable differentiation among species. Although many biological molecules in the cells absorb at the UV-Vis region, only a few of them can be detected in whole cells by their intrinsic fluorescence. Among these molecules are the amino acids phenylalanine, tyrosine, and tryptophan. In this work, we develop a rapid method for bacterial identification by synchronous fluorescence. We show that we can quantify the concentration for the 3 amino acids without any significant interference from other fluorophores in the cells and that we can differentiate among 6 pathogenic bacterial species by using the concentrations of their amino acids as a bacterial fingerprint. Fluorescent amino acids exist in all living cells. Therefore, this method has the potential to be applicative for the rapid identification of cells from all kinds of organisms.

Surface-enhanced Raman spectroscopy for bioanalysis and diagnosis

In recent years, bioanalytical surface-enhanced Raman spectroscopy (SERS) has blossomed into a fast-growing research area. Owing to its high sensitivity and outstanding multiplexing ability, SERS is an effective analytical technique that has excellent potential in bioanalysis and diagnosis, as demonstrated by its increasing applications in vivo. SERS allows the rapid detection of molecular species based on direct and indirect strategies. Because it benefits from the tunable surface properties of nanostructures, it finds a broad range of applications with clinical relevance, such as biological sensing, drug delivery and live cell imaging assays. Of particular interest are early-stage-cancer detection and the fast detection of pathogens. Here, we present a comprehensive survey of SERS-based assays, from basic considerations to bioanalytical applications. Our main focus is on SERS-based pathogen detection methods as point-of-care solutions for early bacterial infection detection and chronic disease diagnosis. Additionally, various promising in vivo applications of SERS are surveyed. Furthermore, we provide a brief outlook of recent endeavours and we discuss future prospects and limitations for SERS, as a reliable approach for rapid and sensitive bioanalysis and diagnosis.

Rapid Detection Method for Pathogenic Candida Captured by Magnetic Nanoparticles and Identified Using SERS via AgNPs. Int J Nanomedicine 2021;16:941-950. [PMID: 33603361 PMCID: PMC7884937 DOI: 10.2147/ijn.s285339]

Purpose

Candidemia infection is common in the clinic and has a high mortality rate. Candida albicans, Candida tropicalis, and Candida krusei are very important and common pathogenic species. Candida is difficult to isolate from clinical samples and culture, and immunological detection cannot distinguish these related strains. Furthermore, Candida has a complex cell wall, which causes difficulties in the extraction of DNA for nucleic acid detection. The purpose of this study was to establish a protocol for the direct identification of Candida from serum.

Materials and Methods

We synthesized Fe₃O₄@PEI (where PEI stands for polyethylenimine) magnetic nanoparticles to capture Candida and prepared positively charged silver nanoparticles (AgNPs⁺) as the substrate for surface-enhanced Raman scattering (SERS). Candida was directly identified from serum by SERS detection.

Results

Orthogonal partial least squares discriminant analysis (OPLS-DA) was used as the multivariate analysis tool. Principal component analysis confirmed that this method can clearly distinguish common Candida. After 10-fold cross-validation, the accuracy of training data in this model was 100% and the accuracy of test data was 99.8%, indicating that the model has good classification ability.

Conclusion

The detection could be completed within 40 minutes using Fe₃O₄@PEI and AgNPs⁺ prepared in advance. This is the first time that Fe₃O₄@PEI was used in the detection of Candida by SERS. We report the first rapid method to identify fungi directly from serum without breaking the cell wall to extract DNA from the fungi.