Ultrasensitive Dual ELONA/SERS-RPA Multiplex Diagnosis of Antimicrobial Resistance.

Antimicrobial resistance (AMR) is a significant global health threat concern, necessitating healthcare practitioners to accurately prescribe the most effective antimicrobial agents with correct doses to combat resistant infections. This is necessary to improve the therapeutic outcomes for patients and prevent further increase in AMR. Consequently, there is an urgent need to implement rapid and sensitive clinical diagnostic methods to identify resistant pathogenic strains and monitor the efficacy of antimicrobials. In this study, we report a novel proof-of-concept magnetic scaffold-recombinase polymerase amplification (RPA) technique, coupled with an enzyme-linked oligonucleotide assay (ELONA) and surface-enhanced Raman scattering (SERS) detection, aimed at selectively amplifying and detecting the DNA signature of three resistant carbapenemase genes, VIM, KPC, and IMP. To achieve this, streptavidin-coated magnetic beads were functionalized with biotin-modified forward primers. RPA was conducted on the surface of the beads, resulting in an immobilized duplex amplicon featuring a single overhang tail specific to each gene. These tails were subsequently hybridized with recognition HRP probes conjugated to a complementary single-stranded oligonucleotide and detected colorimetrically. Additionally, they underwent hybridization with similar selective SERS probes and were measured using a handheld Raman spectrometer. The resulting quantification limits were at subpicomolar level for both assays, allowing the potential for early diagnosis. Moreover, we demonstrated the platform capability to conduct a multiplex RPA-SERS detection of the three genes in a single tube. Compared to similar approaches like PCR, RPA offers advantages of speed, affordability, and isothermal operation at 37 °C, eliminating the need for a thermal cycler. The whole assay was completed within <2 h. Therefore, this novel magnetic scaffold ELONA/SERS-RPA platform, for DNA detection, demonstrated excellent capability for the rapid monitoring of AMR in point-of-care applications, in terms of sensitivity, portability, and speed of analysis.

Multiplex detection of the big five carbapenemase genes using solid-phase recombinase polymerase amplification.

Five carbapenemase enzymes, coined the 'big five', have been identified as the biggest threat to worldwide antibiotic resistance based on their broad substrate affinity and global prevalence. Here we show the development of a molecular detection method for the gene sequences from the five carbapenemases utilising the isothermal amplification method of recombinase polymerase amplification (RPA). We demonstrate the successful detection of each of the big five carbapenemase genes with femtomolar detection limits using a spatially separated multiplex amplification strategy. The approach uses tailed oligonucleotides for hybridisation, reducing the complexity and cost of the assay compared to classical RPA detection strategies. The reporter probe, horseradish peroxidase, generates the measureable output on a benchtop microplate reader, but more notably, our study leverages the power of a portable Raman spectrometer, enabling up to a 19-fold enhancement in the limit of detection. Significantly, the development approach employed a solid-phase RPA format, wherein the forward primers targeting each of the five carbapenemase genes are immobilised to a streptavidin-coated microplate. The adoption of this solid-phase methodology is pivotal for achieving a successful developmental pathway when employing this streamlined approach. The assay takes 2 hours until result, including a 40 minutes RPA amplification step at 37 °C. This is the first example of using solid-phase RPA for the detection of the big five and represents a milestone towards the developments of an automated point-of-care diagnostic for the big five using RPA.

Recent advances in antibiotic resistance diagnosis using SERS: focus on the "Big 5" challenges.

Antibiotic resistant bacteria constitute a global health threat. It is essential for healthcare professionals to prescribe the correct dose of an effective antibiotic to mitigate the bacterial infection in a timely manner to improve the therapeutic outcomes to the patient and prevent the dissemination of antibiotic resistance. To achieve this, there is a need to implement a rapid and ultra-sensitive clinical diagnosis to identify resistant bacterial strains and monitor the effect of antibiotics. In this review, we highlight the use of surface enhanced Raman scattering (SERS) as a powerful diagnostic technique for bacterial detection and evaluation. Initially, this is viewed through a lens covering why SERS can surpass other traditional techniques for bacterial diagnosis. This is followed by different SERS substrates design, detection strategies that have been used for various bacterial biomarkers, how SERS can be combined with other diagnostic platforms to improve its performance towards the bacterial detection and the application of SERS for antibiotic resistance diagnosis. Finally, the recent progress in SERS detection methods in the last decade for the "Big 5" antibiotic resistant challenges as demonstrators of public health major threats is reviewed, namely: Methicillin-resistant Staphylococcus aureus (MRSA), Carbapenem-resistant Enterobacteriaceae (CRE)/Extended-spectrum beta-lactamases (ESBLs), Mycobacterium tuberculosis (TB), Vancomycin-resistant Enterococcus (VRE) and Neisseria Gonorrhoea (NG). This review provides a comprehensive view of the current state of the art with regard to using SERS for assessing antibiotic resistance with a future outlook on where the field go head in the coming years.

Label-free identification of Erythropoietin isoforms by surface enhanced Raman spectroscopy.

We present a sensitive label-free surface enhanced Raman spectroscopy (SERS) method for the discrimination between the recombinant and endogenous human Erythropoietin (EPO) isoforms. The proposed methodology comprises a lectin-functionalised extractor chip for the extraction of the recombinant human EPO (rhuEPO) and the endogenous EPO (enEPO) from blood plasma. The disulfide bond molecular structure of the purified isoforms was modified to chemisorb the biomolecules onto a SERS substrate in a unified orientation, thus maximizing the reproducibility and sensitivity of the SERS measurements. The acquired SERS spectra of the EPO isoforms showed diagnostic Raman bands that allowed for the discrimination between rhuEPO and enEPO. The method was also used for the SERS quantification of rhuEPO and enEPO down to 0.1 pM and 0.5 pM, respectively. The SERS determination of the protein isoforms was cross validated against ELISA. The new SERS method has strong potential for the rapid screening of rhuEPO doping in athletes and for the therapeutic drug monitoring of rhuEPO treatment in cancer patients.

Rapid ultra-sensitive diagnosis of clostridium difficile infection using a SERS-based lateral flow assay.

Clostridium difficile (C. diff) infection is one of the most contagious diseases associated with high morbidity and mortality rates in hospitalised patients. Accurate diagnosis can slow its spread by determining the most effective treatment. Herein, we report a novel testing platform as a proof-of-concept for the selective, sensitive, rapid and cost-effective diagnosis of C. diff infection (CDI) based on a duplex measurement. This was achieved by detecting two specific biomarkers, surface layer protein A (SlpA) and toxin B (ToxB), using a surface enhanced Raman scattering-based lateral flow assay (SERS-based LFA). The simultaneous duplex detection of SlpA with ToxB has not been described for the clinical diagnosis of CDI previously. The SlpA biomarker "AKDGSTKEDQLVDALA" was first reported by our group in 2018 as a species-specific identification tool. The second biomarker, ToxB, is the essential virulence biomarker of C. diff pathogenic strains and is required to confirm true infection pathogenicity. The proposed SERS-based LFA platform enabled rapid duplex detection of SlpA and ToxB on separate test lines using a duplex LF test strip within 20 minutes. The use of a handheld Raman spectrometer to scan test lines allowed for the highly sensitive quantitative detection of both biomarkers with a lowest observable concentration of 0.01 pg µL-1. The use of a handheld device in this SERS-based LFA instead of benchtop machine paves the way for rapid, selective, sensitive and cheap clinical evaluation of CDI at the point of care (POC) with minimal sample backlog.

Toward Label-Free SERS Detection of Proteins through Their Disulfide Bond Structure.

The molecular structure of many proteins contains disulfide bonds between their cysteine residues. In this work we demonstrate the utilization of the disulfide bond structure of proteins for their label-free determination by surface-enhanced Raman spectroscopy (SERS). The new approach for label-free SERS detection of proteins is demonstrated for human insulin. The protein was selectively extracted from spiked plasma samples using target-specific functionalized nanomaterial. Enzyme-linked immune assay (ELISA) was used to detect insulin in the blood plasma and cross-validate the SERS method. The disulfide bonds in the molecular structure of the protein were chemically reduced and used for their chemisorption onto the gold-coated copper oxide substrate in a unified orientation at a very short distance from the hotspots. The oriented chemisorption of the protein caused significant enhancement to the signal intensity of its Raman vibration modes. This is attributed to the strong short-range electromagnetic and chemical enhancement effects that are experienced by the immobilized protein. Using this approach, label-free and reproducible SERS detection of insulin, down to 10 zM (relative standard deviation [RSD] = 5.52%), was achieved. Sixty-five percent of proteins contain disulfide bonds in their molecular structure. Therefore, the new label-free SERS detection method has strong potential for the determination of ultralow concentrations of proteins at pathology labs and in biology research.

Spectroelectrochemical Nanosensor for the Determination of Cystatin C in Human Blood.

The detection of protein biomarkers for the clinical diagnosis of diseases requires selective and sensitive methodologies and biosensors that can be easily used at pathology laboratories and points of care. An ideal methodology would be able to conduct multimode screening of low and high concentrations of proteins in biological fluids using recyclable platforms. In this work, we demonstrate a novel nanosensing methodology for the dual detection of cystatin C (CST-C), as a protein biomarker model, in blood plasma by surface-enhanced Raman spectroscopy and electrochemistry. The new methodology utilizes the thiol chemistry of biomolecules to develop a target-specific and recyclable extractor chip for the rapid isolation of protein biomarkers from blood plasma. This is followed by the rapid reduction of the disulfide bonds within the isolated protein to influence its oriented immobilization onto a conductive gold coated silicon nanopillar substrate via stable gold-sulfur (Au-S) bonds. The oriented immobilization led to reproducible surface-enhanced Raman spectroscopy (SERS) measurements of the reduced protein (RSD = 3.8%) and allowed for its direct electrochemical determination. After the SERS measurement, differential pulse voltammetry (DPV) was used to desorb the analyte from the substrate and generate a reduction current that is proportional to its concentration. CST-C was determined down to 1 pM and 62.5 nM by SERS and DPV, respectively, which satisfies the requirements for monitoring Alzheimer's and kidney failure diseases. The new dual nanosensing methodology has strong potential for miniaturization in a lab-on-a-chip platform for the screening of many protein biomarkers that have a disulfide bond structure.

An electrochemical biosensor for the rapid detection of erythropoietin in blood.

A label free electrochemical detection method for the rapid detection of recombinant human erythropoietin (rhuEPO) has been developed. In this method, we modified the rhuEPO structure for its direct sensing without using a complex signal amplification strategy. The protein was selectively extracted from blood plasma sample using target-specific magnetic beads. After releasing rhuEPO from the magnetic beads, its disulfide bonds were electrochemically reduced and the protein was spontaneously assembled onto a nanostructured gold electrode via Au-S bonds formation. For electrochemical quantification, the reduced protein was desorbed from the electrode surface using differential pulse voltammetry (DPV). The desorption current was proportional to the concentration of rhuEPO in the range 1-1000 p.M. By cross-validating against ELISA, we found a 104.85 ±â€¯3.35% agreement between the results obtained using the electrochemical biosensor and ELISA. Therefore the developed method has a strong potential for the sensitive detection of rhuEPO doping in sports as well as its rapid screening and pathology labs.

Gold nanomaterials for the selective capturing and SERS diagnosis of toxins in aqueous and biological fluids.

A highly sensitive nanosensing method for the combined selective capture and SERS detection of Microcystin-LR (MC-LR) in blood plasma has been developed. The new method utilizes gold coated magnetic nanoparticles that are functionalized with anti MC-LR antibody Fab' fragments for the selective capture of MC-LR from aqueous media and blood plasma. Using an oriented immobilization approach, the Fab' fragments are covalently attached to gold surface to form a monolayer with high capture efficiency towards the toxin. After the selective capture, the purified MC-LR molecules were released from the extractor nanoparticles within 5min by manipulating the pH environment of the nanoparticles. The regenerated extractor nanoparticles maintained their capture efficiency and, therefore, were re-used to capture of MC-LR from successive samples. The released purified toxin was screened within 10min on gold coated silicon nanopillars and a new paper-based SERS substrate by handheld Raman spectrometer. The SERS enhancement factors of the nanopillars and the new paper-based substrate were 2.5×106 and 3×105 respectively. The lower limit of quantification (LOQ) of MC-LR by SERS on the nanopillar substrate was 10fM (R2=0.9975) which is well below the clinically required detection limit of the toxin. The SERS determination of MC-LR was cross validated against ELISA. By using antibody fragments that are specific to the target biomolecule, the new methodology can be extended to the rapid extraction and detection of other toxins and proteins.

Chromatographic Study of Azintamide in Bulk Powder and in Pharmaceutical Formulation in the Presence of Its Degradation Form.

Two specific, sensitive, and precise stability-indicating chromatographic methods were developed, optimized, and validated for the determination of Azintamide (AZ) in the presence of its degradation product. The first method was TLC combined with the densitometric determination of the separated bands. Separation was achieved using silica gel 60 F254 TLC plates and chloroform-acetone-glacial acetic acid (7.5 + 2.1 + 0.4, v/v/v) as the developing system. Good correlations were obtained between the integrated peak area of the studied drug and its corresponding concentrations in the linearity range. The second method used HPLC with UV diode-array detection, in which the proposed method was applied for the quantitative determination of AZ in the presence of its acidic degradation product and the quantitative determination of the acid-induced degradation product of AZ (AZ Deg) using pentoxifylline as the internal standard. The proposed components were separated on a reversed-phase C18 analytical column using acetonitrile-water (50 + 50, v/v). The flow rate was maintained at 0.55 mL/min and the detection wavelength was 260 nm. Linear regressions were obtained in the range of 1-30 and 0.3-16 µg/mL for AZ and AZ Deg, respectively. Different parameters affecting the suggested methods were optimized for maximum separation of the cited components. The suggested methods were validated in compliance with the International Conference on Harmonization guidelines and successfully applied for the determination of AZ in its pure powder form and in its pharmaceutical formulation. Both methods were also statistically compared with the reported method with no significant difference in performance observed.

Towards interference free HPLC-SERS for the trace analysis of drug metabolites in biological fluids.

Sofosbuvir metabolite, 2'-deoxy-2'-fluoro-2'-C-methyluridine (PSI-6206) was studied for the first time by surface enhanced Raman spectroscopy (SERS) using the paper-based SERS substrate. The quantification limit of PSI-6206 by SERS was found to be 13ngL-1 (R2 value=0.959, RSD=5.23%). For the structural and quantitative analysis of PSI-6206 in blood plasma, an interference-free HPLC-SERS method was developed and compared to HPLC-DAD and HPLC-MS methods. The SERS quantification of the drug by the paper substrate was 4 orders of magnitude more sensitive than that by the diode array detector. In addition, the SERS detection provided unique structural identification of the drug in blood plasma, similar to Mass spectroscopy detector. Due to the disposable nature of the SERS substrate, the new method does not suffer from the known "memory effect" which is known to lead to false positive identification in traditional HPLC-SERS methods. Therefore, the presented HPLC-paper SERS platform holds great potential for the sensitive and cost effective determination of drugs and their metabolites in biological fluids.