Staphylococcus aureus detection in blood samples by silica nanoparticle-oligonucleotides conjugates

Aptamer decorated PDA@magnetic silica microparticles for bacteria purification

One significant constraint in the advancement of biosensors is the signal-to-noise ratio, which is adversely affected by the presence of interfering factors such as blood in the sample matrix. In the present investigation, a specific aptamer binding was chosen for its affinity, while exhibiting no binding affinity towards non-target bacterial cells. This selective binding property was leveraged to facilitate the production of magnetic microparticles decorated with aptamers. A novel assay was developed to effectively isolate S. pneumoniae from PBS or directly from blood samples using an aptamer with an affinity constant of 72.8 nM. The capture experiments demonstrated efficiencies up to 87% and 66% are achievable for isolating spiked S. pneumoniae in 1 mL PBS and blood samples, respectively.

Direct Detection of Viral Infections from Swab Samples by Probe-Gated Silica Nanoparticle-Based Lateral Flow Assay

Point-of-care diagnosis is crucial to control the spreading of viral infections. Here, universal-modifiable probe-gated silica nanoparticles (SNPs) based lateral flow assay (LFA) is developed in the interest of the rapid and early detection of viral infections. The most superior advantage of the rapid assay is its utility in detecting various sides of the virus directly from the human swab samples and its adaptability to detect various types of viruses. For this purpose, a high concentration of fluorescein and rhodamine B as a reporting material was loaded into SNPs with excellent loading capacity and measured using standard curve, 4.19 μmol ⋅ g-1 and 1.23 μmol ⋅ g-1 , respectively. As a model organism, severe acute respiratory syndrome coronavirus-2 (CoV-2) infections were selected by targeting its nonstructural (NSP9, NSP12) and envelope (E) genes as target sites of the virus. We showed that NSP12-gated SNPs-based LFA significantly outperformed detection of viral infection in 15 minutes from 0.73 pg ⋅ mL-1 synthetic viral solution and with a dilution of 1 : 103 of unprocessed human samples with an increasing test line intensity compared to steady state (n=12). Compared to the RT-qPCR method, the sensitivity, specificity, and accuracy of NSP12-gated SNPs were calculated as 100 %, 83 %, and 92 %, respectively. Finally, this modifiable nanoparticle system is a high-performance sensing technique that could take advantage of upcoming point-of-care testing markets for viral infection detections.

Dual-Modal Biosensor for Staphylococcus aureus Detection Based on a Porphyrin-Based Porous Organic Polymer FePor-TPA with Excellent Peroxidase-like, Catalase-like, and Photoelectrochemical Properties

Bacterial infections seriously harm human health and cause many severe diseases, which triggered urgent demands to exploit specific and sensitive biosensor strategies for Staphylococcus aureus detection. Here, a colorimetric and photoelectrochemical dual-mode biosensor for S. aureus assay based on FePor-TPA was constructed. 2D FePor-TPA thin film and its bulk powder (FePor-TPA) were synthesized by in situ growth on ITO and a solvothermal condition, respectively, both of which exhibited excellent peroxidase-like and catalase-like activity, originating from their metalloporphyrin linkers. Benefiting from the in situ growth on ITO electrodes, the 2D FePor-TPA thin film also possessed a more ordered stacking mode and in turn exhibited good electrical conductivity, stable initial photocurrent, and high sensitivity to O2. As for bulk FePor-TPA, its porous structure and high specific surface area make it a possible scaffold to load an amount of AuNPs, the rabbit anti-Staphylococcus aureus Rosenbach tropina antibody (Ab2), and GOx for constructing the signal probe (GOx/Ab2@Au@FePor-TPA) and realizing catalytic amplification. With these satisfactory features in mind, the 2D FePor-TPA thin film and its bulk powder (FePor-TPA) were utilized to construct a dual and signal-on bioplatform for sensitively and selectively detecting S. aureus, which, as far as we know, has not been reported.

Antibody conjugated Au/Ir@Cu/Zn-MOF probe for bacterial lateral flow immunoassay and precise synergistic antibacterial treatment

Staphylococcus aureus is one of the most prevalent threats to public health. Rapid detection with high sensitivity and targeted killing is crucial to curb its spread. Herein, a metal-bearing nanocomposite, consisting of a bimetallic nanoparticle and a metal-organic framework (Au/Ir@Cu/Zn-MOF) was constructed. Upon conjugation with anti-S. aureus antibody, this nanocomposite (Ab-Au/Ir@Cu/Zn-MOF) was exploited for its dual functions, i.e. as a reporting probe in a lateral flow immunoassay and a high efficiency antibacterial reagent. Benefiting from the enrichment of Au/Ir NPs by the Cu/Zn-MOF, the Au/Ir@Cu/Zn-MOF-based lateral flow immunoassay sensor exhibited a visual limit of detection of 10³ CFU/mL, which was100 times more sensitive than Au/Ir-based sensor. Moreover, the Ab-Au/Ir@Cu/Zn-MOF probe possessed synergistic photothermal-chemodynamic bactericidal effect that specifically targeted against S. aureus. Under a co-treatment by H₂O₂ (0.4 mM) and 808 nm near infrared irradiation (1 W/cm², 5 min), complete sterilization of 5 × 10⁵-10⁶ CFU/mL S. aureus was achieved at a nanocomposite concentration as low as 6.25 μg/mL. The superior antibacterial efficiency was attributable to the three-fold properties of the Ab-Au/Ir@Cu/Zn-MOF probe: (1) enhanced multi-enzyme mimicking activities that promote reactive oxygen species generation, (2) high photothermal activity (efficiency of 53.70%), and (3) bacteria targeting ability via the antibody coating. By changing the antibody, this nanocomposite can be tailored to target a wide range of bacteria species, for detection and for precise antibacterial treatment.

Recent Advances in Aptasensors For Rapid and Sensitive Detection of Staphylococcus Aureus

The infection of Staphylococcus aureus (S.aureus) and the spread of drug-resistant bacteria pose a serious threat to global public health. Therefore, timely, rapid and accurate detection of S. aureus is of great significance for food safety, environmental monitoring, clinical diagnosis and treatment, and prevention of drug-resistant bacteria dissemination. Traditional S. aureus detection methods such as culture identification, ELISA, PCR, MALDI-TOF-MS and sequencing, etc., have good sensitivity and specificity, but they are complex to operate, requiring professionals and expensive and complex machines. Therefore, it is still challenging to develop a fast, simple, low-cost, specific and sensitive S. aureus detection method. Recent studies have demonstrated that fast, specific, low-cost, low sample volume, automated, and portable aptasensors have been widely used for S. aureus detection and have been proposed as the most attractive alternatives to their traditional detection methods. In this review, recent advances of aptasensors based on different transducer (optical and electrochemical) for S. aureus detection have been discussed in details. Furthermore, the applications of aptasensors in point-of-care testing (POCT) have also been discussed. More and more aptasensors are combined with nanomaterials as efficient transducers and amplifiers, which appears to be the development trend in aptasensors. Finally, some significant challenges for the development and application of aptasensors are outlined.

Aptamer-Targeted Drug Delivery for Staphylococcus aureus Biofilm

Treatment of Staphylococcus aureus biofilm infections using conventional antibiotic therapy is challenging as only doses that are sublethal to the biofilm can be administered safely to patients. A potential solution to this challenge is targeted drug delivery. In this study, we tailored an aptamer-targeted liposomal drug delivery system for accumulation and delivery of antibiotics locally in S. aureus biofilm. In our search for a suitable targeting ligand, we identified six DNA aptamers that bound to S. aureus cells in biofilms, and we demonstrated that one of these aptamers could facilitate accumulation of liposomes around S. aureus cells inside the biofilm. Aptamer-targeted liposomes encapsulating a combination of vancomycin and rifampicin were able to eradicate S. aureus biofilm upon 24 h of treatment in vitro. Our results point to that aptamer-targeted drug delivery of antibiotics is a potential new strategy for treatment of S. aureus biofilm infections.

Biomolecules capturing live bacteria from clinical samples

Rapid phenotypic antimicrobial susceptibility testing (AST) requires the enrichment of live bacteria from patient samples, which is particularly challenging in the context of life-threatening bloodstream infections (BSIs) due to low bacterial titers. Over two decades, an extensive array of pathogen-specific biomolecules has been identified to capture live bacteria. The prevailing biomolecules are immune proteins of the complement system, antibodies, aptamers, phage proteins, and antimicrobial peptides. These biomolecules differ by their binder generation technologies and exhibit highly variable specificities, ranging from bacterial strains to most pathogenic bacteria. Here, we summarize how these diverse biomolecules were identified, list examples of successfully reported capture assays, and provide an outlook on the use of nanobodies raised against conserved surface-accessible proteins as promising biomolecules for pathogen capture.

Recent Advances in the Use of Mesoporous Silica Nanoparticles for the Diagnosis of Bacterial Infections

Public awareness of infectious diseases has increased in recent months, not only due to the current COVID-19 outbreak but also because of antimicrobial resistance (AMR) being declared a top-10 global health threat by the World Health Organization (WHO) in 2019. These global issues have spiked the realization that new and more efficient methods and approaches are urgently required to efficiently combat and overcome the failures in the diagnosis and therapy of infectious disease. This holds true not only for current diseases, but we should also have enough readiness to fight the unforeseen diseases so as to avoid future pandemics. A paradigm shift is needed, not only in infection treatment, but also diagnostic practices, to overcome the potential failures associated with early diagnosis stages, leading to unnecessary and inefficient treatments, while simultaneously promoting AMR. With the development of nanotechnology, nanomaterials fabricated as multifunctional nano-platforms for antibacterial therapeutics, diagnostics, or both (known as "theranostics") have attracted increasing attention. In the research field of nanomedicine, mesoporous silica nanoparticles (MSN) with a tailored structure, large surface area, high loading capacity, abundant chemical versatility, and acceptable biocompatibility, have shown great potential to integrate the desired functions for diagnosis of bacterial infections. The focus of this review is to present the advances in mesoporous materials in the form of nanoparticles (NPs) or composites that can easily and flexibly accommodate dual or multifunctional capabilities of separation, identification and tracking performed during the diagnosis of infectious diseases together with the inspiring NP designs in diagnosis of bacterial infections.

Targeted mesoporous silica nanoparticles for improved inhibition of disinfectant resistant Listeria monocytogenes and lower environmental pollution

Benzalkonium chloride (BAC) is a common ingredient of disinfectants used for industrial, medical, food safety and domestic applications. It is a common pollutant detected in surface and wastewaters to induce adverse effects on Human health as well as aquatic and terrestrial life forms. Since disinfectant use is essential in combatting against microorganisms, the best approach to reduce ecotoxicity level is to restrict BAC use. We report here that encapsulation of BAC in mesoporous silica nanoparticles can provide an efficient strategy for inhibition of microbial activity with lower than usual concentrations of disinfectants. As a proof-of-concept, Listeria monocytogenes was evaluated for minimum inhibitory concentration (MIC) of nanomaterial encapsulated BAC. Aptamer molecular gate structures provided a specific targeting of the disinfectant to Listeria cells, leading to high BAC concentrations around bacterial cells, but significantly reduced amounts in total. This strategy allowed to inhibition of BAC resistant Listeria strains with 8 times less the usual disinfectant dose. BAC encapsulated and aptamer functionalized silica nanoparticles (AptBACNP) effectively killed only target bacteria L. monocytogenes, but not the non-target cells, Staphylococcus aureus or Escherichia coli. AptBACNP was not cytotoxic to Human cells as determined by in vitro viability assays.

Nanomaterial application in bio/sensors for the detection of infectious diseases

Infectious diseases are a potential risk for public health and the global economy. Fast and accurate detection of the pathogens that cause these infections is important to avoid the transmission of the diseases. Conventional methods for the detection of these microorganisms are time-consuming, costly, and not applicable for on-site monitoring. Biosensors can provide a fast, reliable, and point of care diagnostic. Nanomaterials, due to their outstanding electrical, chemical, and optical features, have become key players in the area of biosensors. This review will cover different nanomaterials that employed in electrochemical, optical, and instrumental biosensors for infectious disease diagnosis and how these contributed to enhancing the sensitivity and rapidity of the various sensing platforms. Examples of nanomaterial synthesis methods as well as a comprehensive description of their properties are explained. Moreover, when available, comparative data, in the presence and absence of the nanomaterials, have been reported to further highlight how the usage of nanomaterials enhances the performances of the sensor.

Recent Advances and a Roadmap to Aptamer-Based Sensors for Bloodstream Infections

The present review is intended to describe bloodstream infections (BSIs), the major pathogens responsible for BSIs, conventional tests and their limitations, commercially available methods used, and the aptamer and nanomaterials-based approaches developed so far for the detection of BSIs. The advantages associated with aptamers and the aptamer-based sensors, the comparison between the aptamers and the antibodies, and the various types of aptasensors developed so far for the detection of bloodstream infections have been described in detail in the present review. Also, the future outlook and roadmap toward aptamer-based sensors and the challenges associated with the aptamer development have also been concluded in this review.

Sensitive detection of S. Aureus using aptamer- and vancomycin -copper nanoclusters as dual recognition strategy

The proposed aptamer- and antibiotic-based dual detection sensor, combines copper nanoclusters (CuNCs) as an effective approach for the recognition and quantification of Staphylococcus aureus (S. aureus) as a pathogenic bacteria. A facile method for CuNCs based on vancomycin as the template using a fluorescence platform was proposed for the recognition of the S. aureus whole cells via antibiotic and aptamer. Using dual receptor functionalized CuNCs linked to vancomycin and a specific aptamer and during aggregation induce emission process enhanced fluorescence signal linearly with S. aureus concentrations between 10²-10⁸ CFU/mL, and the detection limit was 80 CFU/mL after 45 min as the optimum incubation time. Non-target bacteria generated negative results, proving the high specificity of the presented sensor. This strategy showed recoveries ranging 86%-98% in milk as real sample and can be used for the development of universal detection platforms for efficient and specific S. aureus detection with great potential applications for monitoring pathogenic bacteria.

Development of Highly Sensitive Immunosensor for Detection of Staphylococcus aureus Based on AuPdPt Trimetallic Nanoparticles Functionalized Nanocomposite

The rapid and sensitive detection of Staphylococcus aureus (S. aureus) is essential to ensure food safety and protect humans from foodborne diseases. In this study, a sensitive and facile electrochemical immunosensor using AuPdPt trimetallic nanoparticles functionalized multi-walled carbon nanotubes (MWCNTs-AuPdPt) as the signal amplification platform was designed for the label-free detection of S. aureus. The nanocomposite of MWCNTs-AuPdPt was prepared by an in situ growth method of loading AuPdPt trimetallic nanoparticles on the surface of MWCNTs. The synthesized MWCNTs-AuPdPt featured good conductivity and superior catalytic performance for hydrogen peroxide. The nanocomposite of MWCNTs-AuPdPt with good biocompatibility and high specific surface area was further functionalized by anti-S. aureus antibodies. The immobilized antibodies could efficiently capture S. aureus to the modified electrode by an immune reaction, which resulted in the change of catalytic current intensity to realize the sensitive detection of S. aureus. The designed immunosensor could detect S. aureus in a linear range from 1.1 × 102 to 1.1 × 107 CFU mL-1 with a low detection limit of 39 CFU mL-1. Additionally, the proposed immunosensor was successfully applied to determine S. aureus in actual samples with acceptable results. This strategy provided a promising platform for highly sensitive determination of S. aureus and other pathogens in food products.

Enhanced sensitivity and efficiency of detection of Staphylococcus aureus based on modified magnetic nanoparticles by photometric systems

Staphylococcus aureus is an important infectious factor in the food industry and hospital infections. Many methods are used for detecting bacteria but they are mostly time-consuming, poorly sensitive. In this study, a nano-biosensor based on iron nanoparticles (MNPs) was designed to detect S. aureus. MNPs were synthesized and conjugated to Biosensors. Then S. aureus was lysed and nano-biosensor (MNP-TiO₂-AP-SMCC-Biosensors) was added to the lysed bacteria. After bonding the bacterial genome to the nano-biosensor, MNPs were separated by a magnet. Bacterial DNA was released from the surface of nano-biosensor and researched by Nano-drop spectrophotometry. The results of SEM and DLS revealed that the size of MNPs was 20-25 nm which increased to 38-43 nm after modification and addition of biosensors. The designed nano-biosensor was highly sensitive and specific for the detection of S. aureus. The limit of detection (LOD) was determined as 230 CFU mL^-1. There was an acceptable linear correlation between bacterial concentration and absorption at 3.7 × 10²-3.7× 10⁷ whose linear diagram and regression was Y = 0.242X + 2.08 and R² = .996. Further, in the presence of other bacteria as a negative control, it was absolutely specific. The sensitivity of the designed nano-biosensor was investigated and compared through PCR.

Recent advances in functionalized nanomaterials for the diagnosis and treatment of bacterial infections

The growing problem of resistant infections due to antibiotic misuse is a worldwide concern that poses a grave threat to healthcare systems. Thus, it is necessary to discover new strategies to combat infectious diseases. In this review, we provide a selective overview of recent advances in the use of nanocomposites as alternatives to antibiotics in antimicrobial treatments. Metals and metal oxide nanoparticles (NPs) have been associated with inorganic and organic supports to improve their antibacterial activity and stability as well as other properties. For successful antibiotic treatment, it is critical to achieve a high drug concentration at the infection site. In recent years, the development of stimuli-responsive systems has allowed the vectorization of antibiotics to the site of infection. These nanomaterials can be triggered by various mechanisms (such as changes in pH, light, magnetic fields, and the presence of bacterial enzymes); additionally, they can improve antibacterial efficacy and reduce side effects and microbial resistance. To this end, various types of modified polymers, lipids, and inorganic components (such as metals, silica, and graphene) have been developed. Applications of these nanocomposites in diverse fields ranging from food packaging, environment, and biomedical antimicrobial treatments to diagnosis and theranosis are discussed.

Nanotools for Sepsis Diagnosis and Treatment

Sepsis is one of the leading causes of death worldwide with high mortality rates and a pathological complexity hindering early and accurate diagnosis. Today, laboratory culture tests are the epitome of pathogen recognition in sepsis. However, their consistency remains an issue of controversy with false negative results often observed. Clinically used blood markers, C reactive protein (CRP) and procalcitonin (PCT) are indicators of an acute-phase response and thus lack specificity, offering limited diagnostic efficacy. In addition to poor diagnosis, inefficient drug delivery and the increasing prevalence of antibiotic-resistant microorganisms constitute significant barriers in antibiotic stewardship and impede effective therapy. These challenges have prompted the exploration for alternative strategies that pursue accurate diagnosis and effective treatment. Nanomaterials are examined for both diagnostic and therapeutic purposes in sepsis. The nanoparticle (NP)-enabled capture of sepsis causative agents and/or sepsis biomarkers in biofluids can revolutionize sepsis diagnosis. From the therapeutic point of view, currently existing nanoscale drug delivery systems have proven to be excellent allies in targeted therapy, while many other nanotherapeutic applications are envisioned. Herein, the most relevant applications of nanomedicine for the diagnosis, prognosis, and treatment of sepsis is reviewed, providing a critical assessment of their potentiality for clinical translation.

Prospective Application of Aptamer-based Assays and Therapeutics in Bloodstream Infections

Sepsis is still a severe health problem worldwide with high morbidity and mortality. Blood bacterial culture remains the gold standard for the detection of pathogenic bacteria in bloodstream infections, but it is time-consuming, and both the sophisticated equipment and well-trained personnel are required. Immunoassays and genetic diagnosis are expensive and limited to specificity and sensitivity. Aptamers are single-stranded deoxyribonucleic acid (ssDNA) and ribonucleic acid (RNA) oligonucleotide or peptide sequence generated in vitro based on the binding affinity of aptamer-target by a process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX). By taking several advantages over monoclonal antibodies and other conventional small-molecule therapeutics, such as high specificity and affinity, negligible batch-to-batch variation, flexible modification and production, thermal stability, low immunogenicity and lack of toxicity, aptamers are presently becoming promising novel diagnostic and therapeutic agents. This review describes the prospective application of aptamerbased laboratory diagnostic assays and therapeutics for pathogenic bacteria and toxins in bloodstream infections.

The research of aptamer biosensor technologies for detection of microorganism

The activities and transmissions of microorganisms are closely related to human, and all kinds of diseases caused by pathogenic microorganisms have attracted attention in the world and brought many challenges to human health and public health. The traditional microbial detection technologies have characteristics of longer detection cycle and complicated processes, therefore, which can no longer meet the detection requirements in the field of public health. At present, it is the focus to develop and design a novel, rapid, and simple microbial detection method in the field of public health. Herein, this article summarized the development of aptamer biosensor technologies for detection of microorganism in the aspect of bacteria, viruses, and toxins in detail, including optical aptamer sensors such as fluorometry and colorimetry, electrochemical aptamer sensors, and other technologies combined with aptamer. KEY POINTS: • Aptamer biosensor is a good platform for microbial detection. • Aptamer biosensors include optical sensors and electrochemical sensors. • Aptamer sensors have been widely used in the detection of bacteria, viruses, and other microorganisms.

Antibiotic and mammal IgG based lateral flow assay for simple and sensitive detection of Staphylococcus aureus

Lateral flow assay (LFA), performed with simple devices and short detection time, is popular in field applications. Herein, a novel sandwich type-based LFA was constructed for high sensitivity and selectivity detection of Staphylococcus aureus (S. aureus). Vancomycin-immobilized gold nanoparticles (VAN-Au NPs) were utilized as the first identifier to capture S. aureus and the specificity was guaranteed by the second recognition agent of pig immunoglobulin G (IgG). In addition, gold growth was adopted for signal amplification to further improve the detection sensitivity. S. aureus could be directly assayed by this LFA within the concentration range of 1.0 × 10³-1.0 × 10⁸ cfu mL^-1 with a detection limit of 1.0 × 10³ cfu mL^-1. Furthermore, the novel sandwich LFA realized S. aureus detection in food samples with admissible recoveries and established a rapid, simple, cost-effective and sensitive platform, could meet the demand for on-site testing of S. aureus.

Recent Progress in the Identification of Aptamers Against Bacterial Origins and Their Diagnostic Applications

Aptamers have gained an increasing role as the molecular recognition element (MRE) in diagnostic assay development, since their first conception thirty years ago. The process to screen for nucleic acid-based binding elements (aptamers) was first described in 1990 by the Gold Laboratory. In the last three decades, many aptamers have been identified for a wide array of targets. In particular, the number of reports on investigating single-stranded DNA (ssDNA) aptamer applications in biosensing and diagnostic platforms have increased significantly in recent years. This review article summarizes the recent (2015 to 2020) progress of ssDNA aptamer research on bacteria, proteins, and lipids of bacterial origins that have implications for human infections. The basic process of aptamer selection, the principles of aptamer-based biosensors, and future perspectives will also be discussed.

A metal-organic framework/aptamer system as a fluorescent biosensor for determination of aflatoxin B1 in food samples

The demand of simple, sensitive, selective and reliable assay for aflatoxin B1 (AFB1) detection is ubiquitous in food safety, due to its high toxic. Herein, a novel fluorescent aptasensor using metal-organic frameworks (UiO-66-NH₂) and TAMRA label aptamer as sensing platform for AFB1 detection was developed. The TAMRA aptamer adsorbed on the surface of UiO-66-NH₂ via van der Waals force and its fluorescence was quenched for the charge transfer from fluorescence dye TAMRA to metal ions of UiO-66-NH₂. After introducing AFB1 to the system, the TAMRA aptamer binded to AFB1 and formed TAMRA aptamer/AFB1complex, making its conformation change and resulting in fluorescence recovery. Thus, the quantity of AFB1 could be analyzed according to the fluorescence signal change. Under optimize experimental conditions, the assay exhibited high sensitivity toward AFB1 in range of 0-180 ng mL^-1 with low limit of detection of 0.35 ng mL^-1 and good specificity against other toxins. Moreover, the aptamer/metal-organic frameworks sensing platform could be utilized to determine AFB1 content in food samples such as corn, rice and milk. It provided a reasonable method for other mycotoxin detection by changing the sequence of aptamer.

The potential risks of paclobutrazol residue on yogurt fermentation from the level of chiral enantiomers

In recent years, pesticide residues in food have increasingly become the focus of public attention. However, the standard system of pesticide maximum residue limits in fermented food is imperfect, which can lead to potential safety risks to consumers. In this context, the aim of the study was to assess the potential effects of paclobutrazol residue on the yogurt fermentation process. We examined the stereoselective behaviors of the 2 paclobutrazol enantiomers from the perspective of chirality during the yogurt fermentation process. The results indicated that no significant degradation occurred for either of the 2 enantiomers (2R, 3R-paclobutrazol, 2S, 3S-paclobutrazol), and no visible enantiomer conversion behavior was observed. In addition, the reason paclobutrazol did not significantly degrade was explained from the perspective of the microbial function. Results from 16S rRNA sequencing indicated that paclobutrazol significantly affected the microbial composition and inhibited metabolic function of microorganisms to exogenous substances, which impeded the degradation of residual pesticide in yogurt. Furthermore, the stable residue of exogenous substance may cause potential food safety problems. Microbial α-diversity analysis indicated that fermentation time played a more important role on diversity than did paclobutrazol concentration. Moreover, Staphylococcus was found in yogurt after treatment with paclobutrazol; Staphylococcus aureus causes dangerous infectious diseases in humans. We devised a method to investigate the presence of pesticide residues during food fermentation and provided a theoretical basis for food safety assessment.

Protein corona fingerprinting to differentiate sepsis from non-infectious systemic inflammation

Rapid and accurate diagnosis of sepsis remains clinically challenging. The lack of specific biomarkers that can differentiate sepsis from non-infectious systemic inflammatory diseases often leads to excessive antibiotic treatment. Novel diagnostic tests are urgently needed to rapidly and accurately diagnose sepsis and enable effective treatment. Despite investment in cutting-edge technologies available today, the discovery of disease-specific biomarkers in blood remains extremely difficult. The highly dynamic environment of plasma restricts access to vital diagnostic information that can be obtained by proteomic analysis. Here, we employed clinically used lipid-based nanoparticles (AmBisome®) as an enrichment platform to analyze the human plasma proteome in the setting of sepsis. We exploited the spontaneous interaction of plasma proteins with nanoparticles (NPs) once in contact, called the 'protein corona', to discover previously unknown disease-specific biomarkers for sepsis diagnosis. Plasma samples obtained from non-infectious acute systemic inflammation controls and sepsis patients were incubated ex vivo with AmBisome® liposomes, and the resultant protein coronas were thoroughly characterised and compared by mass spectrometry (MS)-based proteomics. Our results demonstrate that the proposed nanoparticle enrichment technology enabled the discovery of 67 potential biomarker proteins that could reproducibly differentiate non-infectious acute systemic inflammation from sepsis. This study provides proof-of-concept evidence that nanoscale-based 'omics' enrichment technologies have the potential to substantially improve plasma proteomics analysis and to uncover novel biomarkers in a challenging clinical setting.

Inhibitory effects of aptamer targeted teicoplanin encapsulated PLGA nanoparticles for Staphylococcus aureus strains

Emergence of resistance to traditional antibiotic treatments necessitates alternative delivery systems. Teicoplanin is a glycopeptide antibiotic used in the treatments of serious infections caused by Gram-positive bacteria, including Methicillin Resistant Staphylococcus aureus (MRSA). One strategy to keep up with antibiotic resistance development is to limit dose and amount during treatments. Targeted delivery systems of antibiotics have been suggested as a mechanism to slow-down the evolution of resistance and to increase efficiency of the antimicrobials on already resistant pathogens. In this study, we report teicoplanin delivery nanoparticles of Poly Lactic-co-Glycolic Acid (PLGA), which are functionalized with S. aureus specific aptamers. A 32-fold decrease in minimum inhibitory concentration (MIC) values of teicoplanin for S. aureus was demonstrated for susceptible strains and about 64-fold decline in MIC value was achieved for moderately resistant clinical isolates of MRSA upon teicoplanin treatment with aptamer-PLGA nanoparticles. Although teicoplanin delivery in PLGA nanoparticles without targeting demonstrated eightfold decrease in MIC of susceptible strains of S. aureus and S. epidermidis and twofold in MIC of resistant strains, the aptamer targeting specifically decreased MIC for S. aureus, but not for S. epidermidis. Therefore, aptamer-targeted PLGA delivery of antibiotic can be an attractive alternative to combat with some of the multi-drug resistant bacterial pathogens.

Application of magnetic nanoparticles in nucleic acid detection

Nucleic acid is the main material for storing, copying, and transmitting genetic information. Gene sequencing is of great significance in DNA damage research, gene therapy, mutation analysis, bacterial infection, drug development, and clinical diagnosis. Gene detection has a wide range of applications, such as environmental, biomedical, pharmaceutical, agriculture and forensic medicine to name a few. Compared with Sanger sequencing, high-throughput sequencing technology has the advantages of larger output, high resolution, and low cost which greatly promotes the application of sequencing technology in life science research. Magnetic nanoparticles, as an important part of nanomaterials, have been widely used in various applications because of their good dispersion, high surface area, low cost, easy separation in buffer systems and signal detection. Based on the above, the application of magnetic nanoparticles in nucleic acid detection was reviewed.

Directing a rational design of aptamer-based fluorescence anisotropy assay for sensitive detection of immunoglobulin E by site-specific binding study

Mapping aptamer-protein interactions is important for characterization and applications of aptamers against proteins. We describe here probing affinity interactions between aptamer and immunoglobulin E (IgE) with a fluorescence anisotropy (FA) approach using a series of aptamer probes having single fluorescein (FAM) label at individual nucleotide (A, C, T). Studies of binding between IgE and aptamer probes revealed several possible close-contact sites, e.g., T9, T10, T11, T13, C15, and T17 of a 37-nt aptamer with a stem-loop secondary structure. FAM labeling on these sites resulted in much higher FA values (higher than 0.230 for T10, T11, T13 and C15) of aptamer-IgE complexes than the distant sites (e.g., terminals) of aptamer probably because the bound IgE close to these sites significantly restricted local rotation of FAM. Close-contact site labeled aptamer probes with high affinity allowed to develop a more sensitive FA assay for IgE than distant site labeled aptamers. The FA assay using T10-labeled aptamer with a dissociation constant (K_d) about 0.8 nM enabled selective detection of IgE at 20 pM and large FA increase upon IgE addition. We also found A12, C14, A25, and T27 were important for IgE-aptamer binding as FAM labeling at these sites significantly reduced aptamer affinity. FA study showed the loop region of this stem-loop aptamer was crucial for affinity binding, and IgE bound to the loop. This FA method will be helpful for understanding aptamer-protein binding and making a rational design of aptamer affinity assays for proteins.

Aptamers coupled to nanoparticles in the diagnosis and treatment of microbial infections

There are nanoparticles with remarkable antibacterial characteristics and aptamers able to recognize specific pathogenic bacteria with high affinity and specificity. The combination of both systems has been used to design rapid bacterial detection methods with excellent detection limits. Likewise, the synergism between aptamers and nanoparticles have allowed to optimize the antimicrobial activity of antibiotics and other nanostructures providing them with activity bacterium-specific, turning into attractive and promising tools to fight against bacteria resistant to multiple antimicrobials.

Micrococcal-Nuclease-Triggered On-Demand Release of Vancomycin from Intramedullary Implant Coating Eradicates Staphylococcus aureus Infection in Mouse Femoral Canals

Preventing orthopedic implant-associated bacterial infections remains a critical challenge. Current practices of physically blending high-dose antibiotics with bone cements is known for cytotoxicity while covalently tethering antibiotics to implant surfaces is ineffective in eradicating bacteria from the periprosthetic tissue environment due to the short-range bactericidal actions, which are limited to the implant surface. Here, we covalently functionalize poly(ethylene glycol) dimethacrylate hydrogel coatings with vancomycin via an oligonucleotide linker sensitive to Staphylococcus aureus (S. aureus) micrococcal nuclease (MN) (PEGDMA-Oligo-Vanco). This design enables the timely release of vancomycin in the presence of S. aureus to kill the bacteria both on the implant surface and within the periprosthetic tissue environment. Ti6Al4V intramedullary (IM) pins surface-tethered with dopamine methacrylamide (DopaMA) and uniformly coated with PEGDMA-Oligo-Vanco effectively prevented periprosthetic infections in mouse femoral canals inoculated with bioluminescent S. aureus. Longitudinal bioluminescence monitoring, μCT quantification of femoral bone changes, end point quantification of implant surface bacteria, and histological detection of S. aureus in the periprosthetic tissue environment confirmed rapid and sustained bacterial clearance by the PEGDMA-Oligo-Vanco coating. The observed eradication of bacteria was in stark contrast with the significant bacterial colonization on implants and osteomyelitis development found in the absence of the MN-sensitive bactericidal coating. The effective vancomycin tethering dose presented in this on-demand release strategy was >200 times lower than the typical prophylactic antibiotic contents used in bone cements and may be applied to medical implants and bone/dental cements to prevent periprosthetic infections in high-risk clinical scenarios. This study also supports the timely bactericidal action by MN-triggered release of antibiotics as an effective prophylactic method to bypass the notoriously harder to treat periprosthetic biofilms and osteomyelitis.

Detection of pathogenic bacteria via nanomaterials-modified aptasensors

Detection and identification of special cells via aptamer-based nano-conjugates sensors have been revolutionized over the past few years. These sensing platforms rely on selecting aptamers using systematic evolution of ligands by exponential enrichment (SELEX) in vitro, which allows for sensitive detection of cells. Integration of the aptamer-based sensors (aptasensors) with nanomaterials offers enhanced specificity and sensitivity, which in turn, offers great promise for numerous applications, spanning from bioanalysis to biomedical applications. Accordingly, the demand for using aptamer-conjugated nanomaterials for various applications has progressively increased over the past years. In light of this, this Review seeks to highlight the recent advances in the development of aptamer-conjugated nanomaterials and their utilization for the detection of various pathogens involved in infectious diseases and food contamination.

Label-free lateral flow assay for Listeria monocytogenes by aptamer-gated release of signal molecules

Lateral flow assay (LFA) type of biosensors have been popular due to cost-effectiveness and easy-interpretation for instant results, most common examples of applications being pregnancy tests, food safety or medical diagnostics. There are several examples of reports with high sensitivity, including pre-concentration of the sample by magnetic pull-down. However, sensitivity and direct detection designs with aptamers has been a limiting factor for developing aptamers-based LFA assays. In this study, we report a lateral flow design based on aptamer-gated silica nanoparticles to develop high sensitivity and direct bacterial assay by shifting aptamers-target interaction to conjugation pad. Aptamer-gated silica nanoparticles-based biosensors were reported for their high sensitivity, specificity and label-free detection for small molecules and whole cells. This label-free strategy for LFA can determine L. monocytogenes in minced chicken matrix at less than 5 min with a limit of detection (LOD) of 53 cells in one mL samples.

Applications of Iron Oxide-Based Magnetic Nanoparticles in the Diagnosis and Treatment of Bacterial Infections

Diseases caused by bacterial infections, especially drug-resistant bacteria have seriously threatened human health throughout the world. It has been predicted that antimicrobial resistance alone will cause 10 million deaths per year and that early diagnosis and therapy will efficiently decrease the mortality rate caused by bacterial infections. Considering this severity, it is urgent to develop effective methods for the early detection, prevention and treatment of these infections. Until now, numerous efforts based on nanoparticles have been made to detect and kill pathogenic bacteria. Iron oxide-based magnetic nanoparticles (MNPs), as potential platforms for bacteria detection and therapy, have drawn great attention owing to their magnetic property. These MNPs have also been broadly used as bioimaging contrast agents and drug delivery and magnetic hyperthermia agents to diagnose and treat bacterial infections. This review therefore overviews the recent progress on MNPs for bacterial detection and therapy, including bacterial separation and enrichment in vitro, bacterial infection imaging in vivo, and their therapeutic activities on pathogenic bacteria. Furthermore, some bacterial-specific targeting agents, used to selectively target the pathogenic bacteria, are also introduced. In addition, the challenges and future perspective of MNPs for bacterial diagnosis and therapy are given at the end of this review. It is expected that this review will provide a better understanding toward the applications of MNPs in the detection and therapy of bacterial infections.

Enhanced antitumor activity of carbendazim on HeLa cervical cancer cells by aptamer mediated controlled release

Carbendazim, is a broad-spectrum fungicide and also a promising experimental antitumor drug as reproduction and developmental toxicant, which is currently under phase II preclinical trials. In this study, an approach based on controlled and targeted release with aptamers and mesoporous silica nanoparticles was investigated to improve the antitumor activity of carbendazim. To this end, we synthesized aptamer conjugated silica nanoparticles for testing cytotoxicity properties in vitro with human cervical adenocarcinoma (HeLa) cultured cells. Nucleolin (AS1411) binding aptamers were used to entrap carbendazim molecules inside nanopores of MCM-41 type silica nanoparticles to obtain a stimuli-dependent release system. The effect of carbendazim loaded aptamer silica complex was tested and compared to free carbendazim treatment on HeLa cells, demonstrating 3.3 fold increase of toxicity on targeted cells with our delivery system. In addition, cytotoxicity of the complex was determined to be mostly due to increased apoptosis and to a less extend necrosis related pathways.

Carbendazim doped and aptamer-gate functionalized mesoporous silica nanoparticles targeted nucleolin on HeLa cell surface for specific delivery. This delivery system improved antitumor activity of carbendazim by about 3 folds increase of EC₅₀ values.

Design of an aptamer-based magnetic adsorbent and biosensor systems for selective and sensitive separation and detection of thrombin

An aptasensor was designed for sensitive detection of thrombin using in biological fluids by integrating a magnetic aptamer-microbeads. To achieve this goal, the surface of gold plated QCM crystals was coated with L-cysteine and a thrombin binding DNA aptamer was immobilized on the L-cysteine coated QCM crystals surface via glutaraldehyde coupling. The binding interactions of thrombin to QCM crystals were characterized. Magnetic poly(2-hydroxyethyl methacrylate-ethylene glycol dimethacrylate-vinylene carbonate), Mp(HEMA-EGDMA-VC) microbeads were synthesized and thrombin binding aptamer (TBA) was immobilized. The Mp(HEMA-EGDMA-VC)-TBA microbeads were effectively adsorbed thrombin from serum in a relatively short contact time (ca. 5.0 min), and the eluted protein from Mp(HEMA-EGDMA-VC)-TBA was transferred to the QCM aptasensor that showed a specific detection of thrombin from serum. The detection limit of thrombin using aptasensor was 1.00 nmol L^-1. The calculation dissociation constant of the aptasensor was 68.5 nmol L^-1. The selectivity of the aptasensor system was tested with three different proteins (i.e., elastin, immunoglobulin G (IgG) and human serum albumin (HSA)) and showed high specificity to thrombin. The aptasensor was regenerated by washing with NaOH solution, and repeatedly used until 20 cycles without a change in the performance.

Synthesis of amphiphilic poly(fluorene) derivatives for selective imaging of Staphylococcus aureus

Three amphiphilic poly(fluorene-co-phenylene) derivatives with different side chains (PFP-1, PFP-2, PFP-3) were designed and synthesized for exploring their detection and imaging of pathogens. Upon incubation with six kinds of different pathogens, it was found the three polymers could selectively interact with Staphylococcus aureus (S. aureus). Their selective imaging towards S. aureus were thus realized. The selective imaging towards S. aureus was also confirmed even under the blend of microbes. PFP-3 shows stronger fluorescence imaging signal than PFP-1 and PFP-2. Zeta potential and isothermal titration microcalorimetry (ITC) tests demonstrated that both electrostatic interactions and hydrophobic interactions played important roles in the binding between PFPs and pathogens. Thus, amphiphilic PFP-3 exhibits great potential for specific imaging of S. aureus in a simple and rapid manner.

Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases

The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.

Shape Engineering Boosts Magnetic Mesoporous Silica Nanoparticle-Based Isolation and Detection of Circulating Tumor Cells

Magnetic mesoporous silica nanoparticles (M-MSNs) are attractive candidates for the immunomagnetic isolation and detection of circulating tumor cells (CTCs). Understanding of the interactions between the effects of the shape of M-MSNs and CTCs is crucial to maximize the binding capacity and capture efficiency as well as to facilitate the sensitivity and efficiency of detection. In this work, fluorescent M-MSNs were rationally designed with sphere and rod morphologies while retaining their robust fluorescence and uniform surface functionality. After conjugation with the antibody of epithelial cell adhesion molecule (EpCAM), both of the differently shaped M-MSNs-EpCAM obtained achieved efficient enrichment of CTCs and fluorescent-based detection. Importantly, rodlike M-MSNs exhibited faster immunomagnetic isolation as well as better performance in the isolation and detection of CTCs in spiked cells and real clinical blood samples than those of their spherelike counterparts. Our results showed that shape engineering contributes positively toward immunomagnetic isolation, which might open new avenues to the rational design of magnetic-fluorescent nanoprobes for the sensitive and efficient isolation and detection of CTCs.

Aptamer-functionalized capacitance sensors for real-time monitoring of bacterial growth and antibiotic susceptibility

To prevent spread of infection and antibiotic resistance, fast and accurate diagnosis of bacterial infection and subsequent administration of antimicrobial agents are important. However, conventional methods for bacterial detection and antibiotic susceptibility testing (AST) require more than two days, leading to delays that have contributed to an increase in antibiotic-resistant bacteria. Here, we report an aptamer-functionalized capacitance sensor array that can monitor bacterial growth and antibiotic susceptibility in real-time. While E. coli and S. aureus were cultured, the capacitance increased over time, and apparent bacterial growth curves were observed even when 10 CFU/mL bacteria was inoculated. Furthermore, because of the selectivity of aptamers, bacteria could be identified within 1h using the capacitance sensor array functionalized with aptamers. In addition to bacterial growth, antibiotic susceptibility could be monitored in real-time. When bacteria were treated with antibiotics above the minimum inhibitory concentration (MIC), the capacitance decreased because the bacterial growth was inhibited. These results demonstrate that the aptamer-functionalized capacitance sensor array might be applied for rapid ASTs.