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    Surface Plasmon Resonance Aptamer Biosensor for Discriminating Pathogenic Bacteria . Ahn Ji-Young,Lee Kyeong-Ah,Lee Moon-Jong,Sekhon Simranjeet Singh,Rhee Sung-Keun,Cho Sung-Jin,Ko Jung Ho,Lee Lyon,Han Janet,Kim Sang Yong,Min Jiho,Kim Yang-Hoon Journal of nanoscience and nanotechnology In this paper, whole-bacteria SELEX (WB-SELEX) strategy was adopted to isolate specific aptamers against Vibrio parahaemolyticus. Round selection for V. parahaemolyticus was conducted 11 rounds, including two negative selection rounds. It was determined through real-time PCR amplification and post-SELEX experiment. The selected aptmers had high binding property and specificity to V. parahaemolyticus. Of 28 aptamers tested, VPCA-apta#1 had the highest binding affinity compared to other aptamer candidates obtained. To detect V. parahaemolyticus, aptamer based SPR biosensor platform was constructed and pathogenic bacteria sensing was conducted in two steps. The first step was to construct 5'-biotinylated VPCA-apta#1 binding probe. The second step was to incubate V. parahaemolyticus and test microbes in functionalized SA sensor chip in parallel. Our platform showed significant activity for detecting and discriminating V. parahaemolyticus from other enteric species such as Escherichia coli, Listeria monocytogenes, Sigella sonnei, and Vibrio fischeri. This is the first report on the use of whole-SELEX to isolate DNA aptamers specific for V. parahaemolyticus. We demonstrated the feasibility of using aptamer platform for the detection of V. parahaemolyticus in various food supplies. It might be used in multiple points of care for diagnosing Vibriosis. 10.1166/jnn.2018.14212
    Aptamer-Functionalized DNA-Silver Nanocluster Nanofilm for Visual Detection and Elimination of Bacteria. Yang Min,Chen Xu,Zhu Longjiao,Lin Shenghao,Li Chenwei,Li Xiangyang,Huang Kunlun,Xu Wentao ACS applied materials & interfaces As a new type of nanomaterial, DNA-templated silver nanoclusters (DNA-AgNCs) have been widely studied because of their fluorescence and antibacterial properties. In this study, we combined the DNA-AgNCs with aptamers of bacteria to achieve a novel approach for the visual detection and effective elimination of bacteria. The aptamers of () were linked to G-rich sequences to achieve fluorescence enhancement when approaching the DNA-AgNCs. The capture of aptamers not only realized the visual monitoring of bacteria but also promoted the antibacterial effects. Additionally, a fluorescent nanofilm with excellent selectivity and antibacterial activity in the detection and elimination of was developed based on the DNA-AgNCs. These aptamer-functionalized DNA-AgNCs show significant potential for many applications in food packaging and biomedical engineering. 10.1021/acsami.1c05751
    Sensitive detection of S. Aureus using aptamer- and vancomycin -copper nanoclusters as dual recognition strategy. Bagheri Pebdeni Azam,Mousavizadegan Maryam,Hosseini Morteza Food chemistry 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 10-10 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. 10.1016/j.foodchem.2021.130137
    Aptamer-based biosensors for the diagnosis of sepsis. Liu Lubin,Han Zeyu,An Fei,Gong Xuening,Zhao Chenguang,Zheng Weiping,Mei Li,Zhou Qihui Journal of nanobiotechnology Sepsis, the syndrome of infection complicated by acute organ dysfunction, is a serious and growing global problem, which not only leads to enormous economic losses but also becomes one of the leading causes of mortality in the intensive care unit. The detection of sepsis-related pathogens and biomarkers in the early stage plays a critical role in selecting appropriate antibiotics or other drugs, thereby preventing the emergence of dangerous phases and saving human lives. There are numerous demerits in conventional detection strategies, such as high cost, low efficiency, as well as lacking of sensitivity and selectivity. Recently, the aptamer-based biosensor is an emerging strategy for reasonable sepsis diagnosis because of its accessibility, rapidity, and stability. In this review, we first introduce the screening of suitable aptamer. Further, recent advances of aptamer-based biosensors in the detection of bacteria and biomarkers for the diagnosis of sepsis are summarized. Finally, the review proposes a brief forecast of challenges and future directions with highly promising aptamer-based biosensors. 10.1186/s12951-021-00959-5
    Targeted inhibition of methicillin-resistant biofilm formation by a graphene oxide-loaded aptamer/berberine bifunctional complex. Drug delivery Biofilm formation is known to promote drug resistance in methicillin-resistant (MRSA), which is closely related to persistent infections in hospital settings. In this study, a DNA aptamer specific to penicillin-binding protein 2a (PBP2a) with a dissociation constant () of 82.97 ± 8.86 nM was obtained after 14 cycles of systematic evolution of ligands by exponential enrichment (SELEX). Next, a bifunctional complex containing the aptamer intercalated by berberine into the double-strand region was prepared and adsorbed onto the surface of graphene oxide GO) by π-stacking interactions. The GO-loaded aptamer/berberine bifunctional complex showed significantly higher inhibition of MRSA biofilm formation than the control. Furthermore, this study shows that the complex possesses anti-biofilm activity, which can be attributed to the ability of the aptamer to reduce cell-surface attachment by blocking the function of PBP2a and berberine to attenuate the level of the accessory gene regulator () system, which plays an important role in mediating MRSA biofilm formation. Therefore, the simultaneous delivery of berberine and PBP2a-targted aptamer using GO may have potential for the treatment of chronic infections caused by MRSA biofilms. It also provides a new avenue for multitarget treatment of bacterial biofilms. 10.1080/10717544.2022.2079768
    Selection and Characterization of Cell Surface Specific Aptamer and Development of Fluorescence Assay for Detection of Shigella flexneri from Water Samples. Lavu Padma Sudharani,Mondal Bhairab,Ramlal Shylaja Journal of fluorescence The present study demonstrates, development of ssDNA aptamers against whole cell of S. flexneri employing a whole bacterium-based Systemic Evolution of Ligands by Exponential Enrichment (SELEX). After ten rounds of SELEX, cell surface specific aptamer pool was cloned, sequenced and divided based on sequence similarities and secondary structure. Binding affinity of FITC labelled aptamer from different group were carried out by flow cytometry analysis. The dissociation constant (K) values for specific and higher binder were evaluated to range from 144 to 329 nM. Six high binding aptamers with lower dissociation constant was chosen for selectivity study. Aptamer SHI 23, SHI 37 and SHI 42 showed higher selectivity towards S. flexneri in comparison with other related bacteria. Further applicability of selected aptamer was proven by fluorescence assay for convenience detection of target cell from spiked water sample and natural contaminated water samples. Altogether, aptamer generated in this study can be alternative DNA ligands for detection of S. flexneri compared to available ligands. 10.1007/s10895-021-02691-7
    Mycobacterium tuberculosis strain H37Rv Electrochemical Sensor Mediated by Aptamer and AuNPs-DNA. Zhang Xiaoqing,Feng Ye,Duan Shaoyun,Su Lingling,Zhang Jialin,He Fengjiao ACS sensors The accurate and rapid detection of Mycobacterium tuberculosis ( M. tuberculosis) is essential for the effective treatment of tuberculosis. In this article, we propose an electrochemical sensor to detect M. tuberculosis reference strain H37Rv. The sensor contains an H37Rv aptamer and oligonucleotides modified with gold nanoparticles (AuNPs-DNA). An H37Rv aptamer screened by our laboratory was used as the recognition probe. The change in frequency shift mediated by AuNPs-DNA in the presence of H37Rv was detected using a multichannel series piezoelectric quartz crystal (MSPQC) system. Three oligonucleotides modified with gold nanoparticles were designed. These oligonucleotides contained 12, 12, and 13 bases that hybridized with the 37-nt H37Rv aptamer. H37Rv aptamer was immobilized on the gold electrode surface by Au-S bonds. A conductive-layer was then formed by sequential hybridization of the aptamer with the three designed AuNPs-DNAs. When H37Rv was present, it specifically bound to the aptamer, resulting in the detachment of AuNPs-DNA from the electrode. The conductive layer was thereby replaced by a nonconductive complex of aptamer and bacteria. These changes were monitored by the MSPQC system. The proposed sensor is rapid, specific and sensitive, the detection time was 2 h. The detection limit was 100 cfu/mL. This sensor would be of great benefit for the early clinical diagnosis of tuberculosis. 10.1021/acssensors.8b01230
    An aptamer-exonuclease III (Exo III)-assisted amplification-based lateral flow assay for sensitive detection of Escherichia coli O157:H7 in milk. Ren Yuwei,Gao Pingping,Song Yang,Yang Xinyan,Yang Tao,Chen Sihan,Fu Shiqian,Qin Xue,Shao Meili,Man Chaoxin,Jiang Yujun Journal of dairy science Escherichia coli O157:H7 (E. coli O157:H7), one of the most widespread foodborne pathogens, can cause a series of diseases and even lead to death. In this study, a highly sensitive method was developed by combining aptamer-exonuclease III (Exo III)-assisted amplification with lateral flow assay (LFA) based on gold nanoparticles (AuNP). The compound of single-stranded (ss) DNA-anti-E. coli O157:H7 aptamer (ssDNA-aptamer) was formed by hybridization between designed target ssDNA and aptamer. When E. coli O157:H7 was present, target bacteria were bound with the aptamer, and the free target ssDNA was hybridized with the probes of the designed hairpin (HP) structure. Exo III digests the 3' double-stranded blunt end of the complex and releases the enzyme product. Because the remaining sequence of the HP of the designed enzyme product was the same as the target ssDNA sequence, the target ssDNA could be amplified. Finally, the enhanced target ssDNA was combined with AuNP-LFA to achieve visual detection of E. coli O157:H7. The quantitative ability of this platform for E. coli O157:H7 was 7.6 × 10 cfu/mL in pure culture, and the detection limit in milk was 8.35 × 10 cfu/mL. This LFA was highly specific to E. coli O157:H7, and the time for detection of E. coli O157:H7 in milk was 4 h. Hence, this system has important application prospects in the detection of pathogenic bacteria in dairy products. 10.3168/jds.2020-19939
    G-quadruplex-based assay combined with aptamer and gold nanoparticles for Escherichia coli K88 determination. Wang Zefeng,Lu Qiujun,Xu Tao,Wang Feiying,Huang Fangfang,Peng Yanling,Deng Le Mikrochimica acta A colorimetric method was developed using G-quadruplex and gold nanoparticles (AuNPs) for determination of Escherichia coli K88 (ETEC K88). It was composed of two modules: (1) an aptamer as biorecognizing element and (2) a capturing DNA (modified with AuNPs at 5') as a transducer. In the absence of target bacteria, the aptamer can form stable double strands with capturing DNA, preventing the binding of capturing DNA to the G-quadruplex. However, the double strands of capturing DNA and aptamer are untied due to the stronger binding of aptamers to bacteria in the presence of target bacteria. As a result, the G-quadruplex binds to capture DNA and leads to the aggregation and color change of AuNPs, which can be monitored by a spectrophotometer or visualization. The quantitative determination was achieved by monitoring the optical density change of AuNPs solution at 524 nm after target addition. Under optimal conditions, the method has a low detection limit (1.35 × 10 CFU mL) and a linear response in the range 10 to 10 CFU mL. Graphical abstract The manuscripts describe a colorimetric method for the detection of ETEC K88 by using intermolecular G-quadruplex to induce the agglomeration of gold nanoparticles, which can be directly used to determine the presence of bacteria with our naked eyes. 10.1007/s00604-020-04291-x
    Identification of a highly specific DNA aptamer for Vibrio vulnificus using systematic evolution of ligands by exponential enrichment coupled with asymmetric PCR. Yan Wanli,Gu Lide,Liu Shu,Ren Wei,Lyu Mingsheng,Wang Shujun Journal of fish diseases Vibrio vulnificus is an important bacterial pathogen that causes serious infections in fish and is also highly pathogenic to humans. Many effective detection methods targeting this pathogen have previously been designed, but many of these methods are time-consuming, complicated and expensive. Thus, these approaches cannot be widely used by small aqacultural concerns. Although DNA aptamers have been used to detect pathogenic bacteria, these have not been applied to marine bacteria, including V. vulnificus. Therefore, we developed a highly specific DNA aptamer for V. vulnificus detection using systematic evolution of ligands by exponential enrichment (SELEX), coupled with asymmetric PCR. After 13 rounds of cross-selection, we identified a novel DNA aptamer (Vapt2). We evaluated the affinity, specificity and limit of detection (LOD) of this aptamer for V. vulnificus. We found that Vapt2 had a high affinity for V. vulnificus (K = 26.8 ± 5.3 nM) and detected this pathogen at a wide range of concentrations (8-2.0 × 10  cfu/ml). Vapt2 bound to V. vulnificus with high selectivity in the presence of other pathogenic bacteria. Our study increases our knowledge of the possible applications of aptamers with respect to marine bacteria. Moreover, our work might provide a framework for the rapid detection of pathogenic bacteria and water pollution. 10.1111/jfd.12891
    Bioprobes Based on Aptamer and Silica Fluorescent Nanoparticles for Bacteria Salmonella typhimurium Detection. Wang Qiu-Yue,Kang Yan-Jun Nanoscale research letters In this study, we have developed an efficient method based on single-stranded DNA (ssDNA) aptamers along with silica fluorescence nanoparticles for bacteria Salmonella typhimurium detection. Carboxyl-modified Tris(2,2'-bipyridyl)dichlororuthenium(II) hexahydrate (RuBPY)-doped silica nanoparticles (COOH-FSiNPs) were prepared using reverse microemulsion method, and the streptavidin was conjugated to the surface of the prepared COOH-FSiNPs. The bacteria S. typhimurium was incubated with a specific ssDNA biotin-labeled aptamer, and then the aptamer-bacteria conjugates were treated with the synthetic streptavidin-conjugated silica fluorescence nanoprobes (SA-FSiNPs). The results under fluorescence microscopy show that SA-FSiNPs can be applied effectively for the labeling of bacteria S. typhimurium with great photostable property. To further verify the specificity of SA-FSiNPs out of multiple bacterial conditions, variant concentrations of bacteria mixtures composed of bacteria S. typhimurium, Escherichia coli, and Bacillus subtilis were treated with SA-FSiNPs.In addition, the feasibility of SA-FSiNPs for bacteria S. typhimurium detection in chicken samples was assessed. All the results display that the established aptamer-based nanoprobes exhibit the superiority for bacteria S. typhimurium detection, which is referentially significant for wider application prospects in pathogen detection. 10.1186/s11671-016-1359-z
    Dual Recognition Strategy for Specific and Sensitive Detection of Bacteria Using Aptamer-Coated Magnetic Beads and Antibiotic-Capped Gold Nanoclusters. Cheng Dan,Yu Mengqun,Fu Fei,Han Weiye,Li Gan,Xie Jianping,Song Yang,Swihart Mark T,Song Erqun Analytical chemistry Food poisoning and infectious diseases caused by pathogenic bacteria such as Staphylococcus aureus (SA) are serious public health concerns. A method of specific, sensitive, and rapid detection of such bacteria is essential and important. This study presents a strategy that combines aptamer and antibiotic-based dual recognition units with magnetic enrichment and fluorescent detection to achieve specific and sensitive quantification of SA in authentic specimens and in the presence of much higher concentrations of other bacteria. Aptamer-coated magnetic beads (Apt-MB) were employed for specific capture of SA. Vancomycin-stabilized fluorescent gold nanoclusters (AuNCs@Van) were prepared by a simple one-step process and used for sensitive quantification of SA in the range of 32-10(8) cfu/mL with the detection limit of 16 cfu/mL via a fluorescence intensity measurement. And using this strategy, about 70 cfu/mL of SA in complex samples (containing 3 × 10(8) cfu/mL of other different contaminated bacteria) could be successfully detected. In comparison to prior studies, the developed strategy here not only simplifies the preparation procedure of the fluorescent probes (AuNCs@Van) to a great extent but also could sensitively quantify SA in the presence of much higher concentrations of other bacteria directly with good accuracy. Moreover, the aptamer and antibiotic used in this strategy are much less expensive and widely available compared to common-used antibodies, making it cost-effective. This general aptamer- and antibiotic-based dual recognition strategy, combined with magnetic enrichment and fluorescent detection of trace bacteria, shows great potential application in monitoring bacterial food contamination and infectious diseases. 10.1021/acs.analchem.5b03320
    Aptamer-conjugated carbon-based nanomaterials for cancer and bacteria theranostics: A review. Chemico-biological interactions Aptamers are single-stranded oligonucleotides that link to various substrates with great affinity and selectivity, including small molecules, peptides, proteins, cells, and tissues. For this reason, they can be used as imaging agents for cancer imaging techniques. Multifunctional nanomaterials combined with imaging probes and drugs are promising cancer diagnosis and treatment candidates. On the other hand, carbon-based nanomaterials (CNMs), including such as fullerene, carbon nanotubes, carbon-based quantum dots, carbon nanohorns, graphene oxide and its derivatives carbon nanodots, and nanodiamonds, are sort of smart materials that can be used in a variety of theranostic applications, including photo-triggered therapies. The remarkable physical characteristics, functionalizable chemistry, biocompatibility, and optical properties of these nanoparticles have enabled their utilization in less-invasive therapies. The theranostic agents that emerged by combining aptamers with CNMs have opened a novel alternative for personified medicine of cancer, target-specific imaging, and label-free diagnosis of a broad range of cancers, as well as pathogens. Aptamer-functionalized CNMs have been used as nanovesicles for targeted delivery of anti-cancer agents (i.e., doxorubicin and 5-fluorouracil) to tumor sites. Furthermore, these CNMs conjugated with aptamers have shown great advantages over standard CNMs to sensitively detect Mycobacterium tuberculosis, Escherichia coli, staphylococcus aureus, Vibrio parahaemolyticus, Salmonella typhimurium, Pseudomonas aeruginosa, and Citrobacter freundii. Regrettably, CNMs can form compounds defined as NOAA (nano-objects, and their aggregates and agglomerates larger than 100 nm), that accumulate in the body and cause toxic effects. Surface modification and pretreatment with albumin avoid agglomeration and increase the dispersibility of CNMs, so it is needed to guarantee the desirable interactions between functionalized CNMs and blood plasma proteins. This preliminary review aimed to comprehensively discuss the features and uses of aptamer-conjugated CNMs to manage cancer and bacterial infections. 10.1016/j.cbi.2022.109964
    Dual-aptamer-based enzyme linked plasmonic assay for pathogenic bacteria detection. Colloids and surfaces. B, Biointerfaces Development of rapid, sensitive, and selective method for pathogenic bacteria detection is of great importance for food safety, medical diagnostic, and environmental monitoring. Currently, most techniques for low numbers of bacteria detection require advanced instrumentation or skilled operators. Herein, we present a facile colorimetric detection platform for bacterial detection using Ag nanoplates as chromogenic substrate, which takes advantages of the high specificity and affinity of aptamer and the ability of catalase to hydrolyze HO that can etch Ag nanoplates. By introducing catalase to the sandwich structure composed by dual-aptamer recognition strategy, bacteria detection signal is converted to the peak shift of LSPR and colorimetric change. This proposed method allows a fast naked-eye detection of S. aureus at the concentration of 60 CFU/mL based on the combination of streptavidin-biotin system and inherent sensitivity of plasmonic Ag nanoplates. Owing to the high selectivity and sensitivity, as well as the low-cost and good adaptability, this plasmonic assay is expected to be suitable for pathogenic bacteria detection in resource-limited settings. 10.1016/j.colsurfb.2022.112471
    A universal SERS-label immunoassay for pathogen bacteria detection based on FeO@Au-aptamer separation and antibody-protein A orientation recognition. Zhou Zihui,Xiao Rui,Cheng Siyun,Wang Shu,Shi Luoluo,Wang Chongwen,Qi Kezong,Wang Shengqi Analytica chimica acta Rapid, reliable and sensitive detection methods for pathogenic bacteria are strongly demanded. Herein, we proposed a magnetically assisted surface enhanced Raman scattering (SERS)-label immunoassay for the sensitive detection of bacteria by using a universal approach based on free antibody labelling and staphylococcus proteins A (PA)-SERS tags orientation recognition. The SERS biosensor consists of two functional nanomaterials: aptamer-conjugated FeO@Au magnetic nanoparticles (MNPs) as magnetic SERS platform for pathogen enrichment and PA modified-SERS tags (Au@DTNB@PA) as a universal probe for target bacteria quantitative detection. After target bacteria enriched, free antibody was used to specific marking target bacteria and provided numerous Fc fragment, which can guide the PA-SERS tags orientation-dependent binding. With this strategy, FeO@Au/bacteria/SERS tags sandwich immunocomplexes for most bacteria (expect several species of Staphylococcus) were easy constructed. The limits of detection (LODs) of the proposed assay were found to be 10, 10, and 25 cells/mL for three common pathogens Escherichia coli (E. coli), Listeria monocytogenes (L. mono), and Salmonella typhimurium (S. typhi), respectively, in real food samples. The universal method also exhibits the advantages of rapid, robust, and easy to operate, suggesting its great potential for food safety monitoring and infectious diseases diagnosis. 10.1016/j.aca.2021.338421
    An in situ quenching electrochemiluminescence biosensor amplified with aptamer recognition-induced multi-DNA release for sensitive detection of pathogenic bacteria. Liu Shihua,Li Qiuyan,Yang Huili,Wang Po,Miao Xiangmin,Feng Qiumei Biosensors & bioelectronics An in situ quenching electrochemiluminescence (ECL) biosensor sensitized with the aptamer recognition-induced multi-DNA release was designed for pathogenic bacterial detection. Benefitting from the high binding ability of the aptamer to targets and large enrichment capacity of magnetic bead separation, the proposed sensing system not only exhibited outstanding identification to Staphylococcus aureus (S. aureus) among various bacteria, but also released abundant signal transduction DNAs. One S. aureus initiated the dissociation of four kinds of DNA sequences, achieving a one-to-multiple amplification effect. These multi-DNA strands were further hybridized with capture DNA, which were assembled to an electrode modified with Ru(bpy)-conjugated silica nanoparticles (RuSi NPs). Then, glucose oxidase (GOD) was introduced via the functional conjugation of GOD-multi-DNA, leading to the presence of HO by in situ catalysis of GOD on glucose. Relying on the ECL quenching of HO in the Ru(bpy) system, S. aureus was quantified with a linear range from 10 to 10 CFU/mL. In addition, the negative results of non-target bacteria and good recovery efficiency in real samples revealed the system's remarkable selectivity and potential application in infectious food tests. 10.1016/j.bios.2021.113744
    An aptamer cocktail-functionalized photocatalyst with enhanced antibacterial efficiency towards target bacteria. Song Min Young,Jurng Jongsoo,Park Young-Kwon,Kim Byoung Chan Journal of hazardous materials We developed TiO2 particles conjugated with an Escherichia coli surface-specific ssDNA aptamer cocktail (composed of three different aptamers isolated from E. coli) for targeted and enhanced disinfection of E. coli. We examined the target-specific and enhanced inactivation of this composite (TiO2-Apc), which were compared to those of TiO2 conjugated with a single aptamer (one of the three different aptamers, TiO2-Aps) and non-modified TiO2. We found that TiO2-Apc enhanced the inactivation of targeted E. coli under UV irradiation compared to both the non-modified TiO2 and TiO2-Aps. A higher number of TiO2-Apc than TiO2-Aps particles was observed on the surface of E. coli. The amount of TiO2-Apc required to inactivate ∼99.9% of E. coli (10(6) CFU/ml) was 10 times lower than that of non-modified TiO2. The close proximity of functionalized particles with E. coli resulting from the interaction between the target surface and the aptamer induced the efficient and fast transfer of reactive oxygen species to the cells. In a mixed culture of different bacteria (E. coli and Staphylococcus epidermidis), TiO2-Apc enhanced the inactivation of only E. coli. Taken together, these results support the use of aptamer cocktail-conjugated TiO2 for improvement of the target-specific inactivation of bacteria. 10.1016/j.jhazmat.2016.07.016
    Electrochemical Immuno- and Aptamer-Based Assays for Bacteria: Pros and Cons over Traditional Detection Schemes. Jamal Rimsha Binte,Shipovskov Stepan,Ferapontova Elena E Sensors (Basel, Switzerland) Microbiological safety of the human environment and health needs advanced monitoring tools both for the specific detection of bacteria in complex biological matrices, often in the presence of excessive amounts of other bacterial species, and for bacteria quantification at a single cell level. Here, we discuss the existing electrochemical approaches for bacterial analysis that are based on the biospecific recognition of whole bacterial cells. Perspectives of such assays applications as emergency-use biosensors for quick analysis of trace levels of bacteria by minimally trained personnel are argued. 10.3390/s20195561
    Rapid and Selective Detection of Pathogenic Bacteria in Bloodstream Infections with Aptamer-Based Recognition. Shen Haijing,Wang Jie,Liu Haoyang,Li Zhihao,Jiang Fenglei,Wang Fu-Bing,Yuan Quan ACS applied materials & interfaces Sepsis and bacteremia are life-threatening clinical syndromes associated with significant patient morbidity and mortality. Rapid and sensitive detection of pathogenic bacteria is the key to improve patient survival rates. Herein, we have rationally constructed a simple aptamer-based capture platform to shorten the time needed for confirmation of bacterial bloodstream infection in clinical blood samples. This capture platform is made of a mesoporous TiO2-coated magnetic nanoparticle and is modified with target aptamer. It features excellent bacterial enrichment efficiency of about 80% even at low bacterial concentrations (10-2000 CFU mL(-1)). More importantly, the bacteria can be enriched within 2 h, and the time for bacterial identification is effectively shortened in comparison to the "gold standard" in clinical diagnosis of bloodstream infection. The aptamer-based capture platform may pave a way for the detection of biomarkers and find potential applications in disease diagnosis. 10.1021/acsami.6b06671
    Aptamer-assisted tumor localization of bacteria for enhanced biotherapy. Geng Zhongmin,Cao Zhenping,Liu Rui,Liu Ke,Liu Jinyao,Tan Weihong Nature communications Despite bacterial-mediated biotherapies have been widely explored for treating different types of cancer, their implementation has been restricted by low treatment efficacy, due largely to the absence of tumor-specific accumulation following administration. Here, the conjugation of aptamers to bacterial surface is described by a simple and cytocompatible amidation procedure, which can significantly promote the localization of bacteria in tumor site after systemic administration. The surface density of aptamers can be easily adjusted by varying feed ratio and the conjugation is able to increase the stability of anchored aptamers. Optimal bacteria conjugated with an average of 2.8 × 10 aptamers per cell present the highest specificity to tumor cells in vitro, separately generating near 2- and 4-times higher accumulation in tumor tissue at 12 and 60 hours compared to unmodified bacteria. In both 4T1 and H22 tumor-bearing mouse models, aptamer-conjugated attenuated Salmonella show enhanced antitumor efficacy, along with highly activated immune responses inside the tumor. This work demonstrates how bacterial behaviors can be tuned by surface conjugation and supports the potential of aptamer-conjugated bacteria for both targeted intratumoral localization and enhanced tumor biotherapy. 10.1038/s41467-021-26956-8
    Aptamer Affinity-Bead Mediated Capture and Displacement of Gram-Negative Bacteria Using Acoustophoresis. Lee SangWook,Kim Byung Woo,Shin Hye-Su,Go Anna,Lee Min-Ho,Lee Dong-Ki,Kim Soyoun,Jeong Ok Chan Micromachines Here, we report a simple and effective method for capturing and displacement of gram-negative bacteria using aptamer-modified microbeads and acoustophoresis. As acoustophoresis allows for simultaneous washing and size-dependent separation in continuous flow mode, we efficiently obtained gram-negative bacteria that showed high affinity without any additional washing steps. The proposed device has a simple and efficient channel design, utilizing a long, square-shaped microchannel that shows excellent separation performance in terms of the purity, recovery, and concentration factor. Microbeads (10 µm) coated with the GN6 aptamer can specifically bind gram-negative bacteria. After incubation of bacteria culture sample with aptamer affinity bead, gram-negative bacteria-bound microbeads, and other unbound/contaminants can be separated by size with high purity and recovery. The device demonstrated excellent separation performance, with high recovery (up to 98%), high purity (up to 99%), and a high-volume rate (500 µL/min). The acoustophoretic separation performances were conducted using 5 Gram-negative bacteria and 5 Gram-positive bacteria. Thanks to GN6 aptamer's binding affinity, aptamer affinity bead also showed binding affinity to multiple strains of gram-negative bacteria, but not to gram-positive bacteria. GN6 coated bead can capture Gram-negative bacteria but not Gram-positive bacteria. This study may present a different perspective in the field of early diagnosis in bacterial infectious diseases. In addition to detecting living bacteria or bacteria-derived biomarkers, this protocol can be extended to monitoring the contamination of water resources and may aid quick responses to bioterrorism and pathogenic bacterial infections. 10.3390/mi10110770
    A novel method combining aptamer-AgNPs based microfluidic biochip with bright field imaging for detection of KPC-2-expressing bacteria. Chen Jing,Li Hui,Xie Hexin,Xu Danke Analytica chimica acta The β-lactam drugs resistance poses a serious threat to human health throughout the world. Klebsiella pneumoniae carbapenemase 2 (KPC-2) is a carbapenemase that produced in bacteria can hydrolyze carbapenems, which typically considered as the antibiotics of last resort. Therefore, there is an urgent need to quickly and accurately detect whether bacteria express KPC-2. In this paper, a PDMS/glass microfluidic biochip integrated with aptamer-modified AgNPs nano-biosensors was developed for rapid, simple and specific pathogenic bacteria detection, more importantly, the biochip was combined with bright field imaging, then the captured bacteria could be observed and counted directly without using extra chemical labeling. KPC-2-expressing Escherichia coli (KPC-2 E.coli) was used as the target bacterium with a detected limit of 10 CFU and capture efficiency exceeded 90%. This method is remarkably specific towards KPC-2 E.coli over other non-resistant bacteria, and pathogen assay only takes ∼1 h to complete in a ready-to-use microfluidic biochip. Furthermore, the effective capture and fast counting of microfluidic biochip system demonstrates its potential for the rapid detection of antibiotic-resistant bacteria. 10.1016/j.aca.2020.07.061
    Aptamer-based hydrogel barcodes for the capture and detection of multiple types of pathogenic bacteria. Xu Yueshuang,Wang Huan,Luan Chengxin,Liu Yuxiao,Chen Baoan,Zhao Yuanjin Biosensors & bioelectronics Rapid and sensitive diagnosing hematological infections based on the separation and detection of pathogenic bacteria in the patient's blood is a significant challenge. To address this, we herein present a new barcodes technology that can simultaneously capture and detect multiple types of pathogenic bacteria from a complex sample. The barcodes are poly (ethylene glycol) (PEG) hydrogel inverse opal particles with characteristic reflection peak codes that remain stable during bacteria capture on their surfaces. As the spherical surface of the particles has ordered porous nanostructure, the barcodes can provide not only more surface area for probe immobilization and reaction, but also a nanopatterned platform for highly efficient bioreactions. In addition, the PEG hydrogel scaffold could decrease the non-specificity adsorption by its anti-adhesive effect, and the decorated aptamer probes in the scaffolds could increase the sensitivity, reliability, and specificity of the bacteria capture and detection. Moreover, the tagged magnetic nanoparticles in the PEG scaffold could impart the barcodes with controllable movement under magnetic fields, which can be used to significantly increase the reaction speed and simplify the processing of the bioassays. Based on the describe barcodes, it was demonstrated that the bacteria could be captured and identified even at low bacterial concentrations (100 CFU mL) within 2.5h, which is effectively shortened in comparison with the "gold standard" in clinic. These features make the barcodes ideal for capturing and detecting multiple bacteria from clinical samples for hematological infection diagnostics. 10.1016/j.bios.2017.09.032
    Light-up RNA aptamer signaling-CRISPR-Cas13a-based mix-and-read assays for profiling viable pathogenic bacteria. Zhang Ting,Zhou Wenhu,Lin Xiaoya,Khan Mohammad Rizwan,Deng Sha,Zhou Mi,He Guiping,Wu Chengyong,Deng Ruijie,He Qiang Biosensors & bioelectronics Viable pathogenic bacteria cause serious human diseases via systemic infections and food poisoning. Herein, we constructed a light-up RNA aptamer signaling-CRISPR-Cas13a assay enabling mix-and-read detection of viable pathogenic bacteria. Directly targeting pathogen RNAs via CRISPR-Cas13a allows precisely discriminating viable bacteria from dead bacteria. We introduced a light-up RNA aptamer, Broccoli, serving as the substate of activated CRISPR-Cas13a to monitor the presence of pathogen RNAs, eliminating the need to use chemically labeled RNA substrate. Sequentially, the assay allows a reverse transcription-free, nucleic acid amplification-free, and label-free quantification of RNA targets and viable pathogenic bacteria. It could detect as low as 10 CFU of Bacillus cereus and precisely quantify viable bacteria with a content ranging from 0% to 100% in 10 CFU total bacteria. The quantification of viable bacteria allows more accurately estimating the ability of B. cereus to spoil food. The RNA assay promises its use in point-of-use detection of viable pathogens and biosafety control. 10.1016/j.bios.2020.112906
    Dual-recognition surface-enhanced Raman scattering(SERS)biosensor for pathogenic bacteria detection by using vancomycin-SERS tags and aptamer-FeO@Au. Pang Yuanfeng,Wan Nan,Shi Luoluo,Wang Chongwen,Sun Zhiwei,Xiao Rui,Wang Shengqi Analytica chimica acta Rapid and reliable detection of pathogenic bacteria is vital to prevent and control bacterial diseases. In this study, we present a magnetically assisted surface-enhanced Raman scattering (SERS) biosensor based on the dual-recognition of bacterial cell by aptamer and antibiotic molecules. Aptamer-FeO@Au magnetic nanoparticles (AuMNPs) were synthesized as magnetic and SERS activated substrate for specific bacteria enrichment, vancomycin-SERS tags (Au@MBA) were prepared for the sensitive quantification of pathogenic bacteria. Due to the Au-shell based dual-SERS enhancement and aptamer/vancomycin based dual-recognition ability, a detection limit of 3 cells/mL with a wide dynamic linear range from 10 to 10 cells/mL can be achieved within 50 min without other non-target bacteria interference. When applied in real samples, the approach shows recoveries from 95.0% to 106.4% with relative standard derivation (RSD) less than 5.3%. The SERS strategy could be used to detect a broad range of bacteria by using different aptamers, moreover, the simple operation and precise quantification ability empower this assay great potential in the application of food safety and infectious disease point-of-care diagnosis. 10.1016/j.aca.2019.05.059
    Recent advances on aptamer-based biosensors for detection of pathogenic bacteria. Li Danliang,Liu Luyao,Huang Qiaoling,Tong Ting,Zhou You,Li Zhongyu,Bai Qinqin,Liang Hao,Chen Lili World journal of microbiology & biotechnology As a significant constituent in biosphere, bacteria have a great influence on human activity. The detection of pathogen bacteria is closely related to the human health. However, the traditional methods for detection of pathogenic bacteria are time-consuming and difficult for quantification, although they are practical and reliable. Therefore, novel strategies for rapid, sensitive, and cost-effective detection are in great demand. Aptamer is a kind of oligonucleotide that selected by repeated screening in vitro or systematic evolution of ligands by exponential enrichment (SELEX) technology. Over the past years, owing to high affinity and specificity of aptamers, a variety of aptamer-based biosensors have been designed and applied for pathogen detection. In this review, we have discussed the recent advances on the applications of aptamer-based biosensors in detection of pathogenic bacteria. In addition, we also point out some problems in current methods and look forward to the further development of aptamer-based biosensors for pathogen detection. 10.1007/s11274-021-03002-9