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Using Gd-Enhanced β-NaYF4:Yb,Er Fluorescent Nanorods Coupled to Reduced TiO2 for the NIR-Triggered Photocatalytic Inactivation of Escherichia coli. Catalysts 2021. [DOI: 10.3390/catal11020184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
β-NaYF4:Yb,Er,Gd fluorescent nanorods were successfully coupled to a reduced TiO2 (UCNPs@R-TiO2) nanocomposite and applied to visible-light catalytic sterilization under 980 nm near-infrared (NIR) light illumination. The UCNPs (β-NaYF4:Yb,Er,Gd) absorb the NIR light and emit red and green light. The visible light can be absorbed by the R-TiO2 (Eg = 2.8 eV) for the photocatalytic reaction. About 98.1% of Escherichia coli were effectively killed upon 12 min of NIR light irradiation at a minimum inhibitory concentration (MIC) of 40 μg/mL UCNPs@R-TiO2 nanocomposite. The bactericidal properties were further evaluated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. We found that the high bactericidal activity was due to the synergistic effect between the UCNPs and R-TiO2. Moreover, the UCNPs show excellent upconversion luminance properties, and the introduction of visible-light-absorbed R-TiO2 nanoparticles (2.8 eV) was conducive to the efficient separation and utilization of photogenerated electron-hole pairs.
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Zhen D, Liu Y, Grimes CA, Cai Q. Reduced titania nanosheets as an effective visible-light germicide. NANOTECHNOLOGY 2019; 30:405602. [PMID: 31247609 DOI: 10.1088/1361-6528/ab2d69] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Two-dimensional reduced titania nanosheets (RTNs), synthesized by a solvothermal method, reveal significant visible light-activated germicidal activity. XRD, XPS, EPR, TEM and Raman show successful reduction of anatase TiO2, resulting in Ti3+ formation as well as an increase in the concentration of {001} facets. The RTNs possess a bandgap energy of approximately 2.86 eV, and demonstrate strong absorption over the visible spectrum. Under simulated solar light (λ = 320-780 nm, 70 mW cm-2) the RTNs are found to completely inactivate Escherichia coli bacteria within 1 h. Our study indicates the RTNs have significant potential for ameliorating antibiotic-resistant bacteria in clinical settings under ambient lighting conditions.
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Affiliation(s)
- Deshuai Zhen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, People's Republic of China. College of Chemistry and Chemical Engineering, Qiannan Normal University for Nationalities, Duyun 558000, People's Republic of China
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Sandrin TR, Demirev PA. Characterization of microbial mixtures by mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:321-349. [PMID: 28509357 DOI: 10.1002/mas.21534] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 05/27/2023]
Abstract
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.
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Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona
| | - Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
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Magalhães P, Pinto L, Gonçalves A, Araújo JE, Santos HM, Capelo JL, Saénz Y, de Toro M, Torres C, Chambon C, Hébraud M, Poeta P, Igrejas G. Could transformation mechanisms of acetylase-harboring pMdT1 plasmid be evaluated through proteomic tools in Escherichia coli? J Proteomics 2016; 145:103-111. [PMID: 27072110 DOI: 10.1016/j.jprot.2016.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/22/2016] [Accepted: 03/29/2016] [Indexed: 11/19/2022]
Abstract
UNLABELLED Escherichia coli is a commensal microorganism of the gastrointestinal tract of animals and humans and it is an excellent model organism for the study of antibiotic resistance mechanisms. The resistance transmission and other characteristics of bacteria are based on different types of gene transfer occurring throughout the bacterial evolution. One of which is horizontal gene transfer that allows us to understand the ability of bacteria to acquire new genes. One dimensional and two dimensional electrophoresis (2-DE) techniques were performed in order to identify and characterize the proteome of two E. coli strains: Electromax DH10B, a transformation-ready strain; and TF-Se20, the Electromax DH10B that contains the aac(6')-Ib-cr4-harboring pMdT1 plasmid. After 2-DE and subsequent analysis by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), it was possible to identify 76 distinct proteins on the TF-Se20 strain, whereas 71 had a known function. From Electromax DH10B strain, 72 different proteins were identified of which 71 were associated with a biological process. The protein of interest, aminoglycoside N-(6')-acetyltransferase type 1, was identified by MALDI-TOF MS. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique was performed to determine its sequence. Seventy six percent of the acetylase sequence was reconstructed only in the TF-Se20 strain, representing the single protein associated to antibiotic resistance. MALDI-TOF MS and LC-MS/MS approaches allowed us to determine the total proteome of both strains, as well as the acetylase sequence. Both of them enhance the ability to obtain more accurate information about the mechanisms of antimicrobial resistance. The pMdT1 plasmid brings a new perspective in understanding the metabolic processes that lead to antibiotic resistance. BIOLOGICAL SIGNIFICANCE This study highlights the importance of proteomics and bioinformatics in understanding mechanisms of gene transfer and antibiotic resistance. These two approaches allow to compare the protein expression in different samples, as well as different biological processes related to each protein.
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Affiliation(s)
- Pedro Magalhães
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Luís Pinto
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Alexandre Gonçalves
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - José Eduardo Araújo
- UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal
| | - Hugo M Santos
- UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal; ProteoMass Scientific Society, Faculty of Sciences and Technology, Caparica, Portugal
| | - José Luis Capelo
- UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal; ProteoMass Scientific Society, Faculty of Sciences and Technology, Caparica, Portugal
| | - Yolanda Saénz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain
| | - María de Toro
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain; Instituto de Biomedicina y Biotecnologia de Cantabria IBBTEC, Universidad de Cantabria/CSIC, Santander, Spain
| | - Carmen Torres
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), Logroño, Spain; Department of Food and Agriculture, Biochemistry and Molecular Biology, University of La Rioja, Logroño, Spain
| | - Christophe Chambon
- Institut National de la Recherche Agronomique, Centre Auvergne-Rhône-Alpes, Plate-Forme d'Exploration du Métabolisme composante protéomique (PFEMcp), France
| | - Michel Hébraud
- Institut National de la Recherche Agronomique, Centre Auvergne-Rhône-Alpes, Plate-Forme d'Exploration du Métabolisme composante protéomique (PFEMcp), France; Institut National de la Recherche Agronomique, Centre Auvergne-Rhône-Alpes, UR454 Microbiologie, France
| | - Patrícia Poeta
- UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal; Veterinary Science Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Gilberto Igrejas
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal; UCIBIO-REQUIMTE, Faculty of Science and Technology, University NOVA of Lisbon, Caparica, Portugal.
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Charretier Y, Schrenzel J. Mass spectrometry methods for predicting antibiotic resistance. Proteomics Clin Appl 2016; 10:964-981. [PMID: 27312049 DOI: 10.1002/prca.201600041] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/09/2016] [Accepted: 06/13/2016] [Indexed: 11/10/2022]
Abstract
Developing elaborate techniques for clinical applications can be a complicated process. Whole-cell MALDI-TOF MS revolutionized reliable microorganism identification in clinical microbiology laboratories and is now replacing phenotypic microbial identification. This technique is a generic, accurate, rapid, and cost-effective growth-based method. Antibiotic resistance keeps emerging in environmental and clinical microorganisms, leading to clinical therapeutic challenges, especially for Gram-negative bacteria. Antimicrobial susceptibility testing is used to reliably predict antimicrobial success in treating infection, but it is inherently limited by the need to isolate and grow cultures, delaying the application of appropriate therapies. Antibiotic resistance prediction by growth-independent methods is expected to reduce the turnaround time. Recently, the potential of next-generation sequencing and microarrays in predicting microbial resistance has been demonstrated, and this review evaluates the potential of MS in this field. First, technological advances are described, and the possibility of predicting antibiotic resistance by MS is then illustrated for three prototypical human pathogens: Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Clearly, MS methods can identify antimicrobial resistance mediated by horizontal gene transfers or by mutations that affect the quantity of a gene product, whereas antimicrobial resistance mediated by target mutations remains difficult to detect.
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Affiliation(s)
- Yannick Charretier
- Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals.
| | - Jacques Schrenzel
- Genomic Research Laboratory, Division of Infectious Diseases, Geneva University Hospitals
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Niyompanich S, Srisanga K, Jaresitthikunchai J, Roytrakul S, Tungpradabkul S. Utilization of Whole-Cell MALDI-TOF Mass Spectrometry to Differentiate Burkholderia pseudomallei Wild-Type and Constructed Mutants. PLoS One 2015; 10:e0144128. [PMID: 26656930 PMCID: PMC4685992 DOI: 10.1371/journal.pone.0144128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/14/2015] [Indexed: 01/19/2023] Open
Abstract
Whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (whole-cell MALDI-TOF MS) has been widely adopted as a useful technology in the identification and typing of microorganisms. This study employed the whole-cell MALDI-TOF MS to identify and differentiate wild-type and mutants containing constructed single gene mutations of Burkholderia pseudomallei, a pathogenic bacterium causing melioidosis disease in both humans and animals. Candidate biomarkers for the B. pseudomallei mutants, including rpoS, ppk, and bpsI isolates, were determined. Taxon-specific and clinical isolate-specific biomarkers of B. pseudomallei were consistently found and conserved across all average mass spectra. Cluster analysis of MALDI spectra of all isolates exhibited separate distribution. A total of twelve potential mass peaks discriminating between wild-type and mutant isolates were identified using ClinProTools analysis. Two peaks (m/z 2721 and 2748 Da) were specific for the rpoS isolate, three (m/z 3150, 3378, and 7994 Da) for ppk, and seven (m/z 3420, 3520, 3587, 3688, 4623, 4708, and 5450 Da) for bpsI. Our findings demonstrated that the rapid, accurate, and reproducible mass profiling technology could have new implications in laboratory-based rapid differentiation of extensive libraries of genetically altered bacteria.
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Affiliation(s)
- Suthamat Niyompanich
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kitima Srisanga
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Janthima Jaresitthikunchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Pathum Thani, Thailand
| | - Sumalee Tungpradabkul
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- * E-mail:
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7
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Hart PJ, Wey E, McHugh TD, Balakrishnan I, Belgacem O. A method for the detection of antibiotic resistance markers in clinical strains of Escherichia coli using MALDI mass spectrometry. J Microbiol Methods 2015; 111:1-8. [PMID: 25633625 DOI: 10.1016/j.mimet.2015.01.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/23/2015] [Accepted: 01/24/2015] [Indexed: 11/25/2022]
Abstract
Matrix-assisted laser-desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is one of the most widely used mass spectrometry based approaches for bacterial identification and classification. The relatively simple sample preparation requirements and the speed of analysis which can usually be completed within a few minutes have resulted in the adoption and assimilation of MALDI-TOF MS into the routine diagnostic workflow of Clinical microbiology laboratories worldwide. This study describes the facilitation of bacterial discrimination based on antibiotic resistance markers through the implementation of MALDI-TOF MS. The periplasmic compartment of whole bacterial cells contains several proteins which confer antibiotic resistance in the Enterobacteriaceae. In order to reduce the complexity of the sample to be analysed via MALDI-TOF MS, the periplasm was extracted and subjected to in solution tryptic digestion followed by nano-LC separation. This method, established that peptide sequence biomarkers from several classes of antibiotic resistance proteins could be predicted using protein/peptide database tools such as Mascot. Biomarkers for a CTX-M-1 group extended spectrum β-lactamase, CMY-2 an Amp-C β-lactamase, VIM a metallo-β-lactamase, TEM a β-lactamase and KanR an aminoglycoside modifying enzyme were detected. This allowed for discrimination at a species level and at an almost identical strain level where the only difference between strains was the carriage of a modified antibiotic resistance carrying plasmid. This method also was able to detect some of these biomarkers in clinical strains where multiple resistance mechanisms were present.
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Affiliation(s)
- Philippa J Hart
- Shimadzu, Wharfside, Trafford Wharf Road, Manchester M17 1GP, UK
| | | | - Timothy D McHugh
- UCL Centre for Clinical Microbiology, Division of Infection and Immunity, UK
| | | | - Omar Belgacem
- Shimadzu, Wharfside, Trafford Wharf Road, Manchester M17 1GP, UK.
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Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2013; 51:2182-94. [PMID: 23637301 DOI: 10.1128/jcm.00492-13] [Citation(s) in RCA: 308] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
During the past 5 years, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool for routine identification in many clinical laboratories. We analyzed our 11-year experience in routine identification of clinical isolates (40 months using MALDI-TOF MS and 91 months using conventional phenotypic identification [CPI]). Among the 286,842 clonal isolates, 284,899 isolates of 459 species were identified. The remaining 1,951 isolates were misidentified and required confirmation using a second phenotypic identification for 670 isolates and using a molecular technique for 1,273 isolates of 339 species. MALDI-TOF MS annually identified 112 species, i.e., 36 species/10,000 isolates, compared to 44 species, i.e., 19 species/10,000 isolates, for CPI. Only 50 isolates required second phenotypic identifications during the MALDI-TOF MS period (i.e., 4.5 reidentifications/10,000 isolates) compared with 620 isolates during the CPI period (i.e., 35.2/10,000 isolates). We identified 128 bacterial species rarely reported as human pathogens, including 48 using phenotypic techniques (22 using CPI and 37 using MALDI-TOF MS). Another 75 rare species were identified using molecular methods. MALDI-TOF MS reduced the time required for identification by 55-fold and 169-fold and the cost by 5-fold and 96-fold compared with CPI and gene sequencing, respectively. MALDI-TOF MS was a powerful tool not only for routine bacterial identification but also for identification of rare bacterial species implicated in human infectious diseases. The ability to rapidly identify bacterial species rarely described as pathogens in specific clinical specimens will help us to study the clinical burden resulting from the emergence of these species as human pathogens, and MALDI-TOF MS may be considered an alternative to molecular methods in clinical laboratories.
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Ho YP, Reddy PM. Advances in mass spectrometry for the identification of pathogens. MASS SPECTROMETRY REVIEWS 2011; 30:1203-24. [PMID: 21557290 PMCID: PMC7168406 DOI: 10.1002/mas.20320] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Revised: 08/06/2010] [Accepted: 08/06/2010] [Indexed: 05/25/2023]
Abstract
Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.
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Affiliation(s)
- Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien 97401, Taiwan.
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Wan Y, Zhang D, Wang Y, Qi P, Hou B. Direct immobilisation of antibodies on a bioinspired architecture as a sensing platform. Biosens Bioelectron 2010; 26:2595-600. [PMID: 21163640 DOI: 10.1016/j.bios.2010.11.013] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 10/28/2010] [Accepted: 11/09/2010] [Indexed: 02/07/2023]
Abstract
A sensitive and selective immunosensor for the nonlabeled detection of sulfate-reducing bacteria (SRB) is constructed using a self-polymerised polydopamine film as the immobilisation platform. Self-polymerisation of dopamine is used as a powerful approach for applying multifunctional coatings onto the surface of a gold electrode. The polydopamine film is used not only as the immobilisation platform, but also as a cross-linker reagent for the immobilisation of the anti-SRB antibody. The polydopamine film is loaded with a high density of anti-SRB antibodies linked to the substrate to obtain high response signals. The formation and fabrication of the biosensor and the quantification of antibody anchoring are monitored, and SRB detection is performed by either quartz crystal microbalance (QCM) or electrochemical impedance spectroscopy (EIS). After modeling the impedance Nyquist plots of the SRB/anti-SRB/polydopamine/gold electrode for increasing concentrations of SRB, the electron transfer resistance (R(ct)) is used as a measure of immunocomplex binding. The R(ct) is correlated with the concentration of bacterial cells in the range of 1.8×10(2) to 1.8×10(6) CFU mL(-1); the detection limit is 50 CFU mL(-1). This work demonstrates a new immobilisation platform for the development of a sensitive and label-less impedimetric and piezoelectric immunosensor. This immunosensor may be broadly applied in clinical diagnoses and the monitoring of water environmental pollution. The method proposed is distinct in its ease of application, use of a simple protocol, and mild reaction conditions. These allow it to be applied to a wide variety of materials.
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Affiliation(s)
- Yi Wan
- Key Lab of Corrosion Science, Shandong Province, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
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Seng P, Rolain JM, Fournier PE, La Scola B, Drancourt M, Raoult D. MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol 2010; 5:1733-54. [DOI: 10.2217/fmb.10.127] [Citation(s) in RCA: 283] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost–effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.
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Affiliation(s)
- Piseth Seng
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Jean-Marc Rolain
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Pierre Edouard Fournier
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Bernard La Scola
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Michel Drancourt
- Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille et URMITE UMR CNRS-IRD 6236, IFR48, Faculté de Médecine, Université de la Méditerranée, Marseille, France: URMITE, Faculté de Médecine, 27 Boulevard Jean Moulin, 13385 Marseille cedex 5, France
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Brinkworth CS. Identification of ricin in crude and purified extracts from castor beans using on-target tryptic digestion and MALDI mass spectrometry. Anal Chem 2010; 82:5246-52. [PMID: 20486671 DOI: 10.1021/ac100650g] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ricin is a toxic protein produced in the seeds of the castor bean plant. The toxicity of the protein and the ease in which it can be extracted from the seeds makes it a potential biological warfare agent. There has been extensive work in the development of analytical techniques that can identify the protein robustly and rapidly. On-target tryptic digestion and MALDI MS was used to distinguish ricin from bovine serum albumin and three other type 2 ribsome-inactivating proteins (RIPs), abrin, agglutinin (RCA(120)), and viscumin, using the peptide mass fingerprint. The sequence coverage obtained was enhanced using methanol-assisted tryptic digestion and was particularly useful for the detection of these toxins in complex matrixes. When used in conjunction with intact protein MALDI mass measurement, a positive identification of ricin (or any of the other RIPs) was achieved including confirmation of the integrity of the disulfide bond between the A and B chains. This applicability of this methodology was demonstrated by the identification of ricin in a typical "crude white powder" that may be illicitly produced in a clandestine lab. The analysis on the solubilized sample using this method can be undertaken in around an hour with minimal sample preparation.
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Affiliation(s)
- Craig S Brinkworth
- Human Protection and Performance Division, Defence Science and Technology Organisation, Fishermans Bend, Victoria, Australia, 3207.
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Chen WJ, Tsai PJ, Chen YC. Functional nanoparticle-based proteomic strategies for characterization of pathogenic bacteria. Anal Chem 2009; 80:9612-21. [PMID: 19007241 DOI: 10.1021/ac802042x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) can be employed to rapidly characterize pathogenic bacteria, bacterial cultures are generally required to obtain sufficient quantities of the bacterial cells prior to MALDI MS analysis. If this time-consuming step could be eliminated, the length of time required for identification of bacterial strains would be greatly reduced. In this paper, we propose an effective means of rapidly identifying bacteria--one that does not require bacterial culturing--using functional nanoparticle-based proteomic strategies that are characterized by extremely short analysis time. In this approach, we used titania-coated magnetic iron oxide nanoparticles (Fe(3)O(4)@TiO(2) NPs) as affinity probes to concentrate the target bacteria. The magnetic properties of the Fe(3)O(4)@TiO(2) NPs allow the conjugated target species to be rapidly isolated from the sample solutions under a magnetic field. Taking advantage of the absorption of the magnetic Fe(3)O(4) NPs in the microwave region of the electromagnetic spectrum, we performed the tryptic digestion of the captured bacteria under microwave heating for only 1-1.5 min prior to MALDI MS analysis. We identified the resulting biomarker ions by combining their MS/MS analysis results with protein database searches. Using this technique, we identified potential biomarker ions representing five gram-negative bacteria: Escherichia coli O157:H7, uropathogenic E. coli, Shigella sonnei, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Finally, we demonstrated the practical feasibility of using this approach to rapidly characterize bacteria in clinical samples.
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Affiliation(s)
- Wei-Jen Chen
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu 300, Taiwan
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Dieckmann R, Helmuth R, Erhard M, Malorny B. Rapid classification and identification of salmonellae at the species and subspecies levels by whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry . Appl Environ Microbiol 2008; 74:7767-78. [PMID: 18952875 PMCID: PMC2607147 DOI: 10.1128/aem.01402-08] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Accepted: 10/16/2008] [Indexed: 11/20/2022] Open
Abstract
Variations in the mass spectral profiles of multiple housekeeping proteins of 126 strains representing Salmonella enterica subsp. enterica (subspecies I), S. enterica subsp. salamae (subspecies II), S. enterica subsp. arizonae (subspecies IIIa), S. enterica subsp. diarizonae (subspecies IIIb), S. enterica subsp. houtenae (subspecies IV), and S. enterica subsp. indica (subspecies VI), and Salmonella bongori were analyzed to obtain a phylogenetic classification of salmonellae based on whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometric bacterial typing. Sinapinic acid produced highly informative spectra containing a large number of biomarkers and covering a wide molecular mass range (2,000 to 40,000 Da). Genus-, species-, and subspecies-identifying biomarker ions were assigned on the basis of available genome sequence data for Salmonella, and more than 200 biomarker peaks, which corresponded mainly to abundant and highly basic ribosomal or nucleic acid binding proteins, were selected. A detailed comparative analysis of the biomarker profiles of Salmonella strains revealed sequence variations corresponding to single or multiple amino acid changes in multiple housekeeping proteins. The resulting mass spectrometry-based bacterial classification was very comparable to the results of DNA sequence-based methods. A rapid protocol that allowed identification of Salmonella subspecies in minutes was established.
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Affiliation(s)
- Ralf Dieckmann
- Federal Institute for Risk Assessment, National Salmonella Reference Laboratory, Diedersdorfer Weg 1, D-12277 Berlin, Germany
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Demirev PA, Fenselau C. Mass spectrometry in biodefense. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1441-57. [PMID: 18720458 DOI: 10.1002/jms.1474] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Potential agents for biological attacks include both microorganisms and toxins. In mass spectrometry (MS), rapid identification of potential bioagents is achieved by detecting the masses of unique biomarkers, correlated to each agent. Currently, proteins are the most reliable biomarkers for detection and characterization of both microorganisms and toxins, and MS-based proteomics is particularly well suited for biodefense applications. Confident identification of an organism can be achieved by top-down proteomics following identification of individual protein biomarkers from their tandem mass spectra. In bottom-up proteomics, rapid digestion of intact protein biomarkers is again followed by MS/MS to provide unambiguous bioagent identification and characterization. Bioinformatics obviates the need for culturing and rigorous control of experimental variables to create and use MS fingerprint libraries for various classes of bioweapons. For specific applications, MS methods, instruments and algorithms have also been developed for identification based on biomarkers other than proteins and peptides.
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Affiliation(s)
- Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD 20723, USA.
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Demirev PA, Fenselau C. Mass spectrometry for rapid characterization of microorganisms. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:71-93. [PMID: 20636075 DOI: 10.1146/annurev.anchem.1.031207.112838] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Advances in instrumentation, proteomics, and bioinformatics have contributed to the successful applications of mass spectrometry (MS) for detection, identification, and classification of microorganisms. These MS applications are based on the detection of organism-specific biomarker molecules, which allow differentiation between organisms to be made. Intact proteins, their proteolytic peptides, and nonribosomal peptides have been successfully utilized as biomarkers. Sequence-specific fragments for biomarkers are generated by tandem MS of intact proteins or proteolytic peptides, obtained after, for instance, microwave-assisted acid hydrolysis. In combination with proteome database searching, individual biomarker proteins are unambiguously identified from their tandem mass spectra, and from there the source microorganism is also identified. Such top-down or bottom-up proteomics approaches permit rapid, sensitive, and confident characterization of individual microorganisms in mixtures and are reviewed here. Examples of MS-based functional assays for detection of targeted microorganisms, e.g., Bacillus anthracis, in environmental or clinically relevant backgrounds are also reviewed.
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Identification of beta-lactamase in antibiotic-resistant Bacillus cereus spores. Appl Environ Microbiol 2007; 74:904-6. [PMID: 18065609 DOI: 10.1128/aem.00788-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Beta-lactamase type I is reported for the first time to occur in the sporulated form in a penicillin-resistant Bacillus species. The enzyme was readily characterized from the B. cereus 5/B line (ATCC 13061) by mass spectrometry and two-dimensional gel electrophoresis.
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