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Klein D, Breuch R, Reinmüller J, Engelhard C, Kaul P. Rapid detection and discrimination of food-related bacteria using IR-microspectroscopy in combination with multivariate statistical analysis. Talanta 2021; 232:122424. [PMID: 34074410 DOI: 10.1016/j.talanta.2021.122424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 10/21/2022]
Abstract
Spoilage microorganisms are of great concern for the food industry. While traditional culturing methods for spoilage microorganism detection are laborious and time-consuming, the development of early detection methods has gained a lot of interest in the last decades. In this work a rapid and non-destructive detection and discrimination method of eight important food-related microorganisms (Bacillus subtilis DSM 10, Bacillus coagulans DSM 1, Escherichia coli K12 DSM 498, Escherichia coli TOP10, Micrococcus luteus DSM 20030, Pseudomonas fluorescens DSM 4358, Pseudomonas fluorescens DSM 50090 and Bacillus thuringiensis israelensis DSM 5724) based on IR-microspectroscopy and chemometric evaluation was developed. Sampling was carried out directly from the surface to be tested, without the need for sample preparation such as purification, singulation, centrifugation and washing steps, as an efficient and inexpensive blotting technique using the sample carrier. IR spectra were recorded directly after the blotting from the surface of the sample carrier without any further pretreatments. A combination of data preprocessing, principal component analysis and canonical discriminant analysis was found to be suitable. The spectral range from 400 to 1750 cm-1 of the IR-microspectrosopic data was determined to be highly sensitive to the time after incubation and sample thickness, resulting in a high standard deviation. Therefore, this area was excluded from the evaluation in favor of the meaningfulness of the chemometric model and, thus, only the spectral range of specific -CH/-NH/-OH excitations (2815-3680 cm-1) was used for model development. This study showed that the differentiation of food-related microorganisms on genera, species and strain level is feasible. A leave-one-out cross-validation of the training data set showed 100% accuracy. The classification of the ungrouped test data showed with an accuracy of 94.5% that, despite the large biological variance of the analytes such as different times after incubation and the presented sampling (including its variance), a robust and meaningful model for the differentiation of food-related bacteria could be developed by data preprocessing and subsequent chemometric evaluation.
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Affiliation(s)
- Daniel Klein
- Bonn-Rhein-Sieg University of Applied Sciences, Institute of Safety and Security Research, von Liebig-Straße 20, 53359, Rheinbach, Germany.
| | - René Breuch
- Bonn-Rhein-Sieg University of Applied Sciences, Institute of Safety and Security Research, von Liebig-Straße 20, 53359, Rheinbach, Germany
| | - Jessica Reinmüller
- Bonn-Rhein-Sieg University of Applied Sciences, Institute of Safety and Security Research, von Liebig-Straße 20, 53359, Rheinbach, Germany
| | - Carsten Engelhard
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, D-57076, Germany; Center of Micro- and Nanochemistry and Engineering, University of Siegen, Adolf-Reichwein-Str. 2, D-57076, Siegen, Germany
| | - Peter Kaul
- Bonn-Rhein-Sieg University of Applied Sciences, Institute of Safety and Security Research, von Liebig-Straße 20, 53359, Rheinbach, Germany
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2
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Kepenek ES, Severcan M, Gozen AG, Severcan F. Discrimination of heavy metal acclimated environmental strains by chemometric analysis of FTIR spectra. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 202:110953. [PMID: 32800227 DOI: 10.1016/j.ecoenv.2020.110953] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Heavy metal acclimated bacteria are profoundly the preferred choice for bioremediation studies. Bacteria get acclimated to toxic concentrations of heavy metals by induction of specific enzymes and genetic selection favoring new metabolic abilities leading to activation of one or several of resistance mechanisms creating bacterial populations with differences in resistance profile and/or level. Therefore, to use in bioremediation processes, it is important to discriminate acclimated bacterial populations and choose a more resistant strain. In this study, we discriminated heavy metal acclimated bacteria by using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy and multivariate analysis methods namely Hierarchical Cluster Analysis (HCA), Principal Component Analysis (PCA) and Soft Independent Modeling of Class Analogy (SIMCA). Two acclimation methods, acute and gradual, were used which cause differences in molecular changes resulting in bacterial populations with different molecular and resistance profiles. Brevundimonas sp., Gordonia sp., and Microbacterium oxydans were exposed to the toxic concentrations of Cd (30 μg/ml) or Pb (90 μg/ml) by using broth medium as a growth media. Our results revealed that PCA and HCA clearly discriminated the acute-acclimated, gradual-acclimated, and control bacteria from each other in protein, carbohydrate, and whole spectral regions. Furthermore, we classified acclimated (acute and gradual) and control bacteria more accurately by using SIMCA with 99.9% confidence. This study demonstrated that heavy metal acclimated and control group bacteria can be discriminated by using chemometric analysis of FTIR spectra in a powerful, cost-effective, and handy way. In addition to the determination of the most appropriate acclimation procedure, this approach can be used in the detection of the most resistant bacterial strains to be used in bioremediation studies.
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Affiliation(s)
- Eda Seyma Kepenek
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Mete Severcan
- Department of Electrical and Electronics Engineering, School of Engineering and Natural Sciences, Altinbas University, Istanbul, Turkey.
| | - Ayse Gul Gozen
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey; Department of Biophysics, Faculty of Medicine, Altinbas University, Istanbul, Turkey
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3
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Martak D, Valot B, Sauget M, Cholley P, Thouverez M, Bertrand X, Hocquet D. Fourier-Transform InfraRed Spectroscopy Can Quickly Type Gram-Negative Bacilli Responsible for Hospital Outbreaks. Front Microbiol 2019; 10:1440. [PMID: 31293559 PMCID: PMC6606786 DOI: 10.3389/fmicb.2019.01440] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/07/2019] [Indexed: 12/19/2022] Open
Abstract
The typing of epidemic bacterial pathogens in hospitals relies on DNA-based, expensive, and time-consuming techniques, that are often limited to retrospective studies. However, the quick identification of epidemic pathogens in the routine of the microbiology laboratories would expedite infection control procedures that limit the contamination of new patients. IR Biotyper (Bruker Daltonics GmbH) is a new typing machine based on Fourier-transform infrared (FTIR) spectroscopy which generates spectra, aiming at typing the micro-organisms within 3 h. This technique discriminates the isolates by exploring the differences of the surface cell polysaccharides. In this work, we evaluated the ability of the FTIR spectroscopy to recognize Gram-negative bacilli clones responsible for hospital outbreaks. Isolates of Pseudomonas aeruginosa (n = 100), Klebsiella pneumoniae (n = 16), Enterobacter cloacae (n = 23), and Acinetobacter baumannii (n = 20) were typed by the reference methods Multi-Locus Sequence Typing (defining sequence types – STs) along with or without pulsed field gel electrophoresis (PFGE) (defining pulsotypes), and by FTIR spectroscopy. The congruence of FTIR spectroscopy clustering was compared to those of MLST and PFGE by Adjusted Rand index and Adjusted Wallace coefficient. We found that FTIR spectroscopy accurately clustered P. aeruginosa, K. pneumoniae, and E. cloacae isolates belonging to the same ST. The performance of the FTIR spectroscopy was slightly lower for A. baumannii. Furthermore, FTIR spectroscopy also correctly clustered P. aeruginosa isolates having a similar pulsotype. Overall, the IR Biotyper can quickly (in less than 3 h) detect the spread of clones of P. aeruginosa, K. pneumoniae, E. cloacae, and A. baumannii. The use of this technique by clinical microbiology laboratories may help to tackle the spread of epidemic clones by the quick implementation of infection control measures.
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Affiliation(s)
- Daniel Martak
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Benoît Valot
- UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Marlène Sauget
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
| | - Pascal Cholley
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Michelle Thouverez
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Xavier Bertrand
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France
| | - Didier Hocquet
- Laboratoire d'Hygiène Hospitalière, Centre Hospitalier Régional Universitaire, Besançon, France.,UMR 6249, Laboratoire Chrono-Environnement, Centre National de la Recherche Scientifique-Université de Franche-Comté, Besançon, France.,Centre de Ressources Biologiques - Filière Microbiologique de Besançon, Centre Hospitalier Régional Universitaire, Besançon, France
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Marques V, Cunha B, Couto A, Sampaio P, Fonseca LP, Aleixo S, Calado CRC. Characterization of gastric cells infection by diverse Helicobacter pylori strains through Fourier-transform infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 210:193-202. [PMID: 30453195 DOI: 10.1016/j.saa.2018.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
The infection of Helicobacter pylori, covering 50% of the world-population, leads to diverse gastric diseases as ulcers and cancer along the life-time of the human host. To promote the discovery of biomarkers of bacterial infection, in the present work, Fourier-transform infrared spectra were acquired from adenocarcinoma gastric cells, incubated with H. pylori strains presenting different genotypes concerning the virulent factors cytotoxin associated gene A and vacuolating cytotoxin A. Defined absorbance ratios were evaluated by diverse methods of statistical inference, according to the fulfillment of the tests assumptions. It was possible to define from the gastric cells, diverse absorbance ratios enabling to discriminate: i) The infection; ii) the bacteria genotype; and iii) the gastric disease of the patients from which the bacteria were isolated. These biomarkers could fasten the knowledge of the complex infection process while promoting a platform for a new diagnostic method, rapid but also specific and sensitive towards the diagnosis of both infection and bacterial virulence.
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Affiliation(s)
- Vanda Marques
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Bernardo Cunha
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal; IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Andreia Couto
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Pedro Sampaio
- Faculty of Engineering, Lusophone University of Humanities and Technology, Campo Grande, 376, 1749-019 Lisbon, Portugal
| | - Luís P Fonseca
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sandra Aleixo
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal; Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Cecília R C Calado
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal.
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Novais Â, Freitas AR, Rodrigues C, Peixe L. Fourier transform infrared spectroscopy: unlocking fundamentals and prospects for bacterial strain typing. Eur J Clin Microbiol Infect Dis 2018; 38:427-448. [DOI: 10.1007/s10096-018-3431-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/11/2018] [Indexed: 01/25/2023]
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6
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Granato D, Putnik P, Kovačević DB, Santos JS, Calado V, Rocha RS, Cruz AGD, Jarvis B, Rodionova OY, Pomerantsev A. Trends in Chemometrics: Food Authentication, Microbiology, and Effects of Processing. Compr Rev Food Sci Food Saf 2018; 17:663-677. [PMID: 33350122 DOI: 10.1111/1541-4337.12341] [Citation(s) in RCA: 246] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 11/27/2022]
Abstract
In the last decade, the use of multivariate statistical techniques developed for analytical chemistry has been adopted widely in food science and technology. Usually, chemometrics is applied when there is a large and complex dataset, in terms of sample numbers, types, and responses. The results are used for authentication of geographical origin, farming systems, or even to trace adulteration of high value-added commodities. In this article, we provide an extensive practical and pragmatic overview on the use of the main chemometrics tools in food science studies, focusing on the effects of process variables on chemical composition and on the authentication of foods based on chemical markers. Pattern recognition methods, such as principal component analysis and cluster analysis, have been used to associate the level of bioactive components with in vitro functional properties, although supervised multivariate statistical methods have been used for authentication purposes. Overall, chemometrics is a useful aid when extensive, multiple, and complex real-life problems need to be addressed in a multifactorial and holistic context. Undoubtedly, chemometrics should be used by governmental bodies and industries that need to monitor the quality of foods, raw materials, and processes when high-dimensional data are available. We have focused on practical examples and listed the pros and cons of the most used chemometric tools to help the user choose the most appropriate statistical approach for analysis of complex and multivariate data.
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Affiliation(s)
- Daniel Granato
- Dept. of Food Engineering, State Univ. of Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, Brazil
| | - Predrag Putnik
- Faculty of Food Technology and Biotechnology, Univ. of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia
| | - Danijela Bursać Kovačević
- Faculty of Food Technology and Biotechnology, Univ. of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia
| | - Jânio Sousa Santos
- Dept. of Food Engineering, State Univ. of Ponta Grossa, Av. Carlos Cavalcanti, 4748, 84030-900, Ponta Grossa, Brazil
| | - Verônica Calado
- School of Chemistry, Federal Univ. of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ramon Silva Rocha
- Dept. de Alimentos, Inst. Federal de Educação, Ciência e Tecnologia (IFRJ), 20270-021, Rio de Janeiro, Brazil
| | - Adriano Gomes Da Cruz
- Dept. de Alimentos, Inst. Federal de Educação, Ciência e Tecnologia (IFRJ), 20270-021, Rio de Janeiro, Brazil
| | - Basil Jarvis
- Dept. of Food and Nutrition Sciences, School of Chemistry, Food and Pharmacy, The Univ. of Reading, Whiteknights, Reading, Berkshire RG6 6AP, U.K
| | - Oxana Ye Rodionova
- Semenov Inst. of Chemical Physics RAS, Kosygin str. 4, 119991, Moscow, Russia
| | - Alexey Pomerantsev
- Semenov Inst. of Chemical Physics RAS, Kosygin str. 4, 119991, Moscow, Russia
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Quintelas C, Ferreira EC, Lopes JA, Sousa C. An Overview of the Evolution of Infrared Spectroscopy Applied to Bacterial Typing. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700449] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/18/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Cristina Quintelas
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - Eugénio C. Ferreira
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - João A. Lopes
- Dr. J. A. Lopes; Research Institute for Medicines (iMed.ULisboa); Faculdade de Farmácia; Universidade de Lisboa; Lisboa Portugal
| | - Clara Sousa
- Dr. C. Sousa; LAQV/REQUIMTE; Departamento de Ciências Químicas Faculdade de Farmácia; Universidade do Porto; Rua Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
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Rosa F, Sales KC, Cunha BR, Couto A, Lopes MB, Calado CRC. A comprehensive high-throughput FTIR spectroscopy-based method for evaluating the transfection event: estimating the transfection efficiency and extracting associated metabolic responses. Anal Bioanal Chem 2015; 407:8097-108. [PMID: 26329279 DOI: 10.1007/s00216-015-8983-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/29/2015] [Accepted: 08/14/2015] [Indexed: 12/11/2022]
Abstract
Reporter genes are routinely used in every laboratory for molecular and cellular biology for studying heterologous gene expression and general cellular biological mechanisms, such as transfection processes. Although well characterized and broadly implemented, reporter genes present serious limitations, either by involving time-consuming procedures or by presenting possible side effects on the expression of the heterologous gene or even in the general cellular metabolism. Fourier transform mid-infrared (FT-MIR) spectroscopy was evaluated to simultaneously analyze in a rapid (minutes) and high-throughput mode (using 96-wells microplates), the transfection efficiency, and the effect of the transfection process on the host cell biochemical composition and metabolism. Semi-adherent HEK and adherent AGS cell lines, transfected with the plasmid pVAX-GFP using Lipofectamine, were used as model systems. Good partial least squares (PLS) models were built to estimate the transfection efficiency, either considering each cell line independently (R (2) ≥ 0.92; RMSECV ≤ 2 %) or simultaneously considering both cell lines (R (2) = 0.90; RMSECV = 2 %). Additionally, the effect of the transfection process on the HEK cell biochemical and metabolic features could be evaluated directly from the FT-IR spectra. Due to the high sensitivity of the technique, it was also possible to discriminate the effect of the transfection process from the transfection reagent on KEK cells, e.g., by the analysis of spectral biomarkers and biochemical and metabolic features. The present results are far beyond what any reporter gene assay or other specific probe can offer for these purposes.
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Affiliation(s)
- Filipa Rosa
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Kevin C Sales
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Bernardo R Cunha
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Andreia Couto
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Marta B Lopes
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal.,Instituto de Telecomunicações, Instituto Superior Técnico, 1049-001, Lisbon, Portugal
| | - Cecília R C Calado
- Instituto Superior de Engenharia de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal.
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Cho IH, Radadia AD, Farrokhzad K, Ximenes E, Bae E, Singh AK, Oliver H, Ladisch M, Bhunia A, Applegate B, Mauer L, Bashir R, Irudayaraj J. Nano/micro and spectroscopic approaches to food pathogen detection. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:65-88. [PMID: 24896312 DOI: 10.1146/annurev-anchem-071213-020249] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Despite continuing research efforts, timely and simple pathogen detection with a high degree of sensitivity and specificity remains an elusive goal. Given the recent explosion of sensor technologies, significant strides have been made in addressing the various nuances of this important global challenge that affects not only the food industry but also human health. In this review, we provide a summary of the various ongoing efforts in pathogen detection and sample preparation in areas related to Fourier transform infrared and Raman spectroscopy, light scattering, phage display, micro/nanodevices, and nanoparticle biosensors. We also discuss the advantages and potential limitations of the detection methods and suggest next steps for further consideration.
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Affiliation(s)
- Il-Hoon Cho
- Bindley Bioscience and Birck Nanotechnology Center; Departments of
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