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Dinçtürk E. Determination of Raman spectrum under different culture conditions: preliminary research on bacterial fish pathogens. Anim Biotechnol 2024; 35:2299733. [PMID: 38166494 DOI: 10.1080/10495398.2023.2299733] [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] [Indexed: 01/04/2024]
Abstract
The intensive labour and time required for conventional methods to identify bacterial fish pathogens have revealed the need to develop alternative methods. Raman spectroscopy has been used in the rapid optical identification of bacterial pathogens in recent years as an alternative method in microbiology. Strains of bacterial fish pathogens (Vibrio anguillarum, Lactococcus garvieae and Yersinia ruckeri) that often cause infectious diseases in fish were here identified and analyzed in terms of their biochemical structures in different media and at different incubation times, and the data were specified by using Raman spectroscopy. The results demonstrated that Raman spectroscopy presents species-specific Raman spectra of each disease-causing bacteria and that it would be more appropriate to choose general microbiological media over selective media for routine studies. Additionally, it was found that species-specific band regions did not differ in 24- and 48-hour cultures, but there could be a difference in peak intensity which may lead to difficult characterization of spectrum. The current study, conducted for the first time with bacterial fish pathogens under different incubation conditions, is believed to provide a basis for the routine use of Raman spectroscopy for quick pathogen identification and the precise determination of the methodology for further research.
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Affiliation(s)
- Ezgi Dinçtürk
- Fish Disease and Biotechnology Laboratory, Department of Aquaculture, Izmir Katip Celebi University, Izmir, Türkiye
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2
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Jeon G, Kim S, Kim YJ, Kim S, Han K, Oh K, Lee HJ, Choi J. Identification of fluoroquinolone-resistant Mycobacterium tuberculosis through high-level data fusion of Raman and laser-induced breakdown spectroscopy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:6349-6355. [PMID: 39221494 DOI: 10.1039/d4ay01331j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Accurate and rapid diagnosis of drug susceptibility of Mycobacterium tuberculosis is crucial for the successful treatment of tuberculosis, a persistent global public health threat. To shorten diagnosis times and enhance accuracy, this study introduces a fusion model combining laser-induced breakdown spectroscopy (LIBS) and Raman spectroscopy. This model offers a rapid and accurate method for diagnosing drug-resistance. LIBS and Raman spectroscopy provide complementary information, enabling accurate identification of drug resistance in tuberculosis. Although individual use of LIBS or Raman spectroscopy achieved approximately 90% accuracy in identifying drug resistance, the fusion model significantly improved identification accuracy to 98.3%. Given the fast measurement capabilities of both techniques, this fusion approach is expected to markedly decrease the time required for diagnosis.
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Affiliation(s)
- Gookseon Jeon
- Industrial Transformation Technology Department, Research Institute of Sustainable Development Technology, Korea Institute of Industrial Technology, 89, Yangdaegiro-gil, Ipjang-myeon, Seobuk-gu, Cheonan-Si, Chungcheongnam-do 31056, Republic of Korea.
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Soogeun Kim
- Advanced Photonics Research Institute (APRI), Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Hospital, Seoul, Republic of Korea
| | - Seungmo Kim
- Laboratory Medicine Center, Korean National Tuberculosis Association, The Korean Institute of Tuberculosis, Cheongju, Republic of Korea
| | - Kyungmin Han
- Clinical Laboratory Medicine Center, Korean National Tuberculosis Association, Seoul, Republic of Korea.
| | - Kyunghwan Oh
- Photonic Device Physics Laboratory, Institute of Physics and Applied Physics, Yonsei University, 50, Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hee Joo Lee
- Clinical Laboratory Medicine Center, Korean National Tuberculosis Association, Seoul, Republic of Korea.
| | - Janghee Choi
- Industrial Transformation Technology Department, Research Institute of Sustainable Development Technology, Korea Institute of Industrial Technology, 89, Yangdaegiro-gil, Ipjang-myeon, Seobuk-gu, Cheonan-Si, Chungcheongnam-do 31056, Republic of Korea.
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3
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Wang P, Sun H, Yang W, Fang Y. Optical Methods for Label-Free Detection of Bacteria. BIOSENSORS 2022; 12:bios12121171. [PMID: 36551138 PMCID: PMC9775963 DOI: 10.3390/bios12121171] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 05/27/2023]
Abstract
Pathogenic bacteria are the leading causes of food-borne and water-borne infections, and one of the most serious public threats. Traditional bacterial detection techniques, including plate culture, polymerase chain reaction, and enzyme-linked immunosorbent assay are time-consuming, while hindering precise therapy initiation. Thus, rapid detection of bacteria is of vital clinical importance in reducing the misuse of antibiotics. Among the most recently developed methods, the label-free optical approach is one of the most promising methods that is able to address this challenge due to its rapidity, simplicity, and relatively low-cost. This paper reviews optical methods such as surface-enhanced Raman scattering spectroscopy, surface plasmon resonance, and dark-field microscopic imaging techniques for the rapid detection of pathogenic bacteria in a label-free manner. The advantages and disadvantages of these label-free technologies for bacterial detection are summarized in order to promote their application for rapid bacterial detection in source-limited environments and for drug resistance assessments.
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Affiliation(s)
- Pengcheng Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou 221004, China
| | - Hao Sun
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Wei Yang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
| | - Yimin Fang
- Key Laboratory of Cardiovascular & Cerebrovascular Medicine, School of Pharmacy, Nanjing Medical University, Nanjing 211166, China
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4
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He Q, Yang W, Luo W, Wilhelm S, Weng B. Label-Free Differentiation of Cancer and Non-Cancer Cells Based on Machine-Learning-Algorithm-Assisted Fast Raman Imaging. BIOSENSORS 2022; 12:250. [PMID: 35448310 PMCID: PMC9031282 DOI: 10.3390/bios12040250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/17/2022]
Abstract
This paper proposes a rapid, label-free, and non-invasive approach for identifying murine cancer cells (B16F10 melanoma cancer cells) from non-cancer cells (C2C12 muscle cells) using machine-learning-assisted Raman spectroscopic imaging. Through quick Raman spectroscopic imaging, a hyperspectral data processing approach based on machine learning methods proved capable of presenting the cell structure and distinguishing cancer cells from non-cancer muscle cells without compromising full-spectrum information. This study discovered that biomolecular information-nucleic acids, proteins, and lipids-from cells could be retrieved efficiently from low-quality hyperspectral Raman datasets and then employed for cell line differentiation.
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Affiliation(s)
- Qing He
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73072, USA
| | - Wen Yang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK 73072, USA; (W.Y.); (S.W.)
| | - Weiquan Luo
- Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50010, USA;
| | - Stefan Wilhelm
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK 73072, USA; (W.Y.); (S.W.)
| | - Binbin Weng
- School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK 73072, USA
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5
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Shen H, Rösch P, Popp J. Fiber Probe-Based Raman Spectroscopic Identification of Pathogenic Infection Microorganisms on Agar Plates. Anal Chem 2022; 94:4635-4642. [PMID: 35254815 DOI: 10.1021/acs.analchem.1c04507] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid identification of microorganisms is clinically meaningful, and it helps to decelerate the spread of drug resistance and improve patient treatment. In this study, we present a rapid fiber probe-based Raman technique with an excitation wavelength of 785 nm, which is applied to classify and identify nine different species of microorganisms. The cost-effective fiber probe compresses the dimension of the system and provides a more reliable and stable database. All microorganisms were simply cultivated on Luria-Bertani (LB) agar, and Raman spectra were obtained directly from the microbial colonies with the fiber probe within 30 s. The classification model consists of principal component analysis (PCA) in combination with linear discriminant analysis (LDA) and was examined by applying leave-one-batch-out cross-validation (LOBOCV). This model achieved an accuracy of 98.9%. In addition, the validation and identification processes based on independent replicates achieved accuracies of 99.8% and 100%, respectively. The results demonstrated that fiber probe Raman spectroscopy in combination with chemometric analysis allowed a rapid classification and identification of microorganisms only with a normal culture. Therefore, it is promising especially for medical applications and could moreover be helpful to investigate and identify microorganisms rapidly in further studies.
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Affiliation(s)
- Haodong Shen
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany.,Leibniz Institute of Photonic Technology Jena - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Str. 9, D-07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany.,Leibniz Institute of Photonic Technology Jena - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Str. 9, D-07745 Jena, Germany
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6
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Xu J, Yi X, Jin G, Peng D, Fan G, Xu X, Chen X, Yin H, Cooper JM, Huang WE. High-Speed Diagnosis of Bacterial Pathogens at the Single Cell Level by Raman Microspectroscopy with Machine Learning Filters and Denoising Autoencoders. ACS Chem Biol 2022; 17:376-385. [PMID: 35026119 DOI: 10.1021/acschembio.1c00834] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate and rapid identification of infectious bacteria is important in medicine. Raman microspectroscopy holds great promise in performing label-free identification at the single-cell level. However, due to the naturally weak Raman signal, it is a challenge to build extensive databases and achieve both accurate and fast identification. Here, we used signal-to-noise ratio (SNR) as a standard indicator for Raman data quality and performed bacterial identification using 11, 141 single-cell Raman spectra from nine bacterial strains. Subsequently, using two machine learning methods, a simple filter, and a neural network-based denoising autoencoder (DAE), we demonstrated 92% (simple filter using 1 s/cell spectra) and 84% (DAE using 0.1 s/cell spectra) identification accuracy. Our machine learning-aided Raman analysis paves the way for high-speed Raman microspectroscopic clinical diagnostics.
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Affiliation(s)
- Jiabao Xu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K
| | - Xiaofei Yi
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Guilan Jin
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Di Peng
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Gaoya Fan
- Shanghai Hesen Biotechnology Co., Ltd, Shanghai 201802, China
- Shanghai D-band Medical Instrument Co., Ltd, Shanghai 201802, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xin Chen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Huabing Yin
- James Watt School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - Jonathan M. Cooper
- James Watt School of Engineering, University of Glasgow, Glasgow G12 8LT, U.K
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, U.K
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7
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Raman spectroscopic analysis of skin as a diagnostic tool for Human African Trypanosomiasis. PLoS Pathog 2021; 17:e1010060. [PMID: 34780575 PMCID: PMC8629383 DOI: 10.1371/journal.ppat.1010060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 11/29/2021] [Accepted: 10/23/2021] [Indexed: 02/08/2023] Open
Abstract
Human African Trypanosomiasis (HAT) has been responsible for several deadly epidemics throughout the 20th century, but a renewed commitment to disease control has significantly reduced new cases and motivated a target for the elimination of Trypanosoma brucei gambiense-HAT by 2030. However, the recent identification of latent human infections, and the detection of trypanosomes in extravascular tissues hidden from current diagnostic tools, such as the skin, has added new complexity to identifying infected individuals. New and improved diagnostic tests to detect Trypanosoma brucei infection by interrogating the skin are therefore needed. Recent advances have improved the cost, sensitivity and portability of Raman spectroscopy technology for non-invasive medical diagnostics, making it an attractive tool for gambiense-HAT detection. The aim of this work was to assess and develop a new non-invasive diagnostic method for T. brucei through Raman spectroscopy of the skin. Infections were performed in an established murine disease model using the animal-infective Trypanosoma brucei brucei subspecies. The skin of infected and matched control mice was scrutinized ex vivo using a confocal Raman microscope with 532 nm excitation and in situ at 785 nm excitation with a portable field-compatible instrument. Spectral evaluation and Principal Component Analysis confirmed discrimination of T. brucei-infected from uninfected tissue, and a characterisation of biochemical changes in lipids and proteins in parasite-infected skin indicated by prominent Raman peak intensities was performed. This study is the first to demonstrate the application of Raman spectroscopy for the detection of T. brucei by targeting the skin of the host. The technique has significant potential to discriminate between infected and non-infected tissue and could represent a unique, non-invasive diagnostic tool in the goal for elimination of gambiense-HAT as well as for Animal African Trypanosomiasis (AAT). Human African Trypanosomiasis (HAT), also known as sleeping sickness, is a disease caused by the parasite Trypanosoma brucei and has been responsible for the death of millions of people across Africa in the 20th century. It is also a major economic burden for countries endemic for trypanosomiasis, affecting livestock productivity in rural areas (Animal African Trypanosomiasis). A long-term international collaboration with the help of the World Health Organisation has resulted in the rate of human infection decreasing to less than 1000 new cases per year. However, the human disease continues to spread within remote villages. Current diagnosis is based on the detection of parasites in blood and serum samples, but this is challenging during chronic human infections with low or non-detectable parasitaemia. However, the recent discovery of extravascular skin-dwelling trypanosomes indicates that a reservoir of infection remains undetected, threatening the effort to eliminate the disease. In this study we have targeted the skin as a site for diagnosis using Raman spectroscopy and demonstrate that this method showed great promise in the laboratory, laying the foundation for field studies to examine its potential to strengthen current diagnostic strategies for detecting HAT cases.
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Larios G, Ribeiro M, Arruda C, Oliveira SL, Canassa T, Baker MJ, Marangoni B, Ramos C, Cena C. A new strategy for canine visceral leishmaniasis diagnosis based on FTIR spectroscopy and machine learning. JOURNAL OF BIOPHOTONICS 2021; 14:e202100141. [PMID: 34423902 DOI: 10.1002/jbio.202100141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Visceral leishmaniasis is a neglected disease caused by protozoan parasites of the genus Leishmania. The successful control of the disease depends on its accurate and early diagnosis, which is usually made by combining clinical symptoms with laboratory tests such as serological, parasitological, and molecular tests. However, early diagnosis based on serological tests may exhibit low accuracy due to lack of specificity caused by cross-reactivities with other pathogens, and sensitivity issues related, among other reasons, to disease stage, leading to misdiagnosis. In this study was investigated the use of mid-infrared spectroscopy and multivariate analysis to perform a fast, accurate, and easy canine visceral leishmaniasis diagnosis. Canine blood sera of 20 noninfected, 20 Leishmania infantum, and eight Trypanosoma evansi infected dogs were studied. The data demonstrate that principal component analysis with machine learning algorithms achieved an overall accuracy above 85% in the diagnosis.
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Affiliation(s)
- Gustavo Larios
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Matheus Ribeiro
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Carla Arruda
- Laboratório de Parasitologia Humana, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Samuel L Oliveira
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Thalita Canassa
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Matthew J Baker
- Pure and Applied Chemistry, University of Stratchclyde, Technology and Innovation Centre, Glasgow, UK
| | - Bruno Marangoni
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Carlos Ramos
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Cícero Cena
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
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Chen K, Liu Z, Wang X, Yu C, Ye J, Yu C, Wang F, Shen C. Enhancement of perchloroethene dechlorination by a mixed dechlorinating culture via magnetic nanoparticle-mediated isolation method. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 786:147421. [PMID: 33964769 DOI: 10.1016/j.scitotenv.2021.147421] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/25/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Highly enriched active dechlorinating cultures are important in advancing microbial remediation technology. This study attempted to enrich a rapid perchloroethene (PCE) dechlorinating culture via magnetic nanoparticle-mediated isolation (MMI). MMI is a novel method that can separate the fast-growing and slow-growing population in a microbial community without labelling. In the MMI process, PCE dechlorination was enhanced but the subsequent trichloroethene (TCE) dechlorination was inhibited, with TCE cumulative rate reached up to 80.6% within 70 days. Meanwhile, the microbial community was also changed, with fast-growing genera like Dehalobacterium and Petrimonas enriched, and slow-growing Methanosarcina almost ruled out. Relative abundances of several major genera including Petrimonas and Methanosarcina were positively related to TCE dechlorination rate and the relative abundance of Dehalococcoides. On the other hand, Dehalobacterium was negatively related to TCE dechlorination rate and Dehalococcoides abundance, suggesting potential competition between Dehalobacterium and Dehalococcoides. The regrowth of Methanosarcina coupled well with the recovery of TCE dechlorination capacity, which implied the important role of methanogens in TCE dechlorination. Via MMI method, a simpler but more active microbial consortium could be established to enhance PCE remediation efficiency. Methanogens may act as the indicators or biomarkers for TCE dechlorination, suggesting that methanogenic activity should also be monitored when enriching dechlorination cultures and remediating PCE contaminated sites. CAPSULE: A rapid perchloroethene dechlorinator was gotten via magnetic nanoparticles and dechlorination of trichloroethene coupled well with growth of Methanosarcina.
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Affiliation(s)
- Kezhen Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zefan Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaomin Wang
- Ecological Environmental Science Design and Research Institute of Zhejiang Province, Hangzhou 310007, China
| | - Chungui Yu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Junxiang Ye
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chunna Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Feier Wang
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chaofeng Shen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory for Water Pollution Control and Environmental Safety, Hangzhou 310058, China.
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10
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Tang JW, Liu QH, Yin XC, Pan YC, Wen PB, Liu X, Kang XX, Gu B, Zhu ZB, Wang L. Comparative Analysis of Machine Learning Algorithms on Surface Enhanced Raman Spectra of Clinical Staphylococcus Species. Front Microbiol 2021; 12:696921. [PMID: 34531835 PMCID: PMC8439569 DOI: 10.3389/fmicb.2021.696921] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/30/2021] [Indexed: 12/13/2022] Open
Abstract
Raman spectroscopy (RS) is a widely used analytical technique based on the detection of molecular vibrations in a defined system, which generates Raman spectra that contain unique and highly resolved fingerprints of the system. However, the low intensity of normal Raman scattering effect greatly hinders its application. Recently, the newly emerged surface enhanced Raman spectroscopy (SERS) technique overcomes the problem by mixing metal nanoparticles such as gold and silver with samples, which greatly enhances signal intensity of Raman effects by orders of magnitudes when compared with regular RS. In clinical and research laboratories, SERS provides a great potential for fast, sensitive, label-free, and non-destructive microbial detection and identification with the assistance of appropriate machine learning (ML) algorithms. However, choosing an appropriate algorithm for a specific group of bacterial species remains challenging, because with the large volumes of data generated during SERS analysis not all algorithms could achieve a relatively high accuracy. In this study, we compared three unsupervised machine learning methods and 10 supervised machine learning methods, respectively, on 2,752 SERS spectra from 117 Staphylococcus strains belonging to nine clinically important Staphylococcus species in order to test the capacity of different machine learning methods for bacterial rapid differentiation and accurate prediction. According to the results, density-based spatial clustering of applications with noise (DBSCAN) showed the best clustering capacity (Rand index 0.9733) while convolutional neural network (CNN) topped all other supervised machine learning methods as the best model for predicting Staphylococcus species via SERS spectra (ACC 98.21%, AUC 99.93%). Taken together, this study shows that machine learning methods are capable of distinguishing closely related Staphylococcus species and therefore have great application potentials for bacterial pathogen diagnosis in clinical settings.
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Affiliation(s)
- Jia-Wei Tang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Qing-Hua Liu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, China
| | - Xiao-Cong Yin
- Department of Laboratory Medicine, School of Medical Technology, Xuzhou Medical University, Xuzhou, China
| | - Ya-Cheng Pan
- School of Life Science, Xuzhou Medical University, Xuzhou, China
| | - Peng-Bo Wen
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Xin Liu
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Xing-Xing Kang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Bing Gu
- Department of Laboratory Medicine, School of Medical Technology, Xuzhou Medical University, Xuzhou, China
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zuo-Bin Zhu
- School of Life Science, Xuzhou Medical University, Xuzhou, China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
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11
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Acri G, Romano C, Costa S, Pellegrino S, Testagrossa B. Raman Spectroscopy Technique: A Non-Invasive Tool in Celiac Disease Diagnosis. Diagnostics (Basel) 2021; 11:diagnostics11071277. [PMID: 34359362 PMCID: PMC8306584 DOI: 10.3390/diagnostics11071277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 01/14/2023] Open
Abstract
Celiac disease (CD) is diagnosed by a combination of specific serology and typical duodenal lesions. The histological confirmation of CD, mandatory in the majority of patients with suspected CD, is based on invasive and poorly tolerated procedures, such as upper gastrointestinal endoscopy. In this study we propose an alternative and non-invasive methodology able to confirm the diagnosis of CD based on the analysis of serum samples using the Raman spectroscopy technique. Three different bands centered at 1650, 1450 and 1003 cm-1 have been considered and the A1450/A1003 and A1650/A1003 ratios have been computed to discriminate between CD and non-CD subjects. The reliability of the methodology was validated by statistical analysis using receiver operating characteristic (ROC) curves. The Youden index was also determined to obtain optimal cut-off points. The obtained results highlighted that the proposed methodology was able to distinguish between CD and non-CD subjects with 98% accuracy. The optimal cut-off points revealed, for both the A1450/A1003 and A1650/A1003 ratios, high values of sensitivity and specificity (>95.0% and >92.0% respectively), confirming that Raman spectroscopy may be considered a valid alternative to duodenal biopsy and demonstrates spectral changes in the secondary structures of the protein network.
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Affiliation(s)
- Giuseppe Acri
- Dipartimento di Scienze Biomediche, Odontoiatriche, e delle Immagini Morfologiche e Funzionali, Università degli Studi di Messina, 98125 Messina, Italy
- Correspondence: (G.A.); (B.T.)
| | - Claudio Romano
- Unità Operativa Semplice Dipartimentale Gastroenterologia Pediatrica e Fibrosi Cistica, Azienda, Ospedaliera Universitaria Policlinico G. Martino, Via Consolare Valeria, 98125 Messina, Italy; (C.R.); (S.C.); (S.P.)
| | - Stefano Costa
- Unità Operativa Semplice Dipartimentale Gastroenterologia Pediatrica e Fibrosi Cistica, Azienda, Ospedaliera Universitaria Policlinico G. Martino, Via Consolare Valeria, 98125 Messina, Italy; (C.R.); (S.C.); (S.P.)
| | - Salvatore Pellegrino
- Unità Operativa Semplice Dipartimentale Gastroenterologia Pediatrica e Fibrosi Cistica, Azienda, Ospedaliera Universitaria Policlinico G. Martino, Via Consolare Valeria, 98125 Messina, Italy; (C.R.); (S.C.); (S.P.)
| | - Barbara Testagrossa
- Dipartimento di Scienze Biomediche, Odontoiatriche, e delle Immagini Morfologiche e Funzionali, Università degli Studi di Messina, 98125 Messina, Italy
- Correspondence: (G.A.); (B.T.)
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12
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Kim S, Kim YJ, Bang A, Kim W, Choi S, Lee HJ. Wavelength-dependent label-free identification of isolated nontuberculous mycobacteria using surface-enhanced Raman spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119186. [PMID: 33248886 DOI: 10.1016/j.saa.2020.119186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/22/2020] [Accepted: 10/31/2020] [Indexed: 06/12/2023]
Abstract
We investigated the effect of Raman excitation wavelengths on the surface-enhanced Raman spectroscopy (SERS)-based identification of isolated nontuberculous mycobacteria (NTM). The SERS spectra with 3 commonly used excitation wavelengths, 532, 638, and 785 nm, were compared across 6 representative NTM species that primarily cause human NTM infections in Korea and the United States; these species were identified. The statistical differences among NTM SERS spectra at each Raman excitation wavelength were verified using 1-way analysis of variance, and the 6 NTM species were identified using principal components-linear discriminant analysis with leave-one-out cross validation. The identification accuracies with aromatic amino acid biomarkers were 99.3%, 91.3%, and 90.7% for 532, 638, and 785 nm, respectively. We believe that the proposed SERS protocol with aromatic amino acid biomarkers at the 532-nm Raman excitation wavelength will enable fast and accurate identification of NTM compared to previous identification methods.
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Affiliation(s)
- Soogeun Kim
- Department of Biomedical Engineering, College of Medicine, Kyung Hee University, Seoul 02447, South Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University Hospital, Kyung Hee University School of Medicine, Seoul 02447, South Korea
| | - Ayoung Bang
- Department of Biomedical Engineering, College of Medicine, Kyung Hee University, Seoul 02447, South Korea
| | - Wansun Kim
- Department of Biomedical Engineering, College of Medicine, Kyung Hee University, Seoul 02447, South Korea
| | - Samjin Choi
- Department of Biomedical Engineering, College of Medicine, Kyung Hee University, Seoul 02447, South Korea.
| | - Hee Joo Lee
- Korean National Tuberculosis Association, Seoul 06763, South Korea.
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13
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An X, Erramilli S, Reinhard BM. Plasmonic nano-antimicrobials: properties, mechanisms and applications in microbe inactivation and sensing. NANOSCALE 2021; 13:3374-3411. [PMID: 33538743 PMCID: PMC8349509 DOI: 10.1039/d0nr08353d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Bacterial, viral and fungal infections pose serious threats to human health and well-being. The continuous emergence of acute infectious diseases caused by pathogenic microbes and the rapid development of resistances against conventional antimicrobial drugs necessitates the development of new and effective strategies for the safe elimination of microbes in water, food or on surfaces, as well as for the inactivation of pathogenic microbes in human hosts. The need for new antimicrobials has triggered the development of plasmonic nano-antimicrobials that facilitate both light-dependent and -independent microbe inactivation mechanisms. This review introduces the relevant photophysical mechanisms underlying these plasmonic nano-antimicrobials, and provides an overview of how the photoresponses and materials properties of plasmonic nanostructures can be applied in microbial pathogen inactivation and sensing applications. Through a systematic analysis of the inactivation efficacies of different plasmonic nanostructures, this review outlines the current state-of-the-art in plasmonic nano-antimicrobials and defines the application space for different microbial inactivation strategies. The advantageous optical properties of plasmonic nano-antimicrobials also enhance microbial detection and sensing modalities and thus help to avoid exposure to microbial pathogens. Sensitive and fast plasmonic microbial sensing modalities and their theranostic and targeted therapeutic applications are discussed.
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Affiliation(s)
- Xingda An
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and The Photonics Center, Boston University, Boston, MA 02215, USA
| | - Shyamsunder Erramilli
- Department of Physics, Boston University, Boston, MA 02215, USA and The Photonics Center, Boston University, Boston, MA 02215, USA
| | - Björn M Reinhard
- Department of Chemistry, Boston University, Boston, MA 02215, USA. and The Photonics Center, Boston University, Boston, MA 02215, USA
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14
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Verkhovskii RA, Kozlova AA, Sindeeva OA, Kozhevnikov IO, Prikhozhdenko ES, Mayorova OA, Grishin OV, Makarkin MA, Ermakov AV, Abdurashitov AS, Tuchin VV, Bratashov DN. Lightsheet-based flow cytometer for whole blood with the ability for the magnetic retrieval of objects from the blood flow. BIOMEDICAL OPTICS EXPRESS 2021; 12:380-394. [PMID: 33659080 PMCID: PMC7899519 DOI: 10.1364/boe.413845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/29/2020] [Accepted: 12/06/2020] [Indexed: 05/04/2023]
Abstract
Detection and extraction of circulating tumor cells and other rare objects in the bloodstream are of great interest for modern diagnostics, but devices that can solve this problem for the whole blood volume of laboratory animals are still rare. Here we have developed SPIM-based lightsheet flow cytometer for the detection of fluorescently-labeled objects in whole blood. The bypass channel between two blood vessels connected with the external flow cell was used to visualize, detect, and magnetically separate fluorescently-labeled objects without hydrodynamic focusing. Carriers for targeted drug delivery were used as model objects to test the device performance. They were injected into the bloodstream of the rat, detected fluorescently, and then captured from the bloodstream by a magnetic separator prior to filtration in organs. Carriers extracted from the whole blood were studied by a number of in vitro methods.
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Affiliation(s)
| | | | - Olga A. Sindeeva
- Saratov State University, 83 Astrakhanskaya str., Saratov 410012, Russia
- Skolkovo Innovation Center, 3 Nobel str., Moscow 121205, Russia
| | | | | | - Oksana A. Mayorova
- Saratov State University, 83 Astrakhanskaya str., Saratov 410012, Russia
| | - Oleg V. Grishin
- Saratov State University, 83 Astrakhanskaya str., Saratov 410012, Russia
| | | | - Alexey V. Ermakov
- Saratov State University, 83 Astrakhanskaya str., Saratov 410012, Russia
| | | | - Valery V. Tuchin
- Saratov State University, 83 Astrakhanskaya str., Saratov 410012, Russia
- National Research Tomsk State University, 36 Lenin Avenue, Tomsk 634050, Russia
- Institute of Precision Mechanics and Control of the RAS, 24 Rabochaya str., Saratov 410028, Russia
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15
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Locke A, Fitzgerald S, Mahadevan-Jansen A. Advances in Optical Detection of Human-Associated Pathogenic Bacteria. Molecules 2020; 25:E5256. [PMID: 33187331 PMCID: PMC7696695 DOI: 10.3390/molecules25225256] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023] Open
Abstract
Bacterial infection is a global burden that results in numerous hospital visits and deaths annually. The rise of multi-drug resistant bacteria has dramatically increased this burden. Therefore, there is a clinical need to detect and identify bacteria rapidly and accurately in their native state or a culture-free environment. Current diagnostic techniques lack speed and effectiveness in detecting bacteria that are culture-negative, as well as options for in vivo detection. The optical detection of bacteria offers the potential to overcome these obstacles by providing various platforms that can detect bacteria rapidly, with minimum sample preparation, and, in some cases, culture-free directly from patient fluids or even in vivo. These modalities include infrared, Raman, and fluorescence spectroscopy, along with optical coherence tomography, interference, polarization, and laser speckle. However, these techniques are not without their own set of limitations. This review summarizes the strengths and weaknesses of utilizing each of these optical tools for rapid bacteria detection and identification.
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Affiliation(s)
- Andrea Locke
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Sean Fitzgerald
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - Anita Mahadevan-Jansen
- Vanderbilt Biophotonics Center, Nashville, TN 37232, USA; (A.L.); (S.F.)
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
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16
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Abstract
Abstract
A potential role of optical technologies in medicine including micro-Raman spectroscopy is diagnosis of bacteria, cells and tissues which is covered in this chapter. The main advantage of Raman-based methods to complement and augment diagnostic tools is that unsurpassed molecular specificity is achieved without labels and in a nondestructive way. Principles and applications of micro-Raman spectroscopy in the context of medicine will be described. First, Raman spectra of biomolecules representing proteins, nucleic acids, lipids and carbohydrates are introduced. Second, microbial applications are summarized with the focus on typing on species and strain level, detection of infections, antibiotic resistance and biofilms. Third, cytological applications are presented to classify single cells and study cell metabolism and drug–cell interaction. Fourth, applications to tissue characterization start with discussion of lateral resolution for Raman imaging followed by Raman-based detection of pathologies and combination with other modalities. Finally, an outlook is given to translate micro-Raman spectroscopy as a clinical tool to solve unmet needs in point-of-care applications and personalized treatment of diseases.
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17
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Stiffness signatures along early stages of Xylella fastidiosa biofilm formation. Colloids Surf B Biointerfaces 2017; 159:174-182. [DOI: 10.1016/j.colsurfb.2017.07.075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/19/2017] [Accepted: 07/26/2017] [Indexed: 01/05/2023]
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18
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Stöckel S, Meisel S, Lorenz B, Kloß S, Henk S, Dees S, Richter E, Andres S, Merker M, Labugger I, Rösch P, Popp J. Raman spectroscopic identification of Mycobacterium tuberculosis. JOURNAL OF BIOPHOTONICS 2017; 10:727-734. [PMID: 27714969 DOI: 10.1002/jbio.201600174] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/22/2016] [Accepted: 09/09/2016] [Indexed: 06/06/2023]
Abstract
In this study, Raman microspectroscopy has been utilized to identify mycobacteria to the species level. Because of the slow growth of mycobacteria, the per se cultivation-independent Raman microspectroscopy emerges as a perfect tool for a rapid on-the-spot mycobacterial diagnostic test. Special focus was laid upon the identification of Mycobacterium tuberculosis complex (MTC) strains, as the main causative agent of pulmonary tuberculosis worldwide, and the differentiation between pathogenic and commensal nontuberculous mycobacteria (NTM). Overall the proposed model considers 26 different mycobacteria species as well as antibiotic susceptible and resistant strains. More than 8800 Raman spectra of single bacterial cells constituted a spectral library, which was the foundation for a two-level classification system including three support vector machines. Our model allowed the discrimination of MTC samples in an independent validation dataset with an accuracy of 94% and could serve as a basis to further improve Raman microscopy as a first-line diagnostic point-of-care tool for the confirmation of tuberculosis disease.
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Affiliation(s)
- Stephan Stöckel
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, 07743, Jena, Germany
- InfectoGnostics Forschungscampus Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Susann Meisel
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, 07743, Jena, Germany
- InfectoGnostics Forschungscampus Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Björn Lorenz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, 07743, Jena, Germany
- InfectoGnostics Forschungscampus Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Sandra Kloß
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, 07743, Jena, Germany
- InfectoGnostics Forschungscampus Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Sandra Henk
- Alere Technologies GmbH, Löbstedter Straße 103-105, 07749, Jena, Germany
| | - Stefan Dees
- Alere Technologies GmbH, Löbstedter Straße 103-105, 07749, Jena, Germany
| | - Elvira Richter
- National Reference Center for Mycobacteria, Research Center Borstel, Parkallee 1-40, 23845, Borstel, Germany
- Present address: Laboratory Dr. Limbach, Heidelberg, Germany
| | - Sönke Andres
- National Reference Center for Mycobacteria, Research Center Borstel, Parkallee 1-40, 23845, Borstel, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1-40, 23845, Borstel, Germany
| | - Ines Labugger
- Alere Technologies GmbH, Löbstedter Straße 103-105, 07749, Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, 07743, Jena, Germany
- InfectoGnostics Forschungscampus Jena, Philosophenweg 7, 07743, Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, 07743, Jena, Germany
- InfectoGnostics Forschungscampus Jena, Philosophenweg 7, 07743, Jena, Germany
- Leibniz-Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745, Jena, Germany
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19
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Harrison JP, Berry D. Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples. Front Microbiol 2017; 8:675. [PMID: 28450860 PMCID: PMC5390015 DOI: 10.3389/fmicb.2017.00675] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/31/2017] [Indexed: 01/08/2023] Open
Abstract
Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.
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Affiliation(s)
- Jesse P Harrison
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry Meets Microbiology", University of ViennaVienna, Austria
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry Meets Microbiology", University of ViennaVienna, Austria
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20
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Abstract
Bacterial sensing is important for understanding the numerous roles bacteria play in nature and in technology, understanding and managing bacterial populations, detecting pathogenic bacterial infections, and preventing the outbreak of illness. Current analytical challenges in bacterial sensing center on the dilemma of rapidly acquiring quantitative information about bacteria with high detection efficiency, sensitivity, and specificity, while operating within a reasonable budget and optimizing the use of ancillary tools, such as multivariate statistics. This review starts from a general description of bacterial sensing methods and challenges, and then focuses on bacterial characterization using optical methods including Raman spectroscopy and imaging, infrared spectroscopy, fluorescence spectroscopy and imaging, and plasmonics, including both extended and localized surface plasmon resonance spectroscopy. The advantages and drawbacks of each method in relation to the others are discussed, as are their applications. A particularly promising direction in bacterial sensing lies in combining multiple approaches to achieve multiplex analysis, and examples where this has been achieved are highlighted.
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Affiliation(s)
- Jiayun Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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21
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Kniggendorf AK, Nogueira R, Kelb C, Schadzek P, Meinhardt-Wollweber M, Ngezahayo A, Roth B. Confocal Raman microscopy and fluorescent in situ hybridization - A complementary approach for biofilm analysis. CHEMOSPHERE 2016; 161:112-118. [PMID: 27423128 DOI: 10.1016/j.chemosphere.2016.06.096] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/24/2016] [Accepted: 06/25/2016] [Indexed: 06/06/2023]
Abstract
We combine confocal Raman microscopy (CRM) of wet samples with subsequent Fluorescent in situ hybridization (FISH) without significant limitations to either technique for analyzing the same sample of a microbial community on a cell-to-cell basis. This combination of techniques allows a much deeper, more complete understanding of complex environmental samples than provided by either technique alone. The minimalistic approach is based on laboratory glassware with micro-engravings for reproducible localization of the sample at cell scale combined with a fixation and de- and rehydration protocol for the respective techniques. As proof of concept, we analyzed a floc of nitrifying activated sludge, demonstrating that the sample can be tracked with cell-scale precision over different measurements and instruments. The collected information includes the microbial content, spatial shape, variant chemical compositions of the floc matrix and the mineral microparticles embedded within. In addition, the direct comparison of CRM and FISH revealed a difference in reported cell size due to the different cell components targeted by the respective technique. To the best of our knowledge, this is the first report of a direct cell-to-cell comparison of confocal Raman microscopy and Fluorescent in situ hybridization analysis performed on the same sample. An adaptation of the method to include native samples as a starting point is planned for the near future. The micro-engraving approach itself also opens up the possibility of combining other, functionally incompatible techniques as required for further in-depth investigations of low-volume samples.
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Affiliation(s)
- Ann-Kathrin Kniggendorf
- Hannover Centre for Optical Technologies, Gottfried-Wilhelm-Leibniz Universität Hannover, Nienburger Str. 2, 30167 Hannover, Germany.
| | - Regina Nogueira
- Institut für Siedlungswasserwirtschaft und Abfalltechnik, Gottfried-Wilhelm-Leibniz Universität Hannover, Welfengarten 1, 30167 Hannover, Germany.
| | - Christian Kelb
- Hannover Centre for Optical Technologies, Gottfried-Wilhelm-Leibniz Universität Hannover, Nienburger Str. 2, 30167 Hannover, Germany.
| | - Patrik Schadzek
- Institute for Biophysics, Gottfried-Wilhelm-Leibniz Universität Hannover, Herrenhäuser Str. 2, 30149 Hannover, Germany.
| | - Merve Meinhardt-Wollweber
- Hannover Centre for Optical Technologies, Gottfried-Wilhelm-Leibniz Universität Hannover, Nienburger Str. 2, 30167 Hannover, Germany.
| | - Anaclet Ngezahayo
- Institute for Biophysics, Gottfried-Wilhelm-Leibniz Universität Hannover, Herrenhäuser Str. 2, 30149 Hannover, Germany.
| | - Bernhard Roth
- Hannover Centre for Optical Technologies, Gottfried-Wilhelm-Leibniz Universität Hannover, Nienburger Str. 2, 30167 Hannover, Germany.
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22
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Kogermann K, Putrinš M, Tenson T. Single-cell level methods for studying the effect of antibiotics on bacteria during infection. Eur J Pharm Sci 2016; 95:2-16. [PMID: 27577009 DOI: 10.1016/j.ejps.2016.08.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 08/17/2016] [Accepted: 08/23/2016] [Indexed: 12/11/2022]
Abstract
Considerable evidence about phenotypic heterogeneity among bacteria during infection has accumulated during recent years. This heterogeneity has to be considered if the mechanisms of infection and antibiotic action are to be understood, so we need to implement existing and find novel methods to monitor the effects of antibiotics on bacteria at the single-cell level. This review provides an overview of methods by which this aim can be achieved. Fluorescence label-based methods and Raman scattering as a label-free approach are discussed in particular detail. Other label-free methods that can provide single-cell level information, such as impedance spectroscopy and surface plasmon resonance, are briefly summarized. The advantages and disadvantages of these different methods are discussed in light of a challenging in vivo environment.
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Affiliation(s)
- Karin Kogermann
- Institute of Pharmacy, University of Tartu, Nooruse 1, 50411 Tartu, Estonia.
| | - Marta Putrinš
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia.
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia.
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23
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McIlvenna D, Huang WE, Davison P, Glidle A, Cooper J, Yin H. Continuous cell sorting in a flow based on single cell resonance Raman spectra. LAB ON A CHIP 2016; 16:1420-9. [PMID: 26974400 DOI: 10.1039/c6lc00251j] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Single cell Raman spectroscopy measures a spectral fingerprint of the biochemistry of cells, and provides a powerful method for label-free detection of living cells without the involvement of a chemical labelling strategy. However, as the intrinsic Raman signals of cells are inherently weak, there is a significant challenge in discriminating and isolating cells in a flowing stream. Here we report an integrated Raman-microfluidic system for continuous sorting of a stream of cyanobacteria, Synechocystis sp. PCC6803. These carotenoid-containing microorganisms provide an elegant model system enabling us to determine the sorting accuracy using the subtly different resonance Raman spectra of microorganism cultured in a (12)C or (13)C carbon source. Central to the implementation of continuous flow sorting is the use of "pressure dividers" that eliminate fluctuations in flow in the detection region. This has enabled us to stabilise the flow profile sufficiently to allow automated operation with synchronisation of Raman acquisition, real-time classification and sorting at flow rates of ca. <100 μm s(-1), without the need to "trap" the cells. We demonstrate the flexibility of this approach in sorting mixed cell populations with the ability to achieve 96.3% purity of the selected cells at a speed of 0.5 Hz.
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Affiliation(s)
- David McIlvenna
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK
| | - Paul Davison
- Kroto Research Institute, Department of Civil and Structural Engineering, North Campus, The University of Sheffield, Broad Lane, Sheffield S3 7HQ, UK
| | - Andrew Glidle
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Jon Cooper
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK.
| | - Huabing Yin
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8QQ, UK.
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24
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Gonchukov S, Baikova T, Alushin M, Svistunova T, Minaeva S, Ionin A, Kudryashov S, Saraeva I, Zayarny D. SINGLE BACTERIUM DETECTION USING SERS. ACTA ACUST UNITED AC 2016. [DOI: 10.1088/1742-6596/691/1/012010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Near-infrared spectroscopy and variable selection techniques to discriminate Pseudomonas aeruginosa strains in clinical samples. Microchem J 2016. [DOI: 10.1016/j.microc.2015.09.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Assmann C, Kirchhoff J, Beleites C, Hey J, Kostudis S, Pfister W, Schlattmann P, Popp J, Neugebauer U. Identification of vancomycin interaction with Enterococcus faecalis within 30 min of interaction time using Raman spectroscopy. Anal Bioanal Chem 2015; 407:8343-52. [DOI: 10.1007/s00216-015-8912-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/30/2015] [Accepted: 07/09/2015] [Indexed: 12/22/2022]
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27
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Pahlow S, Meisel S, Cialla-May D, Weber K, Rösch P, Popp J. Isolation and identification of bacteria by means of Raman spectroscopy. Adv Drug Deliv Rev 2015; 89:105-20. [PMID: 25895619 DOI: 10.1016/j.addr.2015.04.006] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 04/02/2015] [Accepted: 04/10/2015] [Indexed: 01/10/2023]
Abstract
Bacterial detection is a highly topical research area, because various fields of application will benefit from the progress being made. Consequently, new and innovative strategies which enable the investigation of complex samples, like body fluids or food stuff, and improvements regarding the limit of detection are of general interest. Within this review the prospects of Raman spectroscopy as a reliable tool for identifying bacteria in complex samples are discussed. The main emphasis of this work is on important aspects of applying Raman spectroscopy for the detection of bacteria like sample preparation and the identification process. Several approaches for a Raman compatible isolation of bacterial cells have been developed and applied to different matrices. Here, an overview of the limitations and possibilities of these methods is provided. Furthermore, the utilization of Raman spectroscopy for diagnostic purposes, food safety and environmental issues is discussed under a critical view.
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28
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Kloß S, Lorenz B, Dees S, Labugger I, Rösch P, Popp J. Destruction-free procedure for the isolation of bacteria from sputum samples for Raman spectroscopic analysis. Anal Bioanal Chem 2015; 407:8333-41. [DOI: 10.1007/s00216-015-8743-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/13/2015] [Accepted: 04/27/2015] [Indexed: 11/25/2022]
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29
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Eberhardt K, Stiebing C, Matthäus C, Schmitt M, Popp J. Advantages and limitations of Raman spectroscopy for molecular diagnostics: an update. Expert Rev Mol Diagn 2015; 15:773-87. [PMID: 25872466 DOI: 10.1586/14737159.2015.1036744] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Over the last decade, Raman spectroscopy has gained more and more interest in research as well as in clinical laboratories. As a vibrational spectroscopy technique, it is complementary to the also well-established infrared spectroscopy. Through specific spectral patterns, substances can be identified and molecular changes can be observed with high specificity. Because of a high spatial resolution due to an excitation wavelength in the visible and near-infrared range, Raman spectroscopy combined with microscopy is very powerful for imaging biological samples. Individual cells can be imaged on the subcellular level. In vivo tissue examinations are becoming increasingly important for clinical applications. In this review, we present currently ongoing research in different fields of medical diagnostics involving linear Raman spectroscopy and imaging. We give a wide overview over applications for the detection of atherosclerosis, cancer, inflammatory diseases and pharmacology, with a focus on developments over the past 5 years. Conclusions drawn from Raman spectroscopy are often validated by standard methods, for example, histopathology or PCR. The future potential of Raman spectroscopy and its limitations are discussed in consideration of other non-linear Raman techniques.
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Affiliation(s)
- Katharina Eberhardt
- Leibniz Institute of Photonic Technology (IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
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Baikova TV, Minaeva SA, Sundukov AV, Svistunova TS, Bagratashvili VN, Alushin MV, Gonchukov SA. Detection of single bacteria – causative agents of meningitis using raman microscopy. ACTA ACUST UNITED AC 2015. [DOI: 10.1088/1742-6596/594/1/012029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Detection of vancomycin resistances in enterococci within 3 ½ hours. Sci Rep 2015; 5:8217. [PMID: 25645753 PMCID: PMC4314646 DOI: 10.1038/srep08217] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/29/2014] [Indexed: 12/26/2022] Open
Abstract
Vancomycin resistant enterococci (VRE) constitute a challenging problem in health care institutions worldwide. Novel methods to rapidly identify resistances are highly required to ensure an early start of tailored therapy and to prevent further spread of the bacteria. Here, a spectroscopy-based rapid test is presented that reveals resistances of enterococci towards vancomycin within 3.5 hours. Without any specific knowledge on the strain, VRE can be recognized with high accuracy in two different enterococci species. By means of dielectrophoresis, bacteria are directly captured from dilute suspensions, making sample preparation very easy. Raman spectroscopic analysis of the trapped bacteria over a time span of two hours in absence and presence of antibiotics reveals characteristic differences in the molecular response of sensitive as well as resistant Enterococcus faecalis and Enterococcus faecium. Furthermore, the spectroscopic fingerprints provide an indication on the mechanisms of induced resistance in VRE.
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Silge A, Schumacher W, Rösch P, Da Costa Filho PA, Gérard C, Popp J. Identification of water-conditioned Pseudomonas aeruginosa by Raman microspectroscopy on a single cell level. Syst Appl Microbiol 2014; 37:360-7. [DOI: 10.1016/j.syapm.2014.05.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 11/16/2022]
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33
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Münchberg U, Rösch P, Bauer M, Popp J. Raman spectroscopic identification of single bacterial cells under antibiotic influence. Anal Bioanal Chem 2014; 406:3041-50. [DOI: 10.1007/s00216-014-7747-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/12/2014] [Accepted: 03/04/2014] [Indexed: 11/30/2022]
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I-Fang Cheng, Chang HC, Chen TY, Hu C, Yang FL. Rapid (<5 min) identification of pathogen in human blood by electrokinetic concentration and surface-enhanced Raman spectroscopy. Sci Rep 2014; 3:2365. [PMID: 23917638 PMCID: PMC3734443 DOI: 10.1038/srep02365] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/15/2013] [Indexed: 01/12/2023] Open
Abstract
This study reports a novel microfluidic platform for rapid and long-ranged concentration of rare-pathogen from human blood for subsequent on-chip surface-enhanced Raman spectroscopy (SERS) identification/discrimination of bacteria based on their detected fingerprints. Using a hybrid electrokinetic mechanism, bacteria can be concentrated at the stagnation area on the SERS-active roughened electrode, while blood cells were excluded away from this region at the center of concentric circular electrodes. This electrokinetic approach performs isolation and concentration of bacteria in about three minutes; the density factor is increased approximately a thousand fold in a local area of ~5000 μm2 from a low bacteria concentration of 5 × 103 CFU/ml. Besides, three genera of bacteria, S. aureus, E. coli, and P. aeruginosa that are found in most of the isolated infections in bacteremia were successfully identified in less than one minute on-chip without the use of any antibody/chemical immobilization and reaction processes.
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Affiliation(s)
- I-Fang Cheng
- National Nano Device Laboratories, National Applied Research Laboratories, Tainan, Taiwan, ROC.
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35
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Kusić D, Kampe B, Rösch P, Popp J. Identification of water pathogens by Raman microspectroscopy. WATER RESEARCH 2014; 48:179-189. [PMID: 24103393 DOI: 10.1016/j.watres.2013.09.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/12/2013] [Accepted: 09/13/2013] [Indexed: 05/27/2023]
Abstract
Legionella species can be found living in water mostly in a viable but nonculturable state or associated with protozoa and complex biofilm formations. Isolation and afterwards identification of these pathogens from environmental samples by using common identification procedures based on cultivation are extremely difficult and prolonged. The development of fast and sensitive method based on the cultivation free identification of bacteria is necessary. In this study Raman microspectroscopy combined with multiclass support vector machines have been used to discriminate between Legionella and other common aquatic bacteria, to distinguish among clinically relevant Legionella species and to classify unknown Raman spectra for a fast and reliable identification. Recorded Raman spectra of the twenty-two Legionella species as well as the Raman spectra of Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa were utilized to build the classification model. Afterwards, independent Raman spectra of eleven species were used to identify them on the basis of the classification model that was created. The present study shows that Raman microspectroscopy can be used as a rapid and reliable method to distinguish between Legionella species recognized as human pathogens and to identify samples which are unknown to the model based on multiclass support vector machines (MC-SVM).
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Affiliation(s)
- Dragana Kusić
- Institut für Physikalische Chemie and Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, D-07743 Jena, Germany
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36
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Neugebauer U, Kloß S, Schröder UC, Rösch P, Popp J. Fast and Selective Against Bacteria. ACTA ACUST UNITED AC 2013. [DOI: 10.1002/opph.201300031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Diem M, Mazur A, Lenau K, Schubert J, Bird B, Miljković M, Krafft C, Popp J. Molecular pathology via IR and Raman spectral imaging. JOURNAL OF BIOPHOTONICS 2013; 6:855-86. [PMID: 24311233 DOI: 10.1002/jbio.201300131] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/03/2013] [Indexed: 05/21/2023]
Abstract
During the last 15 years, vibrational spectroscopic methods have been developed that can be viewed as molecular pathology methods that depend on sampling the entire genome, proteome and metabolome of cells and tissues, rather than probing for the presence of selected markers. First, this review introduces the background and fundamentals of the spectroscopies underlying the new methodologies, namely infrared and Raman spectroscopy. Then, results are presented in the context of spectral histopathology of tissues for detection of metastases in lymph nodes, squamous cell carcinoma, adenocarcinomas, brain tumors and brain metastases. Results from spectral cytopathology of cells are discussed for screening of oral and cervical mucosa, and circulating tumor cells. It is concluded that infrared and Raman spectroscopy can complement histopathology and reveal information that is available in classical methods only by costly and time-consuming steps such as immunohistochemistry, polymerase chain reaction or gene arrays. Due to the inherent sensitivity toward changes in the bio-molecular composition of different cell and tissue types, vibrational spectroscopy can even provide information that is in some cases superior to that of any one of the conventional techniques.
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Affiliation(s)
- Max Diem
- Laboratory for Spectral Diagnosis LSpD, Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115, USA
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38
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Schröder UC, Ramoji A, Glaser U, Sachse S, Leiterer C, Csaki A, Hübner U, Fritzsche W, Pfister W, Bauer M, Popp J, Neugebauer U. Combined dielectrophoresis-Raman setup for the classification of pathogens recovered from the urinary tract. Anal Chem 2013; 85:10717-24. [PMID: 24125497 DOI: 10.1021/ac4021616] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rapid and effective methods of pathogen identifications are of major interest in clinical microbiological analysis to administer timely tailored antibiotic therapy. Raman spectroscopy as a label-free, culture-independent optical method is suitable to identify even single bacteria. However, the low bacteria concentration in body fluids makes it difficult to detect their characteristic molecular fingerprint directly in suspension. Therefore, in this study, Raman spectroscopy is combined with dielectrophoresis, which enables the direct translational manipulation of bacteria in suspensions with spatial nonuniform electrical fields so as to perform specific Raman spectroscopic characterization. A quadrupole electrode design is used to capture bacteria directly from fluids in well-defined microsized regions. With live/dead fluorescence viability staining, it is verified, that the bacteria survive this procedure for the relevant range of field strengths. The dielectrophoretic enrichment of bacteria allows for obtaining high quality Raman spectra in dilute suspensions with an integration time of only one second. As proof-of-principle study, the setup was tested with Escherichia coli and Enterococcus faecalis, two bacterial strains that are commonly encountered in urinary tract infections. Furthermore, to verify the potential for dealing with real world samples, pathogens from patients' urine have been analyzed. With the additional help of multivariate statistical analysis, a robust classification model could be built and allowed the classification of those two strains within a few minutes. In contrast, the standard microbiological diagnostics are based on very time-consuming cultivation tests. This setup holds the potential to reduce the crucial parameter diagnosis time by orders of magnitude.
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Kloß S, Kampe B, Sachse S, Rösch P, Straube E, Pfister W, Kiehntopf M, Popp J. Culture Independent Raman Spectroscopic Identification of Urinary Tract Infection Pathogens: A Proof of Principle Study. Anal Chem 2013; 85:9610-6. [DOI: 10.1021/ac401806f] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sandra Kloß
- Institute of Physical
Chemistry and Abbe Center of Photonics, University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
| | - Bernd Kampe
- Institute of Physical
Chemistry and Abbe Center of Photonics, University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
| | - Svea Sachse
- Institute of Medical
Microbiology, Jena University Hospital, Erlanger Allee 101, D-07747 Jena, Germany
| | - Petra Rösch
- Institute of Physical
Chemistry and Abbe Center of Photonics, University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
| | - Eberhard Straube
- Institute of Medical
Microbiology, Jena University Hospital, Erlanger Allee 101, D-07747 Jena, Germany
| | - Wolfgang Pfister
- Institute of Medical
Microbiology, Jena University Hospital, Erlanger Allee 101, D-07747 Jena, Germany
| | - Michael Kiehntopf
- Institute
of Clinical
Chemistry and Laboratory Diagnostics, Jena University Hospital, Erlanger Allee
101, D-07747 Jena, Germany
| | - Jürgen Popp
- Institute of Physical
Chemistry and Abbe Center of Photonics, University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- Institute of Photonic Technology, Albert-Einstein-Straße
9, D-07745 Jena, Germany
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Schie IW, Huser T. Methods and applications of Raman microspectroscopy to single-cell analysis. APPLIED SPECTROSCOPY 2013; 67:813-28. [PMID: 23876720 DOI: 10.1366/12-06971] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Raman spectroscopy is a powerful biochemical analysis technique that allows for the dynamic characterization and imaging of living biological cells in the absence of fluorescent stains. In this review, we summarize some of the most recent developments in the noninvasive biochemical characterization of single cells by spontaneous Raman scattering. Different instrumentation strategies utilizing confocal detection optics, multispot, and line illumination have been developed to improve the speed and sensitivity of the analysis of single cells by Raman spectroscopy. To analyze and visualize the large data sets obtained during such experiments, sophisticated multivariate statistical analysis tools are necessary to reduce the data and extract components of interest. We highlight the most recent applications of single cell analysis by Raman spectroscopy and their biomedical implications that have enabled the noninvasive characterization of specific metabolic states of eukaryotic cells, the identification and characterization of stem cells, and the rapid identification of bacterial cells. We conclude the article with a brief look into the future of this rapidly evolving research area.
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Affiliation(s)
- Iwan W Schie
- Center For Biophotonics, Science, and Technology, University of California-Davis, Sacramento, CA 95817, USA.
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41
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Sathyavathi R, Dingari NC, Barman I, Prasad PSR, Prabhakar S, Rao DN, Dasari RR, Undamatla J. Raman spectroscopy provides a powerful, rapid diagnostic tool for the detection of tuberculous meningitis in ex vivo cerebrospinal fluid samples. JOURNAL OF BIOPHOTONICS 2013; 6:567-72. [PMID: 22887773 PMCID: PMC4094343 DOI: 10.1002/jbio.201200110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/11/2012] [Accepted: 07/12/2012] [Indexed: 05/25/2023]
Abstract
In this letter, we propose a novel method for diagnosis of tuberculous meningitis using Raman spectroscopy. The silicate Raman signature obtained from Mycobacterium tuberculosis positive cases enables specific and sensitive detection of tuberculous meningitis from acquired cerebrospinal fluid samples. The association of silicates with the tuberculosis mycobacterium is discussed. We envision that this new method will facilitate rapid diagnosis of tuberculous meningitis without application of exogenous reagents or dyes and can be aptly used as a complementary screening tool to the existing gold standard methods.
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Affiliation(s)
- R. Sathyavathi
- School of Physics, University of Hyderabad, Hyderabad, India
| | - Narahara Chari Dingari
- George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, USA
| | - Ishan Barman
- George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, USA
| | - P. S. R. Prasad
- National Geophysical Research Institute (Council for Scientific and Industrial Research), Hyderabad, India
| | | | - D. Narayana Rao
- School of Physics, University of Hyderabad, Hyderabad, India
| | - Ramachandra R. Dasari
- George R. Harrison Spectroscopy Laboratory, Massachusetts Institute of Technology, Cambridge, USA
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Maurice CF, Turnbaugh PJ. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales. FEMS Microbiol Rev 2013; 37:830-48. [PMID: 23550823 DOI: 10.1111/1574-6976.12022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/18/2013] [Accepted: 03/19/2013] [Indexed: 12/15/2022] Open
Abstract
Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small-to-moderate-sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single-cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities.
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Affiliation(s)
- Corinne F Maurice
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, 02138, USA
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Evidence for phenotypic plasticity among multihost Campylobacter jejuni and C. coli lineages, obtained using ribosomal multilocus sequence typing and Raman spectroscopy. Appl Environ Microbiol 2012. [PMID: 23204423 DOI: 10.1128/aem.02521-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Closely related bacterial isolates can display divergent phenotypes. This can limit the usefulness of phylogenetic studies for understanding bacterial ecology and evolution. Here, we compare phenotyping based on Raman spectrometric analysis of cellular composition to phylogenetic classification by ribosomal multilocus sequence typing (rMLST) in 108 isolates of the zoonotic pathogens Campylobacter jejuni and C. coli. Automatic relevance determination (ARD) was used to identify informative peaks in the Raman spectra that could be used to distinguish strains in taxonomic and host source groups (species, clade, clonal complex, and isolate source/host). Phenotypic characterization based on Raman spectra showed a degree of agreement with genotypic classification using rMLST, with segregation accuracy between species (83.95%), clade (in C. coli, 98.41%), and, to some extent, clonal complex (86.89% C. jejuni ST-21 and ST-45 complexes) being achieved. This confirmed the utility of Raman spectroscopy for lineage classification and the correlation between genotypic and phenotypic classification. In parallel analysis, relatively distantly related isolates (different clonal complexes) were assigned the correct host origin irrespective of the clonal origin (74.07 to 96.97% accuracy) based upon different Raman peaks. This suggests that the phenotypic characteristics, from which the phenotypic signal is derived, are not fixed by clonal descent but are influenced by the host environment and change as strains move between hosts.
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Brauchle E, Schenke-Layland K. Raman spectroscopy in biomedicine - non-invasive in vitro analysis of cells and extracellular matrix components in tissues. Biotechnol J 2012; 8:288-97. [PMID: 23161832 PMCID: PMC3644878 DOI: 10.1002/biot.201200163] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/17/2012] [Accepted: 10/17/2012] [Indexed: 12/12/2022]
Abstract
Raman spectroscopy is an established laser-based technology for the quality assurance of pharmaceutical products. Over the past few years, Raman spectroscopy has become a powerful diagnostic tool in the life sciences. Raman spectra allow assessment of the overall molecular constitution of biological samples, based on specific signals from proteins, nucleic acids, lipids, carbohydrates, and inorganic crystals. Measurements are non-invasive and do not require sample processing, making Raman spectroscopy a reliable and robust method with numerous applications in biomedicine. Moreover, Raman spectroscopy allows the highly sensitive discrimination of bacteria. Rama spectra retain information on continuous metabolic processes and kinetics such as lipid storage and recombinant protein production. Raman spectra are specific for each cell type and provide additional information on cell viability, differentiation status, and tumorigenicity. In tissues, Raman spectroscopy can detect major extracellular matrix components and their secondary structures. Furthermore, the non-invasive characterization of healthy and pathological tissues as well as quality control and process monitoring of in vitro-engineered matrix is possible. This review provides comprehensive insight to the current progress in expanding the applicability of Raman spectroscopy for the characterization of living cells and tissues, and serves as a good reference point for those starting in the field.
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Affiliation(s)
- Eva Brauchle
- Department of Cell and Tissue Engineering, Fraunhofer Institute for Interfacial Engineering and Biotechnology (IGB), Stuttgart, Germany
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45
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Liu F, Zhu Y, Liu Y, Wang X, Ping P, Zhu X, Hu H, Li Z, He L. Real-time Raman microspectroscopy scanning of the single live sperm bound to human zona pellucida. Fertil Steril 2012; 99:684-689.e4. [PMID: 23148927 DOI: 10.1016/j.fertnstert.2012.10.035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 10/18/2012] [Accepted: 10/21/2012] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To determine if Raman microspectroscopy (RMS) can distinguish sperm bound to the human zona pellucida (ZP) from those unbound sperm. DESIGN Paired experiments to compare Raman scanning features of ZP-bound and unbound sperm. SETTING Public hospital-based clinical assisted reproduction center. PATIENT(S) Sperm samples from ten fertile donors were used in this study. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Sperm-ZP binding, ZP-induced acrosome reaction, and scanning intensity of various regions of sperm. RESULT(S) The RMS found two slightly low-intensity regions (800-900 and 3,200-4,000 cm(-1)) shifted to high-intensity grade at the acrosome region of the ZP-bound sperm compared with unbound sperm. Moreover, principal component analysis and statistical analysis showed that the RMS can distinguish the ZP-bound sperm from the unbound sperm. CONCLUSION(S) RMS scanning of single live sperm could be used to distinguish ZP-bound sperm from unbound sperm. Thus, RMS may be a useful tool to detect normal functional sperm and to select sperm for intracytoplasmic sperm injection.
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Affiliation(s)
- Feng Liu
- Department of Urology, Renji Hospital, Shanghai Human Sperm Bank, Sperm Development and Genetics Laboratory, Shanghai Institute of Andrology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
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Raman spectroscopy as a potential tool for detection of Brucella spp. in milk. Appl Environ Microbiol 2012; 78:5575-83. [PMID: 22660699 DOI: 10.1128/aem.00637-12] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Detection of Brucella, causing brucellosis, is very challenging, since the applied techniques are mostly time-demanding and not standardized. While the common detection system relies on the cultivation of the bacteria, further classical typing up to the biotype level is mostly based on phenotypic or genotypic characteristics. The results of genotyping do not always fit the existing taxonomy, and misidentifications between genetically closely related genera cannot be avoided. This situation gets even worse, when detection from complex matrices, such as milk, is necessary. For these reasons, the availability of a method that allows early and reliable identification of possible Brucella isolates for both clinical and epidemiological reasons would be extremely useful. We evaluated micro-Raman spectroscopy in combination with chemometric analysis to identify Brucella from agar plates and directly from milk: prior to these studies, the samples were inactivated via formaldehyde treatment to ensure a higher working safety. The single-cell Raman spectra of different Brucella, Escherichia, Ochrobactrum, Pseudomonas, and Yersinia spp. were measured to create two independent databases for detection in media and milk. Identification accuracies of 92% for Brucella from medium and 94% for Brucella from milk were obtained while analyzing the single-cell Raman spectra via support vector machine. Even the identification of the other genera yielded sufficient results, with accuracies of >90%. In summary, micro-Raman spectroscopy is a promising alternative for detecting Brucella. The measurements we performed at the single-cell level thus allow fast identification within a few hours without a demanding process for sample preparation.
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47
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A study of Docetaxel-induced effects in MCF-7 cells by means of Raman microspectroscopy. Anal Bioanal Chem 2012; 403:745-53. [PMID: 22399121 PMCID: PMC3336052 DOI: 10.1007/s00216-012-5887-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Revised: 02/15/2012] [Accepted: 02/17/2012] [Indexed: 11/13/2022]
Abstract
Chemotherapies feature a low success rate of about 25%, and therefore, the choice of the most effective cytostatic drug for the individual patient and monitoring the efficiency of an ongoing chemotherapy are important steps towards personalized therapy. Thereby, an objective method able to differentiate between treated and untreated cancer cells would be essential. In this study, we provide molecular insights into Docetaxel-induced effects in MCF-7 cells, as a model system for adenocarcinoma, by means of Raman microspectroscopy combined with powerful chemometric methods. The analysis of the Raman data is divided into two steps. In the first part, the morphology of cell organelles, e.g. the cell nucleus has been visualized by analysing the Raman spectra with k-means cluster analysis and artificial neural networks and compared to the histopathologic gold standard method hematoxylin and eosin staining. This comparison showed that Raman microscopy is capable of displaying the cell morphology; however, this is in contrast to hematoxylin and eosin staining label free and can therefore be applied potentially in vivo. Because Docetaxel is a drug acting within the cell nucleus, Raman spectra originating from the cell nucleus region were further investigated in a next step. Thereby we were able to differentiate treated from untreated MCF-7 cells and to quantify the cell–drug response by utilizing linear discriminant analysis models. Raman microspectroscopy in combination with powerful chemometric methods (e.g. artificial neural networks) indicates morphological (nucleus fragmentation) and spectral changes in Docetaxel treated breast cancer cells (MCF-7) in comparison to untreated cell samples ![]()
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48
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Raman Spectroscopy of Bacterial Species and Strains Cultivated under Reproducible Conditions. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/540490] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Rapid and reproducible discrimination between bacterial pathogens is a clear goal in microbiological laboratories when processing infected clinical samples. In this study Raman spectra were taken from at least 30 colonies of four strains of bacteria includingStaphylococcus epidermidis(1457 and 9142) andEscherichia coli(K12 and Top 10) using the Renishawin ViaRaman microscope system. Analysis based on principal components suggests that even strain differentiation (e.g., 1457 versus 9142 or K12 versus Top10) is possible.
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49
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Raman spectroscopic detection of physiology changes in plasmid-bearing Escherichia coli with and without antibiotic treatment. Anal Bioanal Chem 2011; 400:2763-73. [DOI: 10.1007/s00216-011-4819-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 01/28/2011] [Accepted: 02/16/2011] [Indexed: 11/26/2022]
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50
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Meisel S, Stöckel S, Elschner M, Rösch P, Popp J. Assessment of two isolation techniques for bacteria in milk towards their compatibility with Raman spectroscopy. Analyst 2011; 136:4997-5005. [DOI: 10.1039/c1an15761b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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