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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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Wasim M, Ghaffar U, Javed MR, Nawaz H, Majeed MI, Ijaz A, Ishtiaq S, Rehman N, Razaq R, Younas S, Bano A, Kanwal N, Imran M. Surface-Enhanced Raman Spectroscopy for Monitoring the Biochemical Changes Due to DNA Mutations Induced by CRISPR-Cas9 Genome Editing in the Aspergillus niger Fungus. ACS OMEGA 2024; 9:15202-15209. [PMID: 38585125 PMCID: PMC10993282 DOI: 10.1021/acsomega.3c09563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/22/2024] [Accepted: 03/04/2024] [Indexed: 04/09/2024]
Abstract
In this study, surface-enhanced Raman spectroscopy (SERS) technique, along with principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA), is used as a simple, quick, and cost-effective analysis method for identifying biochemical changes occurring due to induced mutations in the Aspergillus niger fungus strain. The goal of this study is to identify the biochemical changes in the mutated fungal cells (cell mass) as compared to the control/nonmutated cells. Furthermore, multivariate data analysis tools, including PCA and PLS-DA, are used to further confirm the differentiating SERS spectral features among fungal samples. The mutations are caused in A. niger by the clustered regularly interspaced palindromic repeat CRISPR-Cas9 genomic editing method to improve their biotechnological potential for the production of cellulase enzyme. SERS was employed to detect the changes in the cells of mutated A. niger fungal strains, including one mutant producing low levels of an enzyme and another mutant producing high levels of the enzyme as a result of mutation as compared with an unmutated fungal strain as a control sample. The distinctive features of SERS corresponding to nucleic acids and proteins appear at 546, 622, 655, 738, 802, 835, 959, 1025, 1157, 1245, 1331, 1398, and 1469 cm-1. Furthermore, PLS-DA is used to confirm the 89% accuracy, 87.7% precision, 87% sensitivity, and 88.9% specificity of this method, and the value of the area under the curve (AUROC) is 0.67. It has been shown that surface-enhanced Raman spectroscopy is an effective method for identifying and differentiating biochemical changes in genome-modified fungal samples.
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Affiliation(s)
- Muhammad Wasim
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Usman Ghaffar
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Rizwan Javed
- Biocatalysis
and Protein Engineering Research Group (BPERG), Department of Bioinformatics
and Biotechnology, Government College University
Faisalabad (GCUF), Allama
Iqbal Road, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Irfan Majeed
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Anam Ijaz
- Biocatalysis
and Protein Engineering Research Group (BPERG), Department of Bioinformatics
and Biotechnology, Government College University
Faisalabad (GCUF), Allama
Iqbal Road, Faisalabad 38000, Pakistan
| | - Shazra Ishtiaq
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Nimra Rehman
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Rabeea Razaq
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Sobia Younas
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Aqsa Bano
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Naeema Kanwal
- Department
of Chemistry, University of Agriculture
Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Imran
- Department
of Chemistry, Faculty of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
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3
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Frempong SB, Salbreiter M, Mostafapour S, Pistiki A, Bocklitz TW, Rösch P, Popp J. Illuminating the Tiny World: A Navigation Guide for Proper Raman Studies on Microorganisms. Molecules 2024; 29:1077. [PMID: 38474589 DOI: 10.3390/molecules29051077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 03/14/2024] Open
Abstract
Raman spectroscopy is an emerging method for the identification of bacteria. Nevertheless, a lot of different parameters need to be considered to establish a reliable database capable of identifying real-world samples such as medical or environmental probes. In this review, the establishment of such reliable databases with the proper design in microbiological Raman studies is demonstrated, shining a light into all the parts that require attention. Aspects such as the strain selection, sample preparation and isolation requirements, the phenotypic influence, measurement strategies, as well as the statistical approaches for discrimination of bacteria, are presented. Furthermore, the influence of these aspects on spectra quality, result accuracy, and read-out are discussed. The aim of this review is to serve as a guide for the design of microbiological Raman studies that can support the establishment of this method in different fields.
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Affiliation(s)
- Sandra Baaba Frempong
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Markus Salbreiter
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Sara Mostafapour
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
| | - Aikaterini Pistiki
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Thomas W Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany
- InfectoGnostics Research Campus Jena, Center of Applied Research, Philosophenweg 7, 07743 Jena, Germany
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance-Leibniz Health Technologies, Albert-Einstein-Str. 9, 07745 Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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Rebrosova K, Bernatová S, Šiler M, Mašek J, Samek O, Ježek J, Kizovsky M, Holá V, Zemanek P, Růžička F. Rapid Identification of Pathogens Causing Bloodstream Infections by Raman Spectroscopy and Raman Tweezers. Microbiol Spectr 2023; 11:e0002823. [PMID: 37078868 PMCID: PMC10269886 DOI: 10.1128/spectrum.00028-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/24/2023] [Indexed: 04/21/2023] Open
Abstract
The search for the "Holy Grail" in clinical diagnostic microbiology-a reliable, accurate, low-cost, real-time, easy-to-use method-has brought up several methods with the potential to meet these criteria. One is Raman spectroscopy, an optical, nondestructive method based on the inelastic scattering of monochromatic light. The current study focuses on the possible use of Raman spectroscopy for identifying microbes causing severe, often life-threatening bloodstream infections. We included 305 microbial strains of 28 species acting as causative agents of bloodstream infections. Raman spectroscopy identified the strains from grown colonies, with 2.8% and 7% incorrectly identified strains using the support vector machine algorithm based on centered and uncentred principal-component analyses, respectively. We combined Raman spectroscopy with optical tweezers to speed up the process and captured and analyzed microbes directly from spiked human serum. The pilot study suggests that it is possible to capture individual microbial cells from human serum and characterize them by Raman spectroscopy with notable differences among different species. IMPORTANCE Bloodstream infections are among the most common causes of hospitalizations and are often life-threatening. To establish an effective therapy for a patient, the timely identification of the causative agent and characterization of its antimicrobial susceptibility and resistance profiles are essential. Therefore, our multidisciplinary team of microbiologists and physicists presents a method that reliably, rapidly, and inexpensively identifies pathogens causing bloodstream infections-Raman spectroscopy. We believe that it might become a valuable diagnostic tool in the future. Combined with optical trapping, it offers a new approach where the microorganisms are individually trapped in a noncontact way by optical tweezers and investigated by Raman spectroscopy directly in a liquid sample. Together with the automatic processing of measured Raman spectra and comparison with a database of microorganisms, it makes the whole identification process almost real time.
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Affiliation(s)
- Katarina Rebrosova
- Department of Microbiology, Faculty of Medicine of Masaryk University, St. Anne’s University Hospital, Brno, Czech Republic
| | - Silvie Bernatová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Martin Šiler
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Mašek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Jan Ježek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Martin Kizovsky
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Veronika Holá
- Department of Microbiology, Faculty of Medicine of Masaryk University, St. Anne’s University Hospital, Brno, Czech Republic
| | - Pavel Zemanek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Filip Růžička
- Department of Microbiology, Faculty of Medicine of Masaryk University, St. Anne’s University Hospital, Brno, Czech Republic
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5
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Liu Z, Xue Y, Yang C, Li B, Zhang Y. Rapid identification and drug resistance screening of respiratory pathogens based on single-cell Raman spectroscopy. Front Microbiol 2023; 14:1065173. [PMID: 36778844 PMCID: PMC9909742 DOI: 10.3389/fmicb.2023.1065173] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
Respiratory infections rank fourth in the global economic burden of disease. Lower respiratory tract infections are the leading cause of death in low-income countries. The rapid identification of pathogens causing lower respiratory tract infections to help guide the use of antibiotics can reduce the mortality of patients with lower respiratory tract infections. Single-cell Raman spectroscopy is a "whole biological fingerprint" technique that can be used to identify microbial samples. It has the advantages of no marking and fast and non-destructive testing. In this study, single-cell Raman spectroscopy was used to collect spectral data of six respiratory tract pathogen isolates. The T-distributed stochastic neighbor embedding (t-SNE) isolation analysis algorithm was used to compare the differences between the six respiratory tract pathogens. The eXtreme Gradient Boosting (XGBoost) algorithm was used to establish a Raman phenotype database model. The classification accuracy of the isolated samples was 93-100%, and the classification accuracy of the clinical samples was more than 80%. Combined with heavy water labeling technology, the drug resistance of respiratory tract pathogens was determined. The study showed that single-cell Raman spectroscopy-D2O (SCRS-D2O) labeling could rapidly identify the drug resistance of respiratory tract pathogens within 2 h.
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Affiliation(s)
- Ziyu Liu
- Department of Pediatric Respiratory, The First Hospital of Jilin University, Changchun, China,School of Life Science, Jilin University, Changchun, China
| | - Ying Xue
- HOOKE Instruments Ltd., Changchun, China
| | - Chun Yang
- Department of Laboratory Medicine, First Hospital of Jilin University, Changchun, Jilin, China
| | - Bei Li
- HOOKE Instruments Ltd., Changchun, China,The State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences (CAS), Changchun, China
| | - Ying Zhang
- Department of Pediatric Respiratory, The First Hospital of Jilin University, Changchun, China,*Correspondence: Ying Zhang ✉
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6
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Wang J, Meng S, Lin K, Yi X, Sun Y, Xu X, He N, Zhang Z, Hu H, Qie X, Zhang D, Tang Y, Huang WE, He J, Song Y. Leveraging single-cell Raman spectroscopy and single-cell sorting for the detection and identification of yeast infections. Anal Chim Acta 2023; 1239:340658. [PMID: 36628751 DOI: 10.1016/j.aca.2022.340658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
Invasive fungal infection serves as a great threat to human health. Discrimination between fungal and bacterial infections at the earliest stage is vital for effective clinic practice; however, traditional culture-dependent microscopic diagnosis of fungal infection usually requires several days, meanwhile, culture-independent immunological and molecular methods are limited by the detectable type of pathogens and the issues with high false-positive rates. In this study, we proposed a novel culture-independent phenotyping method based on single-cell Raman spectroscopy for the rapid discrimination between fungal and bacterial infections. Three Raman biomarkers, including cytochrome c, peptidoglycan, and nucleic acid, were identified through hierarchical clustering analysis of Raman spectra across 12 types of most common yeast and bacterial pathogens. Compared to those of bacterial pathogens, the single cells of yeast pathogens demonstrated significantly stronger Raman peaks for cytochrome c, but weaker signals for peptidoglycan and nucleic acid. A two-step protocol combining the three biomarkers was established and able to differentiate fungal infections from bacterial infections with an overall accuracy of 94.9%. Our approach was also used to detect ten raw urinary tract infection samples. Successful identification of fungi was achieved within half an hour after sample obtainment. We further demonstrated the accurate fungal species taxonomy achieved with Raman-assisted cell ejection. Our findings demonstrate that Raman-based fungal identification is a novel, facile, reliable, and with a breadth of coverage approach, that has a great potential to be adopted in routine clinical practice to reduce the turn-around time of invasive fungal disease (IFD) diagnostics.
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Affiliation(s)
- Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Kaicheng Lin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaofei Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yixiang Sun
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Na He
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhiqiang Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Huijie Hu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Xingwang Qie
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jian He
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China.
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7
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Bari RZA, Nawaz H, Majeed MI, Rashid N, Tahir M, ul Hasan HM, Ishtiaq S, Sadaf N, Raza A, Zulfiqar A, Rehman AU, Shahid M. Characterization of Bacteria Inducing Chronic Sinusitis Using Surface-Enhanced Raman Spectroscopy (SERS) with Multivariate Data Analysis. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2130349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Rana Zaki Abdul Bari
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad, Pakistan
| | - Muhammad Tahir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Shazra Ishtiaq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Nimra Sadaf
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ali Raza
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Anam Zulfiqar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Aziz ur Rehman
- Department of Chemistry, Government College University Lahore, Lahore, Pakistan
| | - Muhammad Shahid
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
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8
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Mushtaq A, Nawaz H, Irfan Majeed M, Rashid N, Tahir M, Zaman Nawaz M, Shahzad K, Dastgir G, Zaki Abdul Bari R, Ul Haq A, Saleem M, Akhtar F. Surface-enhanced Raman spectroscopy (SERS) for monitoring colistin-resistant and susceptible E. coli strains. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121315. [PMID: 35576839 DOI: 10.1016/j.saa.2022.121315] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/21/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
The emergence of drug-resistant bacteria is a precarious global health concern. In this study, surface-enhanced Raman spectroscopy (SERS) is used to characterize colistin-resistant and susceptible E. coli strains based on their distinguished SERS spectral features for the development of rapid and cost-effective detection and differentiation methods. For this purpose, three colistin-resistant and three colistin susceptible E. coli strains were analyzed by comparing their SERS spectral signatures. Moreover, multivariate data analysis techniques including Principal component analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) were used to examine the SERS spectral data of colistin-resistant and susceptible strains. PCA technique was employed for differentiating colistin susceptible and resistant E.coli strains due to alteration in biochemical compositions of the bacterial cell. PLS-DA is employed on SERS spectral data sets for discrimination of these resistant and susceptible E. coli strains with 100% specificity, 100% accuracy, 99.8% sensitivity, and 86% area under receiver operating characteristics (AUROC) curve.
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Affiliation(s)
- Aqsa Mushtaq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad 38000, Pakistan.
| | - Muhammad Tahir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Zaman Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Kashif Shahzad
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ghulam Dastgir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Rana Zaki Abdul Bari
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Anwar Ul Haq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Mudassar Saleem
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Farwa Akhtar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
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9
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Saikia D, Jadhav P, Hole AR, Krishna CM, Singh SP. Growth Kinetics Monitoring of Gram-Negative Pathogenic Microbes Using Raman Spectroscopy. APPLIED SPECTROSCOPY 2022; 76:1263-1271. [PMID: 35694822 DOI: 10.1177/00037028221109624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Optical density based measurements are routinely performed to monitor the growth of microbes. These measurements solely depend upon the number of cells and do not provide any information about the changes in the biochemical milieu or biological status. An objective information about these parameters is essential for evaluation of novel therapies and for maximizing the metabolite production. In the present study, we have applied Raman spectroscopy to monitor growth kinetics of three different pathogenic Gram-negative microbes Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii. Spectral measurements were performed under 532 nm excitation with 5 seconds of exposure time. Spectral features suggest temporal changes in the "peptide" and "nucleic acid" content of cells under different growth stages. Using principal component analysis (PCA), successful discrimination between growth phases was also achieved. Overall, the findings are supportive of the prospective adoption of Raman based approaches for monitoring microbial growth.
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Affiliation(s)
- Dimple Saikia
- Department of Biosciences and Bioengineering, 477529Indian Institute of Technology Dharwad, Dharwad, India
| | - Priyanka Jadhav
- Tata Memorial Centre, 29435Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
- Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, India
| | - Arti R Hole
- Tata Memorial Centre, 29435Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
| | - Chilakapati Murali Krishna
- Tata Memorial Centre, 29435Advanced Centre for Treatment Research and Education in Cancer, Navi Mumbai, India
- Training School Complex, Homi Bhabha National Institute, Anushakti Nagar, India
| | - Surya P Singh
- Department of Biosciences and Bioengineering, 477529Indian Institute of Technology Dharwad, Dharwad, India
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10
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Benladghem Z, Seddiki SML, Dergal F, Mahdad YM, Aissaoui M, Choukchou-Braham N. Biofouling of reverse osmosis membranes: assessment by surface-enhanced Raman spectroscopy and microscopic imaging. BIOFOULING 2022; 38:852-864. [PMID: 36314078 DOI: 10.1080/08927014.2022.2139610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 05/26/2023]
Abstract
The decline in the performance of spiral-wound reverse osmosis (SWRO) membranes is frequently due to biofouling. This study focus on qualitative and quantitative diagnosis of SWRO membrane biofouling. Bacterial counts on the different surfaces of the fouled membranes were carried out. Surface enhanced Raman spectroscopy (SERS) was performed to highlight clogging materials as well as their natures and identity. The topography of the fouled membranes and the structures of biofilms were visualized by fluorescence microscopy (FM) and scanning electron microscopy (SEM). The results indicated the presence of bacteria in the different SWRO membrane areas. Those strongly adhered were significantly higher than those weakly. It varied between 26 × 105 and 262 × 105 CFU m-2. However, SERS mapping showed different fouling levels and the thickness of the fouling layer was 5 µm. Microscopic imaging revealed biotic and abiotic deposits. These data can together allow better management of the seawater desalination process.
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Affiliation(s)
- Zakaria Benladghem
- Antifungal Antibiotic: Physico-Chemical Synthesis and Biological Activity laboratory, Biology department, University of Tlemcen, Tlemcen, Algeria
| | - Sidi Mohammed Lahbib Seddiki
- Antifungal Antibiotic: Physico-Chemical Synthesis and Biological Activity laboratory, Biology department, University of Tlemcen, Tlemcen, Algeria
- Laboratory for Sustainable Management of Natural Resources in Arid and Semi-Arid Areas, University Center of Naâma, Naâma, Algeria
| | - Fayçal Dergal
- Scientific and Technical Research Center in Physico-Chemical Analysis, Tipaza, Algeria
- Laboratory of Catalysis and Synthesis in Organic Chemistry, Faculty of Sciences, University of Tlemcen, Algeria
| | - Yassine Moustafa Mahdad
- Laboratory for Sustainable Management of Natural Resources in Arid and Semi-Arid Areas, University Center of Naâma, Naâma, Algeria
- Department of Physiology, Physiopathology and Biochemistry of Nutrition, University of Tlemcen, Tlemcen, Algeria
| | - Mohammed Aissaoui
- Department of Biology, Faculty of Sciences and Technology, University of Tamanghasset, Tamanghasset, Algeria
| | - Noureddine Choukchou-Braham
- Laboratory of Catalysis and Synthesis in Organic Chemistry, Faculty of Sciences, University of Tlemcen, Algeria
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11
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Rebrosova K, Samek O, Kizovsky M, Bernatova S, Hola V, Ruzicka F. Raman Spectroscopy—A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings. Front Cell Infect Microbiol 2022; 12:866463. [PMID: 35531343 PMCID: PMC9072635 DOI: 10.3389/fcimb.2022.866463] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/02/2022] Open
Abstract
Rapid and accurate identification of pathogens causing infections is one of the biggest challenges in medicine. Timely identification of causative agents and their antimicrobial resistance profile can significantly improve the management of infection, lower costs for healthcare, mitigate ever-growing antimicrobial resistance and in many cases, save lives. Raman spectroscopy was shown to be a useful—quick, non-invasive, and non-destructive —tool for identifying microbes from solid and liquid media. Modifications of Raman spectroscopy and/or pretreatment of samples allow single-cell analyses and identification of microbes from various samples. It was shown that those non-culture-based approaches could also detect antimicrobial resistance. Moreover, recent studies suggest that a combination of Raman spectroscopy with optical tweezers has the potential to identify microbes directly from human body fluids. This review aims to summarize recent advances in non-culture-based approaches of identification of microbes and their virulence factors, including antimicrobial resistance, using methods based on Raman spectroscopy in the context of possible use in the future point-of-care diagnostic process.
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Affiliation(s)
- Katarina Rebrosova
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Martin Kizovsky
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Silvie Bernatova
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czechia
| | - Veronika Hola
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
- *Correspondence: Veronika Hola,
| | - Filip Ruzicka
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne’s University Hospital, Brno, Czechia
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12
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Rebrošová K, Bernatová S, Šiler M, Uhlirova M, Samek O, Ježek J, Holá V, Růžička F, Zemanek P. Raman spectroscopy-a tool for rapid differentiation among microbes causing urinary tract infections. Anal Chim Acta 2022; 1191:339292. [PMID: 35033248 DOI: 10.1016/j.aca.2021.339292] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/20/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022]
Abstract
Urinary tract infections belong to the most common infections in the world. Besides community-acquired infections, nosocomial infections pose a high risk especially for patients having indwelling catheters, undergoing urological surgeries or staying at hospital for prolonged time. They can be often complicated by antimicrobial resistance and/or biofilm formation. Therefore, a rapid diagnostic tool enabling timely identification of a causative agent and its susceptibility to antimicrobials is a need. Raman spectroscopy appears to be a suitable method that allows rapid differentiation among microbes and provides a space for further analyses, such as determination of capability of biofilm formation or antimicrobial susceptibility/resistance in tested strains. Our work here presents a possibility to differ among most common microbes causing urinary tract infections (belonging to 20 species). We tested 254 strains directly from colonies grown on Mueller-Hinton agar plates. The results show that it is possible to distinguish among the tested species using Raman spectroscopy, which proves its great potential for future use in clinical diagnostics. Moreover, we present here a pilot study of a real-time analysis and identification (in less than 10 min) of single microbial cells directly in urine employing optical tweezers combined with Raman spectroscopy.
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Affiliation(s)
- Katarína Rebrošová
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne's, University Hospital, Pekařská 53, Brno, 65691, Czech Republic.
| | - Silvie Bernatová
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno, 61264, Czech Republic.
| | - Martin Šiler
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno, 61264, Czech Republic.
| | - Magdalena Uhlirova
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic, Palackého tř. 1946/1, 612 42, Brno, Czech Republic.
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno, 61264, Czech Republic.
| | - Jan Ježek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno, 61264, Czech Republic.
| | - Veronika Holá
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne's, University Hospital, Pekařská 53, Brno, 65691, Czech Republic
| | - Filip Růžička
- Department of Microbiology, Faculty of Medicine of Masaryk University and St. Anne's, University Hospital, Pekařská 53, Brno, 65691, Czech Republic
| | - Pavel Zemanek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno, 61264, Czech Republic.
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13
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Kuzma BA, Pence IJ, Greenfield DA, Ho A, Evans CL. Visualizing and quantifying antimicrobial drug distribution in tissue. Adv Drug Deliv Rev 2021; 177:113942. [PMID: 34437983 DOI: 10.1016/j.addr.2021.113942] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022]
Abstract
The biodistribution and pharmacokinetics of drugs are vital to the mechanistic understanding of their efficacy. Measuring antimicrobial drug efficacy has been challenging as plasma drug concentration is used as a surrogate for tissue drug concentration, yet typically does not reflect that at the intended site(s) of action. Utilizing an image-guided approach, it is feasible to accurately quantify the biodistribution and pharmacokinetics within the desired site(s) of action. We outline imaging modalities used in visualizing drug distribution with examples ranging from in vitro cellular drug uptake to clinical treatment of microbial infections. The imaging modalities of interest are: radio-labeling, magnetic resonance, mass spectrometry imaging, computed tomography, fluorescence, and Raman spectroscopy. We outline the progress, limitations, and future outlook for each methodology. Further advances in these optical approaches would benefit patients and researchers alike, as non-invasive imaging could yield more profound insights with a lower clinical burden than invasive measurement approaches used today.
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Affiliation(s)
- Benjamin A Kuzma
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
| | - Isaac J Pence
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
| | - Daniel A Greenfield
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
| | - Alexander Ho
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA
| | - Conor L Evans
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston 02114, USA.
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14
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Wang L, Liu W, Tang JW, Wang JJ, Liu QH, Wen PB, Wang MM, Pan YC, Gu B, Zhang X. Applications of Raman Spectroscopy in Bacterial Infections: Principles, Advantages, and Shortcomings. Front Microbiol 2021; 12:683580. [PMID: 34349740 PMCID: PMC8327204 DOI: 10.3389/fmicb.2021.683580] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/17/2021] [Indexed: 12/13/2022] Open
Abstract
Infectious diseases caused by bacterial pathogens are important public issues. In addition, due to the overuse of antibiotics, many multidrug-resistant bacterial pathogens have been widely encountered in clinical settings. Thus, the fast identification of bacteria pathogens and profiling of antibiotic resistance could greatly facilitate the precise treatment strategy of infectious diseases. So far, many conventional and molecular methods, both manual or automatized, have been developed for in vitro diagnostics, which have been proven to be accurate, reliable, and time efficient. Although Raman spectroscopy (RS) is an established technique in various fields such as geochemistry and material science, it is still considered as an emerging tool in research and diagnosis of infectious diseases. Based on current studies, it is too early to claim that RS may provide practical guidelines for microbiologists and clinicians because there is still a gap between basic research and clinical implementation. However, due to the promising prospects of label-free detection and noninvasive identification of bacterial infections and antibiotic resistance in several single steps, it is necessary to have an overview of the technique in terms of its strong points and shortcomings. Thus, in this review, we went through recent studies of RS in the field of infectious diseases, highlighting the application potentials of the technique and also current challenges that prevent its real-world applications.
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Affiliation(s)
- Liang Wang
- Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Wei Liu
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Jia-Wei Tang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Jun-Jiao Wang
- 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
| | - Peng-Bo Wen
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
| | - Meng-Meng Wang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, Xuzhou, China
| | - Ya-Cheng Pan
- School of Life Sciences, Xuzhou Medical University, Xuzhou, China
| | - Bing Gu
- Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiao Zhang
- Department of Bioinformatics, School of Medical Informatics and Engineering, Xuzhou Medical University, Xuzhou, China
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15
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Kochan K, Bedolla DE, Perez-Guaita D, Adegoke JA, Chakkumpulakkal Puthan Veettil T, Martin M, Roy S, Pebotuwa S, Heraud P, Wood BR. Infrared Spectroscopy of Blood. APPLIED SPECTROSCOPY 2021; 75:611-646. [PMID: 33331179 DOI: 10.1177/0003702820985856] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The magnitude of infectious diseases in the twenty-first century created an urgent need for point-of-care diagnostics. Critical shortages in reagents and testing kits have had a large impact on the ability to test patients with a suspected parasitic, bacteria, fungal, and viral infections. New point-of-care tests need to be highly sensitive, specific, and easy to use and provide results in rapid time. Infrared spectroscopy, coupled to multivariate and machine learning algorithms, has the potential to meet this unmet demand requiring minimal sample preparation to detect both pathogenic infectious agents and chronic disease markers in blood. This focal point article will highlight the application of Fourier transform infrared spectroscopy to detect disease markers in blood focusing principally on parasites, bacteria, viruses, cancer markers, and important analytes indicative of disease. Methodologies and state-of-the-art approaches will be reported and potential confounding variables in blood analysis identified. The article provides an up to date review of the literature on blood diagnosis using infrared spectroscopy highlighting the recent advances in this burgeoning field.
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Affiliation(s)
- Kamila Kochan
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Diana E Bedolla
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - David Perez-Guaita
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - John A Adegoke
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | | | - Miguela Martin
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Supti Roy
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Savithri Pebotuwa
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Philip Heraud
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Bayden R Wood
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
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16
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Confield LR, Black GP, Wilson BC, Lowe DJ, Theakstone AG, Baker MJ. Vibrational spectroscopic analysis of blood for diagnosis of infections and sepsis: a review of requirements for a rapid diagnostic test. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:157-168. [PMID: 33284291 DOI: 10.1039/d0ay01991g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Infections and sepsis represent a growing global burden. There is a widespread clinical need for a rapid, high-throughput and sensitive technique for the diagnosis of infections and detection of invading pathogens and the presence of sepsis. Current diagnostic methods primarily consist of laboratory-based haematology, biochemistry and microbiology that are time consuming, labour- and resource-intensive, and prone to both false positive and false negative results. Current methods are insufficient for the increasing demands on healthcare systems, causing delays in diagnosis and initiation of treatment, due to the intrinsic time delay in sample preparation, measurement, and analysis. Vibrational spectroscopic techniques can overcome these limitations by providing a rapid, label-free and low-cost method for blood analysis, with limited sample preparation required, potentially revolutionising clinical diagnostics by producing actionable results that enable early diagnosis, leading to improved patient outcomes. This review will discuss the challenges associated with the diagnosis of infections and sepsis, primarily within the UK healthcare system. We will consider the clinical potential of spectroscopic point-of-care technologies to enable blood analysis in the primary-care setting.
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Affiliation(s)
- L R Confield
- CDT Medical Devices, Department of Biomedical Engineering, Wolfson Centre, 106 Rottenrow, G4 0NW, UK
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17
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AlMasoud N, Muhamadali H, Chisanga M, AlRabiah H, Lima CA, Goodacre R. Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing. Analyst 2021; 146:770-788. [DOI: 10.1039/d0an01482f] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.
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Affiliation(s)
- Najla AlMasoud
- Department of Chemistry
- College of Science
- Princess Nourah bint Abdulrahman University
- Riyadh 11671
- Saudi Arabia
| | - Howbeer Muhamadali
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Malama Chisanga
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Haitham AlRabiah
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Cassio A. Lima
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
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18
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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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19
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Shahid S, Razzaq S, Farooq R, Nazli ZIH. Polyhydroxyalkanoates: Next generation natural biomolecules and a solution for the world's future economy. Int J Biol Macromol 2020; 166:297-321. [PMID: 33127548 DOI: 10.1016/j.ijbiomac.2020.10.187] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 02/08/2023]
Abstract
Petrochemical plastics have become a cause of pollution for decades and finding alternative plastics that are environmental friendly. Polyhydroxyalkanoate (PHA), a biopolyester produced by microbial cells, has characteristics (biocompatible, biodegradable, non-toxic) that make it appropriate as a biodegradable plastic substance. The different forms of PHA make it suitable to a wide choice of products, from packaging materials to biomedical applications. The major challenge in commercialization of PHA is the cost of manufacturing. There are a lot of factors that could affect the efficiency of a development method. The development of new strategic parameters for better synthesis, including consumption of low cost carbon substrates, genetic modification of PHA-producing strains, and fermentational strategies are discussed. Recently, many efforts have been made to develop a method for the cost-effective production of PHAs. The isolation, analysis as well as characterization of PHAs are significant factors for any developmental process. Due to the biodegradable and biocompatible properties of PHAs, they are majorly used in biomedical applications such as vascular grafting, heart tissue engineering, skin tissue repairing, liver tissue engineering, nerve tissue engineering, bone tissue engineering, cartilage tissue engineering and therapeutic carrier. The emerging and interesting area of research is the development of self-healing biopolymer that could significantly broaden the operational life and protection of the polymeric materials for a broad range of uses. Biodegradable and biocompatible polymers are considered as the green materials in place of petroleum-based plastics in the future.
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Affiliation(s)
- Salma Shahid
- Department of Biochemistry, Government College Women University Faisalabad, Pakistan.
| | - Sadia Razzaq
- Department of Chemistry, Government College Women University Faisalabad, Pakistan
| | - Robina Farooq
- Department of Chemistry, Government College Women University Faisalabad, Pakistan
| | - Zill-I-Huma Nazli
- Department of Chemistry, Government College Women University Faisalabad, Pakistan
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20
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Jin Z, Xie L, Zhang T, Liu L, Black T, Jones KC, Zhang H, Wang X, Jin N, Zhang D. Interrogating cadmium and lead biosorption mechanisms by Simplicillium chinense via infrared spectroscopy. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 263:114419. [PMID: 32220774 DOI: 10.1016/j.envpol.2020.114419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/29/2020] [Accepted: 03/18/2020] [Indexed: 06/10/2023]
Abstract
Fungi-associated phytoremediation is an environmentally friendly and cost-efficient approach to remove potential toxic elements (PTEs) from contaminated soils. Many fungal strains have been reported to possess PTE-biosorption behaviour which benefits phytoremediation performance. Nevertheless, most studies are limited in rich or defined medium, far away from the real-world scenarios where nutrients are deficient. Understanding fungal PTE-biosorption performance and influential factors in soil environment can expand their application potential and is urgently needed. This study applied attenuated total reflection Fourier-transform infrared (ATR-FTIR) coupled with phenotypic microarrays to study the biospectral alterations of a fungal strain Simplicillium chinense QD10 and explore the mechanisms of Cd and Pb biosorption. Both Cd and Pb were efficiently adsorbed by S. chinense QD10 cultivated with 48 different carbon sources and the biosorption efficiency achieved >90%. As the first study using spectroscopic tools to analyse PTE-biosorption by fungal cells in a high-throughput manner, our results indicated that spectral biomarkers associated with phosphor-lipids and proteins (1745 cm-1, 1456 cm-1 and 1396 cm-1) were significantly correlated with Cd biosorption, suggesting the cell wall components of S. chinense QD10 as the primary interactive targets. In contrast, there was no any spectral biomarker associated with Pb biosorption. Addtionally, adsorption isotherms evidenced a Langmuir model for Cd biosorption but a Freundlich model for Pb biosorption. Accordingly, Pb and Cd biosorption by S. chinense QD10 followed discriminating mechanisms, specific adsorption on cell membrane for Cd and unspecific extracellular precipitation for Pb. This work lends new insights into the mechanisms of PTE-biosorption via IR spectrochemical tools, which provide more comprehensive clues for biosorption behaviour with a nondestructive and high-throughput manner solving the traditional technical barrier regarding the real-world scenarios.
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Affiliation(s)
- Zhongmin Jin
- College of Agriculture, Forestry and Life Science, Qiqihar University, Qiqihar, 161006, PR China; Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Lin Xie
- College of Agriculture, Forestry and Life Science, Qiqihar University, Qiqihar, 161006, PR China
| | - Tuo Zhang
- College of Environmental Science and Engineering, China West Normal University, Nanchong, 637002, PR China
| | - Lijie Liu
- College of Agriculture, Forestry and Life Science, Qiqihar University, Qiqihar, 161006, PR China
| | - Tom Black
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Hao Zhang
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Xinzi Wang
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Naifu Jin
- School of Environment, Tsinghua University, Beijing, 100084, PR China
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, 100084, PR China.
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21
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Mehta M, Liu Y, Waterland M, Holmes G. Characterization of the Degradation of Sheepskin by Monitoring Cytochrome c of Bacteria by Raman Spectroscopy. ANAL LETT 2020. [DOI: 10.1080/00032719.2020.1792476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Megha Mehta
- New Zealand Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
| | - Yang Liu
- New Zealand Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
| | - Mark Waterland
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Geoff Holmes
- New Zealand Leather and Shoe Research Association (LASRA®), Palmerston North, New Zealand
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22
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Kochan K, Lai E, Richardson Z, Nethercott C, Peleg AY, Heraud P, Wood BR. Vibrational Spectroscopy as a Sensitive Probe for the Chemistry of Intra-Phase Bacterial Growth. SENSORS 2020; 20:s20123452. [PMID: 32570941 PMCID: PMC7348983 DOI: 10.3390/s20123452] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/05/2020] [Accepted: 06/15/2020] [Indexed: 01/22/2023]
Abstract
Bacterial growth in batch cultures occurs in four phases (lag, exponential/log, stationary and death phase) that differ distinctly in number of different bacteria, biochemistry and physiology. Knowledge regarding the growth phase and its kinetics is essential for bacterial research, especially in taxonomic identification and monitoring drug interactions. However, the conventional methods by which to assess microbial growth are based only on cell counting or optical density, without any insight into the biochemistry of cells or processes. Both Raman and Fourier transform infrared (FTIR) spectroscopy have shown potential to determine the chemical changes occurring between different bacterial growth phases. Here, we extend the application of spectroscopy and for the first time combine both Raman and FTIR microscopy in a multimodal approach to detect changes in the chemical compositions of bacteria within the same phase (intra-phase). We found a number of spectral markers associated with nucleic acids (IR: 964, 1082, 1215 cm−1; RS: 785, 1483 cm−1), carbohydrates (IR: 1035 cm−1; RS: 1047 cm−1) and proteins (1394 cm−1, amide II) reflecting not only inter-, but also intra-phase changes in bacterial chemistry. Principal component analysis performed simultaneously on FTIR and Raman spectra enabled a clear-cut, time-dependent discrimination between intra-lag phase bacteria probed every 30 min. This demonstrates the unique capability of multimodal vibrational spectroscopy to probe the chemistry of bacterial growth even at the intra-phase level, which is particularly important for the lag phase, where low bacterial numbers limit conventional analytical approaches.
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Affiliation(s)
- Kamila Kochan
- Centre for Biospectroscopy and School of Chemistry, Clayton Campus, Monash University, Clayton, VIC 3800, Australia; (E.L.); (Z.R.); (P.H.)
- Correspondence: (K.K.); (B.R.W.)
| | - Elizabeth Lai
- Centre for Biospectroscopy and School of Chemistry, Clayton Campus, Monash University, Clayton, VIC 3800, Australia; (E.L.); (Z.R.); (P.H.)
| | - Zack Richardson
- Centre for Biospectroscopy and School of Chemistry, Clayton Campus, Monash University, Clayton, VIC 3800, Australia; (E.L.); (Z.R.); (P.H.)
| | - Cara Nethercott
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Clayton Campus, Monash University, Clayton, VIC 3800, Australia; (C.N.); (A.Y.P.)
| | - Anton Y. Peleg
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Clayton Campus, Monash University, Clayton, VIC 3800, Australia; (C.N.); (A.Y.P.)
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, VIC 3004, Australia
| | - Philip Heraud
- Centre for Biospectroscopy and School of Chemistry, Clayton Campus, Monash University, Clayton, VIC 3800, Australia; (E.L.); (Z.R.); (P.H.)
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Clayton Campus, Monash University, Clayton, VIC 3800, Australia; (C.N.); (A.Y.P.)
| | - Bayden R. Wood
- Centre for Biospectroscopy and School of Chemistry, Clayton Campus, Monash University, Clayton, VIC 3800, Australia; (E.L.); (Z.R.); (P.H.)
- Correspondence: (K.K.); (B.R.W.)
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Biochemical characterization of pathogenic bacterial species using Raman spectroscopy and discrimination model based on selected spectral features. Lasers Med Sci 2020; 36:289-302. [PMID: 32500291 DOI: 10.1007/s10103-020-03028-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 04/22/2020] [Indexed: 01/09/2023]
Abstract
This study aimed to evaluate the differences in the Raman spectra of nine clinical species of bacteria isolated from infections (three Gram-positive and six Gram-negative species), correlating the spectra with the chemical composition of each species and to develop a classification model through discriminant analysis to categorize each bacterial strain using the peaks with the most significant differences. Bacteria were cultured in Mueller Hinton agar and a sample of biomass was harvested and placed in an aluminum sample holder. A total of 475 spectra from 115 different strains were obtained through a dispersive Raman spectrometer (830 nm) with exposure time of 50 s. The intensities of the peaks were evaluated by one-way analysis of variance (ANOVA) and the peaks with significant differences were related to the differences in the biochemical composition of the strains. Discriminant analysis based on quadratic distance applied to the peaks with the most significant differences and partial least squares applied to the whole spectrum showed 89.5% and 90.1% of global accuracy, respectively, for classification of the spectra in all the groups. Raman spectroscopy could be a promising technique to identify spectral differences related to the biochemical content of pathogenic microorganisms and to provide a faster diagnosis of infectious diseases.
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24
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Kumar S, Gopinathan R, Chandra GK, Umapathy S, Saini DK. Rapid detection of bacterial infection and viability assessment with high specificity and sensitivity using Raman microspectroscopy. Anal Bioanal Chem 2020; 412:2505-2516. [PMID: 32072214 DOI: 10.1007/s00216-020-02474-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/05/2020] [Accepted: 01/30/2020] [Indexed: 01/15/2023]
Abstract
Infectious diseases caused by bacteria still pose major diagnostic challenges in spite of the availability of various molecular approaches. Irrespective of the type of infection, rapid identification of the causative pathogen with a high degree of sensitivity and specificity is essential for initiating appropriate treatment. While existing methods like PCR possess high sensitivity, they are incapable of identifying the viability status of the pathogen and those which can, like culturing, are inherently slow. To overcome these limitations, we developed a diagnostic platform based on Raman microspectroscopy, capable of detecting biochemical signatures from a single bacterium for identification as well as viability assessment. The study also establishes a decontamination protocol for handling live pathogenic bacteria which does not affect identification and viability testing, showing applicability in the analysis of sputum samples containing pathogenic mycobacterial strains. The minimal sample processing along with multivariate analysis of spectroscopic signatures provides an interface for automatic classification, allowing the prediction of unknown samples by mapping signatures onto available datasets. Also, the novelty of the current work is the demonstration of simultaneous identification and viability assessment at a single bacterial level for pathogenic bacteria. Graphical abstract.
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Affiliation(s)
- Srividya Kumar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Renu Gopinathan
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India
| | - Goutam Kumar Chandra
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India.,Department of Physics, NIT Calicut, Calicut, Kerala, 673601, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India. .,Department of Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, 560012, India.
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012, India. .,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India. .,Centre for Infectious Diseases Research, Indian Institute of Science, Bangalore, 560012, India.
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25
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Verma T, Podder S, Mehta M, Singh S, Singh A, Umapathy S, Nandi D. Raman spectroscopy reveals distinct differences between two closely related bacterial strains, Mycobacterium indicus pranii and Mycobacterium intracellulare. Anal Bioanal Chem 2019; 411:7997-8009. [PMID: 31732785 DOI: 10.1007/s00216-019-02197-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/24/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
A common technique used to differentiate bacterial species and to determine evolutionary relationships is sequencing their 16S ribosomal RNA genes. However, this method fails when organisms exhibit high similarity in these sequences. Two such strains that have identical 16S rRNA sequences are Mycobacterium indicus pranii (MIP) and Mycobacterium intracellulare. MIP is of significance as it is used as an adjuvant for protection against tuberculosis and leprosy; in addition, it shows potent anti-cancer activity. On the other hand, M. intracellulare is an opportunistic pathogen and causes severe respiratory infections in AIDS patients. It is important to differentiate these two bacterial species as they co-exist in immuno-compromised individuals. To unambiguously distinguish these two closely related bacterial strains, we employed Raman and resonance Raman spectroscopy in conjunction with multivariate statistical tools. Phenotypic profiling for these bacterial species was performed in a kinetic manner. Differences were observed in the mycolic acid profile and carotenoid pigments to show that MIP is biochemically distinct from M. intracellulare. Resonance Raman studies confirmed that carotenoids were produced by both MIP as well as M. intracellulare, though the latter produced higher amounts. Overall, this study demonstrates the potential of Raman spectroscopy in differentiating two closely related mycobacterial strains. Graphical abstract.
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Affiliation(s)
- Taru Verma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India
| | - Santosh Podder
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Mansi Mehta
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
| | - Sarman Singh
- All India Institute of Medical Sciences, Bhopal, 462020, India
| | - Amit Singh
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, India
| | - Siva Umapathy
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India.
| | - Dipankar Nandi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, 560012, India.
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, 560012, India.
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
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26
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Gherman AMR, Dina NE, Chiș V, Wieser A, Haisch C. Yeast cell wall - Silver nanoparticles interaction: A synergistic approach between surface-enhanced Raman scattering and computational spectroscopy tools. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 222:117223. [PMID: 31177002 DOI: 10.1016/j.saa.2019.117223] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 06/09/2023]
Abstract
Candida species are becoming one of the pathogens developing antifungal resistance due to inappropriate treatment and overuse of antimycotic drugs in building construction and agriculture. Further, fungal infections are often difficult to detect, also due to slow in vitro growth of the organisms from clinical specimens. Thus, fast detection and discrimination of yeast cells in direct patient materials is essential for an adequate treatment and success rate. In this work, we investigated Candida species isolated from patients, by using surface-enhanced Raman scattering (SERS) combined with computational spectroscopy tools, aiming to detect and discriminate between the three considered species, Candida albicans, Candida glabrata, and Candida parapsilosis. Density functional theory (DFT) was used to calculate Raman spectra of yeasts' main cell wall components for elucidating the origin of the observed bands. Accurate assignments of normal modes helped for a better understanding of the interaction between silver nanoparticles with yeasts' cell wall. Further, SERS spectra were used as samples in a database on which we performed multivariate analyses. By Principal component analysis (PCA), we obtained a maximum variation of 79% between the three samples. Linear discriminant analysis (LDA) was successfully used to discriminate between the three species.
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Affiliation(s)
- Ana Maria Raluca Gherman
- Department of Molecular and Biomolecular Physics, National Institute of R&D of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania; Faculty of Physics, Babeș-Bolyai University, Kogălniceanu 1, 400084 Cluj-Napoca, Romania
| | - Nicoleta Elena Dina
- Department of Molecular and Biomolecular Physics, National Institute of R&D of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania.
| | - Vasile Chiș
- Faculty of Physics, Babeș-Bolyai University, Kogălniceanu 1, 400084 Cluj-Napoca, Romania
| | - Andreas Wieser
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-University, Marchinoninistr. 17, 82377 Munich, Germany; Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU), Leopoldstr. 5, 80802 Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, D-80802 Munich, Germany
| | - Christoph Haisch
- Chair for Analytical Chemistry, Institute of Hydrochemistry, Technische Universität München, Marchioninistrasse 17, 81377 Munich, Germany
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28
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Alunni Cardinali M, Casagrande Pierantoni D, Caponi S, Corte L, Fioretto D, Cardinali G. Meso-Raman approach for rapid yeast cells identification. Biophys Chem 2019; 254:106249. [DOI: 10.1016/j.bpc.2019.106249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/28/2023]
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29
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Rakib F, Ali CM, Yousuf M, Afifi M, Bhatt PR, Ullah E, Al-Saad K, Ali MHM. Investigation of Biochemical Alterations in Ischemic Stroke Using Fourier Transform Infrared Imaging Spectroscopy-A Preliminary Study. Brain Sci 2019; 9:brainsci9110293. [PMID: 31717715 PMCID: PMC6895834 DOI: 10.3390/brainsci9110293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/20/2019] [Accepted: 10/22/2019] [Indexed: 12/26/2022] Open
Abstract
Objective: Brain damage, long-term disability and death are the dreadful consequences of ischemic stroke. It causes imbalance in the biochemical constituents that distorts the brain dynamics. Understanding the sub-cellular alterations associated with the stroke will contribute to deeper molecular understanding of brain plasticity and recovery. Current routine approaches examining lipid and protein biochemical changes post stoke can be difficult. Fourier Transform Infrared (FTIR) imaging spectroscopy can play a vital role in detecting these molecular alterations on a sub-cellular level due to its high spatial resolution, accuracy and sensitivity. This study investigates the biochemical and molecular changes in peri-infract zone (PIZ) (contiguous area not completely damaged by stroke) and ipsi-lesional white matter (WM) (right below the stroke and PIZ regions) nine weeks post photothrombotic ischemic stroke in rats. Materials and Methods: FTIR imaging spectroscopy and transmission electron microscopy (TEM) techniques were applied to investigate brain tissue samples while hematoxylin and eosin (H&E) stained images of adjacent sections were prepared for comparison and examination the morphological changes post stroke. Results: TEM results revealed shearing of myelin sheaths and loss of cell membrane, structure and integrity after ischemic stroke. FTIR results showed that ipsi-lesional PIZ and WM experienced reduction in total protein and total lipid content compared to contra-lesional hemisphere. The lipid/protein ratio reduced in PIZ and adjacent WM indicated lipid peroxidation, which results in lipid chain fragmentation and an increase in olefinic content. Protein structural change is observed in PIZ due to the shift from random coli and α-helical structures to β-sheet conformation. Conclusion: FTIR imaging bio-spectroscopy provide novel biochemical information at sub-cellular levels that be difficult to be obtained by routine approaches. The results suggest that successful therapeutic strategy that is based on administration of anti-oxidant therapy, which could reduce and prevent neurotoxicity by scavenging the lipid peroxidation products. This approach will mitigate tissue damage in chronic ischemic period. FTIR imaging bio-spectroscopy can be used as a powerful tool and offer new approach in stroke and neurodegenerative diseases research.
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Affiliation(s)
- Fazle Rakib
- Department of Chemistry and Earth Sciences, Qatar University, Doha 2713, Qatar; (F.R.); (C.M.A.); (M.A.); (P.R.B.)
| | - Carmen M. Ali
- Department of Chemistry and Earth Sciences, Qatar University, Doha 2713, Qatar; (F.R.); (C.M.A.); (M.A.); (P.R.B.)
| | - Mohammed Yousuf
- Central Laboratory Unit (CLU), Qatar University, Doha 2713, Qatar;
| | - Mohammed Afifi
- Department of Chemistry and Earth Sciences, Qatar University, Doha 2713, Qatar; (F.R.); (C.M.A.); (M.A.); (P.R.B.)
| | - Pooja R. Bhatt
- Department of Chemistry and Earth Sciences, Qatar University, Doha 2713, Qatar; (F.R.); (C.M.A.); (M.A.); (P.R.B.)
| | - Ehsan Ullah
- Qatar Computing Research Institute (QCRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Education City, Doha 34110, Qatar;
| | - Khalid Al-Saad
- Department of Chemistry and Earth Sciences, Qatar University, Doha 2713, Qatar; (F.R.); (C.M.A.); (M.A.); (P.R.B.)
- Correspondence: (K.A.-S.); (M.H.M.A.)
| | - Mohamed H. M. Ali
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha 34110, Qatar
- Qatar National Library, Doha 5825, Qatar
- Correspondence: (K.A.-S.); (M.H.M.A.)
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30
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Matouke MM. FTIR study of the binary effect of titanium dioxide nanoparticles (nTiO 2) and copper (Cu 2+) on the biochemical constituents of liver tissues of catfish ( Clarias gariepinus). Toxicol Rep 2019; 6:1061-1070. [PMID: 31673508 PMCID: PMC6816136 DOI: 10.1016/j.toxrep.2019.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 09/17/2019] [Accepted: 10/03/2019] [Indexed: 11/30/2022] Open
Abstract
The mixture of nanomaterial and essential metal is of concern for freshwater. Co-exposure of titanium dioxide nanoparticles (nTiO2) and copper (Cu2+) revealed. Notable alteration of biochemical constituents and histopathology of liver tissues. FTIR and histological techniques are adequate for the monitoring of changes in fish tissues.
The increasing demand for nanomaterials and essential metals leads to their discharge into the aquatic ecosystems through water run-off and this is of great concern for the aquatic biodiversity. In the present study titanium dioxide nanoparticles (nTiO2) and copper (Cu2+) effects in binary mixture on the biochemical constituents of the liver of Clarias gariepinus by using Fourrier- transform infrared (FT-IR) techniques was examined. The FT-IR revealed significant differences in absorbance intensities between the control and exposed liver tissues demonstrating changes on the critical biochemical constituents such as proteins, lipids and carbohydrates. This result further reveals the binary mixture responsible for the absence of CH3 bending lipids in liver tissues due to their toxic effect. The observed synergistic decreasing ratio of integrated area (1545/3296) for binary mixture exposed liver tissues suggests that lipid degradation predominates over amide formation. In addition, binary mixture causes an alteration in protein secondary structures by decreasing the β turns of liver tissues. Histology in liver showed marked damages. The frequent alteration in the biochemical constituents in the liver tissues of C. gariepinus could be an indication of alteration of existing biochemical components or the expression of new components.
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Abstract
Fourier transform-infrared spectroscopy (FT-IR) represents an attractive molecular diagnostic modality for translation to the clinic, where comprehensive chemical profiling of biological samples may revolutionize a myriad of pathways in clinical settings. Principally, FT-IR provides a rapid, cost-effective platform to obtain a molecular fingerprint of clinical samples based on vibrational transitions of chemical bonds upon interaction with infrared light. To date, considerable research activities have demonstrated competitive to superior performance of FT-IR strategies in comparison to conventional techniques, with particular promise for earlier, accessible disease diagnostics, thereby improving patient outcomes. However, amidst the changing healthcare landscape in times of aging populations and increased prevalence of cancer and chronic disease, routine adoption of FT-IR within clinical laboratories has remained elusive. Hence, this perspective shall outline the significant clinical potential of FT-IR diagnostics and subsequently address current barriers to translation from the perspective of all stakeholders, in the context of biofluid, histopathology, cytology, microbiology, and biomarker discovery frameworks. Thereafter, future perspectives of FT-IR for healthcare will be discussed, with consideration of recent technological advances that may facilitate future clinical translation.
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Affiliation(s)
- Duncan Finlayson
- Centre for Doctoral Training in Medical Devices and Health Technologies, Department of Biomedical Engineering , University of Strathclyde , Wolfson Centre, 106 Rottenrow , Glasgow G4 0NW , U.K.,WestCHEM , Department of Pure and Applied Chemistry , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K
| | - Christopher Rinaldi
- Centre for Doctoral Training in Medical Devices and Health Technologies, Department of Biomedical Engineering , University of Strathclyde , Wolfson Centre, 106 Rottenrow , Glasgow G4 0NW , U.K.,WestCHEM , Department of Pure and Applied Chemistry , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K
| | - Matthew J Baker
- WestCHEM , Department of Pure and Applied Chemistry , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K.,ClinSpec Diagnostics Ltd. , Technology and Innovation Centre, 99 George Street , Glasgow G11RD , U.K
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32
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Taha M, Hassan M, Essa S, Tartor Y. Use of Fourier transform infrared spectroscopy (FTIR) spectroscopy for rapid and accurate identification of Yeasts isolated from human and animals. Int J Vet Sci Med 2019. [DOI: 10.1016/j.ijvsm.2013.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- M. Taha
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Cairo, Egypt
| | - M. Hassan
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Cairo, Egypt
| | - S. Essa
- Department of Microbiology, Research Institute of Animal Health, Dokki, Giza, Egypt
| | - Y. Tartor
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Cairo, Egypt
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Reagent-Free Identification of Clinical Yeasts by Use of Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy. J Clin Microbiol 2019; 57:JCM.01739-18. [PMID: 30787141 DOI: 10.1128/jcm.01739-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 02/06/2019] [Indexed: 12/23/2022] Open
Abstract
Invasive fungal infections by opportunistic yeasts have increased concomitantly with the growth of an immunocompromised patient population. Misidentification of yeasts can lead to inappropriate antifungal treatment and complications. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy is a promising method for rapid and accurate identification of microorganisms. ATR-FTIR spectroscopy is a standalone, inexpensive, reagent-free technique that provides results within minutes after initial culture. In this study, a comprehensive spectral reference database of 65 clinically relevant yeast species was constructed and tested prospectively on spectra recorded (from colonies taken from culture plates) for 318 routine yeasts isolated from various body fluids and specimens received from 38 microbiology laboratories over a 4-month period in our clinical laboratory. ATR-FTIR spectroscopy attained comparable identification performance with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). In a preliminary validation of the ATR-FTIR method, correct identification rates of 100% and 95.6% at the genus and species levels, respectively, were achieved, with 3.5% unidentified and 0.9% misidentified. By expanding the number of spectra in the spectral reference database for species for which isolates could not be identified or had been misidentified, we were able to improve identification at the species level to 99.7%. Thus, ATR-FTIR spectroscopy provides a new standalone method that can rival MALDI-TOF MS for the accurate identification of a broad range of medically important yeasts. The simplicity of the ATR-FTIR spectroscopy workflow favors its use in clinical laboratories for timely and low-cost identification of life-threatening yeast strains for appropriate treatment.
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Rebrošová K, Šiler M, Samek O, Růžička F, Bernatová S, Ježek J, Zemánek P, Holá V. Identification of ability to form biofilm in Candida parapsilosis and Staphylococcus epidermidis by Raman spectroscopy. Future Microbiol 2019; 14:509-517. [PMID: 31025881 DOI: 10.2217/fmb-2018-0297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Aim: Finding rapid, reliable diagnostic methods is a big challenge in clinical microbiology. Raman spectroscopy is an optical method used for multiple applications in scientific fields including microbiology. This work reports its potential in identifying biofilm positive strains of Candida parapsilosis and Staphylococcus epidermidis. Materials & methods: We tested 54 S. epidermidis strains (23 biofilm positive, 31 negative) and 51 C. parapsilosis strains (27 biofilm positive, 24 negative) from colonies on Mueller-Hinton agar plates, using Raman spectroscopy. Results: The accuracy was 98.9% for C. parapsilosis and 96.1% for S. epidermidis. Conclusion: The method showed great potential for identifying biofilm positive bacterial and yeast strains. We suggest that Raman spectroscopy might become a useful aid in clinical diagnostics.
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Affiliation(s)
- Katarína Rebrošová
- Department of Microbiology, Faculty of Medicine, Masaryk University & St. Anne's Faculty Hospital, Pekařská 53, Brno 65691, Czech Republic
| | - Martin Šiler
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno 61264, Czech Republic
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno 61264, Czech Republic
| | - Filip Růžička
- Department of Microbiology, Faculty of Medicine, Masaryk University & St. Anne's Faculty Hospital, Pekařská 53, Brno 65691, Czech Republic
| | - Silvie Bernatová
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno 61264, Czech Republic
| | - Jan Ježek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno 61264, Czech Republic
| | - Pavel Zemánek
- Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i., Královopolská 147, Brno 61264, Czech Republic
| | - Veronika Holá
- Department of Microbiology, Faculty of Medicine, Masaryk University & St. Anne's Faculty Hospital, Pekařská 53, Brno 65691, Czech Republic
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Potocki L, Depciuch J, Kuna E, Worek M, Lewinska A, Wnuk M. FTIR and Raman Spectroscopy-Based Biochemical Profiling Reflects Genomic Diversity of Clinical Candida Isolates That May Be Useful for Diagnosis and Targeted Therapy of Candidiasis. Int J Mol Sci 2019; 20:ijms20040988. [PMID: 30823514 PMCID: PMC6412866 DOI: 10.3390/ijms20040988] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 12/11/2022] Open
Abstract
Despite the fact that Candida albicans is documented to be the main cause of human candidiasis, non-C. albicans Candida (NCAC) species, such as Candida glabrata and Candida tropicalis, are also suggested to be implicated in the etiopathogenesis of opportunistic fungal infections. As biology, epidemiology, pathogenicity, and antifungal resistance of NCAC species may be affected as a result of genomic diversity and plasticity, rapid and unambiguous identification of Candida species in clinical samples is essential for proper diagnosis and therapy. In the present study, 25 clinical isolates of C. albicans, C. glabrata, and C. tropicalis species were characterized in terms of their karyotype patterns, DNA content, and biochemical features. Fourier transform infrared (FTIR) spectra- and Raman spectra-based molecular fingerprints corresponded to the diversity of chromosomal traits and DNA levels that provided correct species identification. Moreover, Raman spectroscopy was documented to be useful for the evaluation of ergosterol content that may be associated with azole resistance. Taken together, we found that vibrational spectroscopy-based biochemical profiling reflects the variability of chromosome patterns and DNA content of clinical Candida species isolates and may facilitate the diagnosis and targeted therapy of candidiasis.
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Affiliation(s)
- Leszek Potocki
- Department of Genetics, Faculty of Biotechnology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
| | - Joanna Depciuch
- Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Poland.
| | - Ewelina Kuna
- Department of Genetics, Faculty of Biotechnology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
| | - Mariusz Worek
- Department of Microbiology, Faculty of Medicine, University of Rzeszow, 35-959 Rzeszow, Poland.
| | - Anna Lewinska
- Department of Cell Biochemistry, Faculty of Biotechnology, University of Rzeszow, 35-310 Rzeszow, Poland.
| | - Maciej Wnuk
- Department of Genetics, Faculty of Biotechnology, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland.
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Leal L, Nogueira M, Canevari R, Carvalho L. Vibration spectroscopy and body biofluids: Literature review for clinical applications. Photodiagnosis Photodyn Ther 2018; 24:237-244. [DOI: 10.1016/j.pdpdt.2018.09.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 09/03/2018] [Accepted: 09/17/2018] [Indexed: 12/19/2022]
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37
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Hrubanova K, Krzyzanek V, Nebesarova J, Ruzicka F, Pilat Z, Samek O. Monitoring Candida parapsilosis and Staphylococcus epidermidis Biofilms by a Combination of Scanning Electron Microscopy and Raman Spectroscopy. SENSORS 2018; 18:s18124089. [PMID: 30469521 PMCID: PMC6308600 DOI: 10.3390/s18124089] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 02/03/2023]
Abstract
The biofilm-forming microbial species Candida parapsilosis and Staphylococcus epidermidis have been recently linked to serious infections associated with implanted medical devices. We studied microbial biofilms by high resolution scanning electron microscopy (SEM), which allowed us to visualize the biofilm structure, including the distribution of cells inside the extracellular matrix and the areas of surface adhesion. We compared classical SEM (chemically fixed samples) with cryogenic SEM, which employs physical sample preparation based on plunging the sample into various liquid cryogens, as well as high-pressure freezing (HPF). For imaging the biofilm interior, we applied the freeze-fracture technique. In this study, we show that the different means of sample preparation have a fundamental influence on the observed biofilm structure. We complemented the SEM observations with Raman spectroscopic analysis, which allowed us to assess the time-dependent chemical composition changes of the biofilm in vivo. We identified the individual spectral peaks of the biomolecules present in the biofilm and we employed principal component analysis (PCA) to follow the temporal development of the chemical composition.
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Affiliation(s)
- Kamila Hrubanova
- Institute of Scientific Instruments of the Czech Academy of Sciences, CZ-61264 Brno, Czech Republic.
| | - Vladislav Krzyzanek
- Institute of Scientific Instruments of the Czech Academy of Sciences, CZ-61264 Brno, Czech Republic.
| | - Jana Nebesarova
- Biology Centre of the Czech Academy of Sciences, CZ-37005 Ceske Budejovice, Czech Republic.
| | - Filip Ruzicka
- Department of Microbiology, Faculty of Medicine, Masaryk University and St. Anne's Faculty Hospital, CZ-65691 Brno, Czech Republic.
| | - Zdenek Pilat
- Institute of Scientific Instruments of the Czech Academy of Sciences, CZ-61264 Brno, Czech Republic.
| | - Ota Samek
- Institute of Scientific Instruments of the Czech Academy of Sciences, CZ-61264 Brno, Czech Republic.
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Suntsova AY, Guliev RR, Popov DA, Vostrikova TY, Dubodelov DV, Shchegolikhin AN, Laypanov BK, Priputnevich TV, Shevelev AB, Kurochkin IN. Identification of microorganisms by Fourier-transform infrared spectroscopy. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2018. [DOI: 10.24075/brsmu.2018.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The need for novel techniques of rapid identification of pathogenic microorganisms arises from the massive spread of drug-resistant nosocomial strains and the emergence of centers for biohazard control. Fourier-transform infrared spectroscopy is a promising alternative to mass spectrometry as it is cost-effective, fast and suitable for field use. The aim of this work was to propose an algorithm for the identification of microorganisms in pure cultures based on the analysis of their Fourier transform infrared spectra. The algorithm is based on the automated principal component analysis of infrared spectra. Unlike its analogues described in the literature, the algorithm is capable of identifying bacteria regardless of the culture medium or growth phase. The training sample included the most prevalent causative agents of infections and sepsis in humans: Staphylococcus aureus (n = 67), Enterococcus faecalis (n = 10), Enterococcus faecium (n = 10), Klebsiella pneumoniae (n = 10), Escherichia coli (n = 10), Serratia marcescens (n = 10), Enterobacter cloacae (n = 10), Acinetobacter baumannii (n = 10), Pseudomonas aeruginosa (n = 10), and Candida albicans (n = 10). The model we built successfully passed a series of blind tests involving clinical isolates of 10 methicillin-resistant (MRSA) and 10 methicillin-sensitive (MSSA) Staphylococcus aureus strains as well as pair mixes of these cultures with clinical isolates of Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae.
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Affiliation(s)
- A. Yu. Suntsova
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow
| | - R. R. Guliev
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow
| | - D. A. Popov
- Bakulev National Medical Research Center of Cardiovascular Surgery, Moscow
| | - T. Yu. Vostrikova
- Bakulev National Medical Research Center of Cardiovascular Surgery, Moscow
| | - D. V. Dubodelov
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow
| | - A. N. Shchegolikhin
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow
| | - B. K. Laypanov
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow
| | - T. V. Priputnevich
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow
| | - A. B. Shevelev
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow
| | - I. N. Kurochkin
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Moscow
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Ayala OD, Wakeman CA, Pence IJ, Gaddy JA, Slaughter JC, Skaar EP, Mahadevan-Jansen A. Drug-Resistant Staphylococcus aureus Strains Reveal Distinct Biochemical Features with Raman Microspectroscopy. ACS Infect Dis 2018; 4:1197-1210. [PMID: 29845863 PMCID: PMC6476553 DOI: 10.1021/acsinfecdis.8b00029] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Staphylococcus aureus ( S. aureus) is a leading cause of hospital-acquired infections, such as bacteremia, pneumonia, and endocarditis. Treatment of these infections can be challenging since strains of S. aureus, such as methicillin-resistant S. aureus (MRSA), have evolved resistance to antimicrobials. Current methods to identify infectious agents in hospital environments often rely on time-consuming, multistep culturing techniques to distinguish problematic strains (i.e., antimicrobial resistant variants) of a particular bacterial species. Therefore, a need exists for a rapid, label-free technique to identify drug-resistant bacterial strains to guide proper antibiotic treatment. Here, our findings demonstrate the ability to characterize and identify microbes at the subspecies level using Raman microspectroscopy, which probes the vibrational modes of molecules to provide a biochemical "fingerprint". This technique can distinguish between different isolates of species such as Streptococcus agalactiae and S. aureus. To determine the ability of this analytical approach to detect drug-resistant bacteria, isogenic variants of S. aureus including the comparison of strains lacking or expressing antibiotic resistance determinants were evaluated. Spectral variations observed may be associated with biochemical components such as amino acids, carotenoids, and lipids. Mutants lacking carotenoid production were distinguished from wild-type S. aureus and other strain variants. Furthermore, spectral biomarkers of S. aureus isogenic bacterial strains were identified. These results demonstrate the feasibility of Raman microspectroscopy for distinguishing between various genetically distinct forms of a single bacterial species in situ. This is important for detecting antibiotic-resistant strains of bacteria and indicates the potential for future identification of other multidrug resistant pathogens with this technique.
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Affiliation(s)
- Oscar D. Ayala
- Biophotonics Center, Vanderbilt University, 410 24th Avenue South, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, Tennessee 37232, United States
| | - Catherine A. Wakeman
- Department of Biological Sciences, Texas Tech University, 2901 Main Street, Lubbock, Texas 79409, United States
| | - Isaac J. Pence
- Biophotonics Center, Vanderbilt University, 410 24th Avenue South, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, Tennessee 37232, United States
| | - Jennifer A. Gaddy
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Nashville, Tennessee 37232, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Nashville, Tennessee 37232, United States
- Tennessee Valley Healthcare Systems, Department of Veterans Affairs, 1310 24th Avenue South, Nashville, Tennessee 37212, United States
| | - James C. Slaughter
- Department of Biostatistics, Vanderbilt University School of Medicine, 2525 West End Avenue, Suite 11000, Nashville, Tennessee 37203, United States
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, Medical Center North, Nashville, Tennessee 37232, United States
| | - Anita Mahadevan-Jansen
- Biophotonics Center, Vanderbilt University, 410 24th Avenue South, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, 5824 Stevenson Center, Nashville, Tennessee 37232, United States
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40
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Chisanga M, Muhamadali H, Ellis DI, Goodacre R. Surface-Enhanced Raman Scattering (SERS) in Microbiology: Illumination and Enhancement of the Microbial World. APPLIED SPECTROSCOPY 2018; 72:987-1000. [PMID: 29569946 DOI: 10.1177/0003702818764672] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The microbial world forms a huge family of organisms that exhibit the greatest phylogenetic diversity on Earth and thus colonize virtually our entire planet. Due to this diversity and subsequent complex interactions, the vast majority of microorganisms are involved in innumerable natural bioprocesses and contribute an absolutely vital role toward the maintenance of life on Earth, whilst a small minority cause various infectious diseases. The ever-increasing demand for environmental monitoring, sustainable ecosystems, food security, and improved healthcare systems drives the continuous search for inexpensive but reproducible, automated and portable techniques for detection of microbial isolates and understanding their interactions for clinical, environmental, and industrial applications and benefits. Surface-enhanced Raman scattering (SERS) is attracting significant attention for the accurate identification, discrimination and characterization and functional assessment of microbial cells at the single cell level. In this review, we briefly discuss the technological advances in Raman and Fourier transform infrared (FT-IR) instrumentation and their application for the analysis of clinically and industrially relevant microorganisms, biofilms, and biological warfare agents. In addition, we summarize the current trends and future prospects of integrating Raman/SERS-isotopic labeling and cell sorting technologies in parallel, to link genotype-to-phenotype in order to define community function of unculturable microbial cells in mixed microbial communities which possess admirable traits such as detoxification of pollutants and recycling of essential metals.
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Affiliation(s)
- Malama Chisanga
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, UK
| | - Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, UK
| | - David I Ellis
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, UK
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, UK
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41
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Lasch P, Stämmler M, Zhang M, Baranska M, Bosch A, Majzner K. FT-IR Hyperspectral Imaging and Artificial Neural Network Analysis for Identification of Pathogenic Bacteria. Anal Chem 2018; 90:8896-8904. [DOI: 10.1021/acs.analchem.8b01024] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter Lasch
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Maren Stämmler
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Miao Zhang
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
| | - Alejandra Bosch
- CINDEFI,
CONICET-CCT
La Plata, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, 1900 La Plata, Buenos Aires, Argentina
| | - Katarzyna Majzner
- ZBS6 Proteomics and Spectroscopy, Robert Koch-Institute, Seestrasse 10, Berlin, D-13353, Germany
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-060 Krakow, Poland
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42
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Montanari LB, Sartori FG, Ribeiro DBM, Leandro LF, Pires RH, Melhem MDSC, de Mello CA, Martins CHG. Yeast isolation and identification in water used in a Brazilian hemodialysis unit by classic microbiological techniques and Raman spectroscopy. JOURNAL OF WATER AND HEALTH 2018; 16:311-320. [PMID: 29676766 DOI: 10.2166/wh.2017.334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The use of poorly treated water in hemodialysis centers may lead to fungal contamination, which poses a serious threat to immunologically debilitated hemodialysis patients. This study aimed to isolate and identify yeast species in the water of a Brazilian hemodialysis center by using classic microbiological techniques and Raman spectroscopy. For 12 months, a total of 288 water samples were collected from different points of the hemodialysis treatment distribution center. One hundred and forty-six yeast species were isolated and identified in the samples that tested positive for the presence of yeasts such as Candida parapsilosis (100 isolates, or 68.50%), C. guilliermondii (17 isolates, or 11.65%), Rhodotorula mucilaginosa (23 isolates, or 15.75%), R. glutinis (three isolates, or 2.05%), and Trichosporon inkin (three isolates, or 2.05%). Yeast susceptibility to the antifungal fluconazole was also assayed. Only two C. guilliermondii isolates were resistant to fluconazole: the minimal inhibitory concentrations were higher than 64 μg/mL. The different yeast species present in the water of a Brazilian hemodialysis center call for more effective water disinfection procedures in this unit. Raman spectroscopy is an excellent tool to identify yeast species and is potentially applicable in routine water monitoring in hemodialysis units.
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Affiliation(s)
- Lilian Bueno Montanari
- Laboratory of Research in Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600 São Paulo, Brazil E-mail:
| | - Flávio Garcia Sartori
- Laboratory of Research in Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600 São Paulo, Brazil E-mail:
| | | | - Luís Fernando Leandro
- Laboratory of Research in Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600 São Paulo, Brazil E-mail:
| | - Regina Helena Pires
- Laboratory of Research in Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600 São Paulo, Brazil E-mail:
| | | | - César Alexandre de Mello
- Nucleus of Research in Sciences and Technology, University of Franca - UNIFRAN, Franca, 14404-600 São Paulo, Brazil
| | - Carlos Henrique Gomes Martins
- Laboratory of Research in Applied Microbiology, University of Franca - UNIFRAN, Franca, 14404-600 São Paulo, Brazil E-mail:
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43
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Pudlas M, Koch S, Bolwien C, Walles H. Raman Spectroscopy as a Tool for Quality and Sterility Analysis for Tissue Engineering Applications like Cartilage Transplants. Int J Artif Organs 2018. [DOI: 10.1177/039139881003300407] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
At present, the production of tissue engineered cartilage requires the concurrent production of two identical transplants. One transplant is used for destructive quality control and the second one is implanted into the patient. A non-invasive characterization of such tissue engineering samples would be a promising tool to achieve a production process of just one transplant that is both implanted and tested. Raman spectroscopy is a method that satisfies this requirement by analyzing cells without lysis, fixation or the use of any chemicals. This pure optical technique is based on inelastic scattering of laser photons by molecular vibrations of biopolymers. Characteristic peaks in Raman spectra of cells could be assigned to typical biochemical molecules present in biological samples. For the analysis of chondrocytes present in cartilage transplants, the determination of the cell vitality as well as the discrimination of another cell type have been studied by Raman spectroscopy. Another bottleneck in such biological processes under GMP conditions is sterility control, as most of the commonly used methods require long cultivation times. Raman spectroscopy provides a good alternative to conventional methods in terms of time saving. In this study, the potential of Raman spectroscopy as a quality and sterility control tool for tissue engineering applications was studied by analyzing and comparing the spectra of cell and bacteria cultures.
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Affiliation(s)
- Marieke Pudlas
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart - Germany
- University of Stuttgart, Medical Interfacial Engineering, Stuttgart - Germany
| | - Steffen Koch
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart - Germany
- University of Stuttgart, Medical Interfacial Engineering, Stuttgart - Germany
| | - Carsten Bolwien
- Fraunhofer Institute for Physical Measurement Techniques, Freiburg - Germany
| | - Heike Walles
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart - Germany
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44
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Dina NE, Gherman AMR, Chiş V, Sârbu C, Wieser A, Bauer D, Haisch C. Characterization of Clinically Relevant Fungi via SERS Fingerprinting Assisted by Novel Chemometric Models. Anal Chem 2018; 90:2484-2492. [PMID: 29356512 DOI: 10.1021/acs.analchem.7b03124] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Nonculture-based tests are gaining popularity and upsurge in the diagnosis of invasive fungal infections (IFI) fostered by their main asset, the reduced analysis time, which enables a more rapid diagnosis. In this project, three different clinical isolates of relevant filamentous fungal species were discriminated by using a rapid (less than 5 min) and sensitive surface-enhanced Raman scattering (SERS)-based detection method, assisted by chemometrics. The holistic evaluation of the SERS spectra was performed by employing appropriate chemometric tools-classical and fuzzy principal component analysis (FPCA) in combination with linear discriminant analysis (LDA) applied to the first relevant principal components. The efficiency of the proposed robust algorithm is illustrated on the data set including three fungal isolates (Aspergillus fumigatus sensu stricto, cryptic A. fumigatus complex species, and Rhizomucor pusillus) that were isolated from patient materials. The accurate and reliable discrimination between species of common fungal pathogen strains suggest that the developed method has the potential as an alternative, spectroscopic-based routine analysis tool in IFI diagnosis.
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Affiliation(s)
- Nicoleta Elena Dina
- Department of Molecular and Biomolecular Physics, National Institute of R&D of Isotopic and Molecular Technologies , 67-103 Donat, 400293 Cluj-Napoca, Romania
| | - Ana Maria Raluca Gherman
- Department of Molecular and Biomolecular Physics, National Institute of R&D of Isotopic and Molecular Technologies , 67-103 Donat, 400293 Cluj-Napoca, Romania.,Faculty of Physics, Babeş-Bolyai University , 1 Kogălniceanu, 400084 Cluj-Napoca, Romania
| | - Vasile Chiş
- Faculty of Physics, Babeş-Bolyai University , 1 Kogălniceanu, 400084 Cluj-Napoca, Romania
| | - Costel Sârbu
- Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University , 11 Arany Janos, 400028 Cluj-Napoca, Romania
| | - Andreas Wieser
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-University ; Marchioninistrasse 17, 82377 Munich, Germany.,Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich (LMU) , Leopoldstrasse 5, 80802 Munich, Germany.,German Center for Infection Research (DZIF) , partner site Munich, 80802 Munich, Germany
| | - David Bauer
- Chair for Analytical Chemistry, Institute of Hydrochemistry, Technische Universität München , Marchioninistrasse 17, 81377 Munich, Germany
| | - Christoph Haisch
- Chair for Analytical Chemistry, Institute of Hydrochemistry, Technische Universität München , Marchioninistrasse 17, 81377 Munich, Germany
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45
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Gurbanov R, Gozen AG, Severcan F. Rapid classification of heavy metal-exposed freshwater bacteria by infrared spectroscopy coupled with chemometrics using supervised method. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 189:282-290. [PMID: 28823969 DOI: 10.1016/j.saa.2017.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/08/2017] [Accepted: 08/13/2017] [Indexed: 05/21/2023]
Abstract
Rapid, cost-effective, sensitive and accurate methodologies to classify bacteria are still in the process of development. The major drawbacks of standard microbiological, molecular and immunological techniques call for the possible usage of infrared (IR) spectroscopy based supervised chemometric techniques. Previous applications of IR based chemometric methods have demonstrated outstanding findings in the classification of bacteria. Therefore, we have exploited an IR spectroscopy based chemometrics using supervised method namely Soft Independent Modeling of Class Analogy (SIMCA) technique for the first time to classify heavy metal-exposed bacteria to be used in the selection of suitable bacteria to evaluate their potential for environmental cleanup applications. Herein, we present the powerful differentiation and classification of laboratory strains (Escherichia coli and Staphylococcus aureus) and environmental isolates (Gordonia sp. and Microbacterium oxydans) of bacteria exposed to growth inhibitory concentrations of silver (Ag), cadmium (Cd) and lead (Pb). Our results demonstrated that SIMCA was able to differentiate all heavy metal-exposed and control groups from each other with 95% confidence level. Correct identification of randomly chosen test samples in their corresponding groups and high model distances between the classes were also achieved. We report, for the first time, the success of IR spectroscopy coupled with supervised chemometric technique SIMCA in classification of different bacteria under a given treatment.
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Affiliation(s)
- Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik S.E. University, 11230 Bilecik, Turkey; Department of Biochemistry, Middle East Technical University, 06800 Ankara, Turkey
| | - Ayse Gul Gozen
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey; Department of Biophysics, Faculty of Medicine, Altinbas University, 34217 Istanbul, Turkey.
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46
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De Bruyne S, Speeckaert MM, Delanghe JR. Applications of mid-infrared spectroscopy in the clinical laboratory setting. Crit Rev Clin Lab Sci 2017; 55:1-20. [PMID: 29239240 DOI: 10.1080/10408363.2017.1414142] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fourier transform mid-infrared (MIR-FTIR) spectroscopy is a nondestructive, label-free, highly sensitive and specific technique that provides complete information on the chemical composition of biological samples. The technique both can offer fundamental structural information and serve as a quantitative analysis tool. Therefore, it has many potential applications in different fields of clinical laboratory science. Although considerable technological progress has been made to promote biomedical applications of this powerful analytical technique, most clinical laboratory analyses are based on spectroscopic measurements in the visible or ultraviolet (UV) spectrum and the potential role of FTIR spectroscopy still remains unexplored. In this review, we present some general principles of FTIR spectroscopy as a useful method to study molecules in specimens by MIR radiation together with a short overview of methods to interpret spectral data. We aim at illustrating the wide range of potential applications of the proposed technique in the clinical laboratory setting with a focus on its advantages and limitations and discussing the future directions. The reviewed applications of MIR spectroscopy include (1) quantification of clinical parameters in body fluids, (2) diagnosis and monitoring of cancer and other diseases by analysis of body fluids, cells, and tissues, (3) classification of clinically relevant microorganisms, and (4) analysis of kidney stones, nails, and faecal fat.
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Affiliation(s)
- Sander De Bruyne
- a Department of Clinical Chemistry , Ghent University Hospital , Ghent , Belgium
| | | | - Joris R Delanghe
- a Department of Clinical Chemistry , Ghent University Hospital , Ghent , Belgium
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47
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Colabella C, Corte L, Roscini L, Shapaval V, Kohler A, Tafintseva V, Tascini C, Cardinali G. Merging FT-IR and NGS for simultaneous phenotypic and genotypic identification of pathogenic Candida species. PLoS One 2017; 12:e0188104. [PMID: 29206226 PMCID: PMC5714347 DOI: 10.1371/journal.pone.0188104] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 10/18/2017] [Indexed: 01/27/2023] Open
Abstract
The rapid and accurate identification of pathogen yeast species is crucial for clinical diagnosis due to the high level of mortality and morbidity induced, even after antifungal therapy. For this purpose, new rapid, high-throughput and reliable identification methods are required. In this work we described a combined approach based on two high-throughput techniques in order to improve the identification of pathogenic yeast strains. Next Generation Sequencing (NGS) of ITS and D1/D2 LSU marker regions together with FTIR spectroscopy were applied to identify 256 strains belonging to Candida genus isolated in nosocomial environments. Multivariate data analysis (MVA) was carried out on NGS and FT-IR data-sets, separately. Strains of Candida albicans, C. parapsilosis, C. glabrata and C. tropicalis, were identified with high-throughput NGS sequencing of ITS and LSU markers and then with FTIR. Inter- and intra-species variability was investigated by consensus principal component analysis (CPCA) which combines high-dimensional data of the two complementary analytical approaches in concatenated PCA blocks normalized to the same weight. The total percentage of correct identification reached around 97.4% for C. albicans and 74% for C. parapsilosis while the other two species showed lower identification rates. Results suggested that the identification success increases with the increasing number of strains actually used in the PLS analysis. The absence of reliable FT-IR libraries in the current scenario is the major limitation in FTIR-based identification of strains, although this metabolomics fingerprint represents a valid and affordable aid to rapid and high-throughput to clinical diagnosis. According to our data, FT-IR libraries should include some tens of certified strains per species, possibly over 50, deriving from diverse sources and collected over an extensive time period. This implies a multidisciplinary effort of specialists working in strain isolation and maintenance, molecular taxonomy, FT-IR technique and chemo-metrics, data management and data basing.
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Affiliation(s)
- Claudia Colabella
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Laura Corte
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Luca Roscini
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
| | - Volha Shapaval
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Achim Kohler
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Valeria Tafintseva
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Norway
| | - Carlo Tascini
- Azienda Ospedaliera dei Colli—Ospedale Cotugno, Napoli, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences—Microbiology, University of Perugia, Perugia (Italy)
- CEMIN, Centre of Excellence on Nanostructured Innovative Materials—Department of Chemistry, Biology and Biotechnology—University of Perugia, Perugia, Italy
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48
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Quintelas C, Ferreira EC, Lopes JA, Sousa C. An Overview of the Evolution of Infrared Spectroscopy Applied to Bacterial Typing. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700449] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/18/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Cristina Quintelas
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - Eugénio C. Ferreira
- Dr. C. Quintelas, Dr. E. C. Ferreira; CEB − Centro de Engenharia Biológica; Universidade do Minho; Braga Portugal
| | - João A. Lopes
- Dr. J. A. Lopes; Research Institute for Medicines (iMed.ULisboa); Faculdade de Farmácia; Universidade de Lisboa; Lisboa Portugal
| | - Clara Sousa
- Dr. C. Sousa; LAQV/REQUIMTE; Departamento de Ciências Químicas Faculdade de Farmácia; Universidade do Porto; Rua Jorge Viterbo Ferreira, 228 4050-313 Porto Portugal
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49
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Rapid identification of staphylococci by Raman spectroscopy. Sci Rep 2017; 7:14846. [PMID: 29093473 PMCID: PMC5665888 DOI: 10.1038/s41598-017-13940-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/03/2017] [Indexed: 12/25/2022] Open
Abstract
Clinical treatment of the infections caused by various staphylococcal species differ depending on the actual cause of infection. Therefore, it is necessary to develop a fast and reliable method for identification of staphylococci. Raman spectroscopy is an optical method used in multiple scientific fields. Recent studies showed that the method has a potential for use in microbiological research, too. Our work here shows a possibility to identify staphylococci by Raman spectroscopy. We present a method that enables almost 100% successful identification of 16 of the clinically most important staphylococcal species directly from bacterial colonies grown on a Mueller-Hinton agar plate. We obtained characteristic Raman spectra of 277 staphylococcal strains belonging to 16 species from a 24-hour culture of each strain grown on the Mueller-Hinton agar plate using the Raman instrument. The results show that it is possible to distinguish among the tested species using Raman spectroscopy and therefore it has a great potential for use in routine clinical diagnostics.
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50
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Sharaha U, Rodriguez-Diaz E, Riesenberg K, Bigio IJ, Huleihel M, Salman A. Using Infrared Spectroscopy and Multivariate Analysis to Detect Antibiotics' Resistant Escherichia coli Bacteria. Anal Chem 2017; 89:8782-8790. [PMID: 28731324 DOI: 10.1021/acs.analchem.7b01025] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial pathogens are one of the primary causes of human morbidity worldwide. Historically, antibiotics have been highly effective against most bacterial pathogens; however, the increasing resistance of bacteria to a broad spectrum of commonly used antibiotics has become a global health-care problem. Early and rapid determination of bacterial susceptibility to antibiotics has become essential in many clinical settings and, sometimes, can save lives. Currently classical procedures require at least 48 h for determining bacterial susceptibility, which can constitute a life-threatening delay for effective treatment. Infrared (IR) microscopy is a rapid and inexpensive technique, which has been used successfully for the detection and identification of various biological samples; nonetheless, its true potential in routine clinical diagnosis has not yet been established. In this study, we evaluated the potential of this technique for rapid identification of bacterial susceptibility to specific antibiotics based on the IR spectra of the bacteria. IR spectroscopy was conducted on bacterial colonies, obtained after 24 h culture from patients' samples. An IR microscope was utilized, and a computational classification method was developed to analyze the IR spectra by novel pattern-recognition and statistical tools, to determine E. coli susceptibility within a few minutes to different antibiotics, gentamicin, ceftazidime, nitrofurantoin, nalidixic acid, ofloxacin. Our results show that it was possible to classify the tested bacteria into sensitive and resistant types, with success rates as high as 85% for a number of examined antibiotics. These promising results open the potential of this technique for faster determination of bacterial susceptibility to certain antibiotics.
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Affiliation(s)
- Uraib Sharaha
- Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - Eladio Rodriguez-Diaz
- Department of Medicine, Section of Gastroenterology, Boston University School of Medicine , Boston, Massachusetts 02118, United States.,USA 2 Section of Gastroenterology, VA Boston Healthcare System , Boston, Massachusetts 02130, United States
| | | | - Irving J Bigio
- Department of Biomedical Engineering, Boston University , Boston, Massachusetts 02215, United States.,Department of Electrical & Computer Engineering, Boston University , Boston, Massachusetts 02215, United States
| | - Mahmoud Huleihel
- Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev , Beer-Sheva 84105, Israel
| | - Ahmad Salman
- Department of Physics, SCE-Shamoon College of Engineering , Beer-Sheva 84100, Israel
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