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Saikia D, Vijay A, Cebajel Bhanwarlal T, Singh SP. Validating the utility of heavy water (Deuterium Oxide) as a potential Raman spectroscopic probe for identification of antibiotic resistance. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 321:124723. [PMID: 38941753 DOI: 10.1016/j.saa.2024.124723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/07/2024] [Accepted: 06/24/2024] [Indexed: 06/30/2024]
Abstract
The impact of microbial infections is increasing over time, and it is one of the major reasons for death in both developed and developing countries. colistin is considered as the antibiotic of last choice for infections brought by major multidrug-resistant (MDR), gram-negative bacteria such as Enterobacter species, Acinetobacter species, and Pseudomonas aeruginosa. Existing approaches to diagnose these resistant species are relatively slow and take up to 2 to 3 days. In this work, we propose a novel interdisciplinary method based on Raman spectroscopy and heavy water to identify colistin-resistant microbes. Our hypothesis is based on the fact that resistant bacteria will be metabolically active in the culture medium containing antibiotics and heavy water, and these bacteria will take up deuterium instead of hydrogen to newly synthesized lipids and proteins. This effect will generate a 'C - D' bond-specific Raman spectral marker. Successful identification of this band in the spectral profile can confirm the presence of colistin-resistant bacteria. We have validated the efficacy of this approach in identifying colistin-resistant bacteria spiked in artificial urine and have compared sensitivity at different bacterial concentrations. Overall findings suggest that heavy water can potentially serve as a suitable Raman probe for identifying metabolically active colistin-resistant bacteria via urine under clinically implementable time and can be used in clinical settings after validation.
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Affiliation(s)
- Dimple Saikia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka 580011, India
| | - Arunsree Vijay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka 580011, India
| | - Tanan Cebajel Bhanwarlal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka 580011, India
| | - S P Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka 580011, India.
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2
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Stanca SE, Mogavero S, Fritzsche W, Krafft C, Hube B, Popp J. Isotope labeled 3D-Raman confocal imaging and atomic force microscopy study on epithelial cells interacting with the fungus Candida albicans. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 59:102750. [PMID: 38734040 DOI: 10.1016/j.nano.2024.102750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/08/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024]
Abstract
The human pathogenic fungus Candida albicans damages epithelial cells during superficial infections. Here we use three-dimensional-sequential-confocal Raman spectroscopic imaging and atomic force microscopy to investigate the interaction of C. albicans wild type cells, the secreted C. albicans peptide toxin candidalysin and mutant cells lacking candidalysin with epithelial cells. The candidalysin is responsible for epithelial cell damage and exhibits in its deuterated form an identifiable Raman signal in a frequency region distinct from the cellular frequency region. Vibration modes at 2100-2200 cm-1 attributed to carbon‑deuterium bending and at 477 cm-1, attributed to the nitrogen‑deuterium out-of-plane bending, found around the nucleus, can be assigned to deuterated candidalysin. Atomic force microscopy visualized 100 nm deep lesions on the cell and force-distance curves indicate the higher adhesion on pore surrounding after incubation with candidalysin. Candidalysin targets the plasma membrane, but is also found inside of the cytosol of epithelial cells during C. albicans infection.
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Affiliation(s)
- Sarmiza Elena Stanca
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany.
| | - Selene Mogavero
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany
| | - Wolfgang Fritzsche
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany.
| | - Bernhard Hube
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll Institute, Beutenbergstraße 11a, 07745 Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany; Institute for Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany.
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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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4
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Zhou Z, Pandey R, Valdez TA. Label-Free Optical Technologies for Middle-Ear Diseases. Bioengineering (Basel) 2024; 11:104. [PMID: 38391590 PMCID: PMC10885954 DOI: 10.3390/bioengineering11020104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/11/2024] [Accepted: 01/16/2024] [Indexed: 02/24/2024] Open
Abstract
Medical applications of optical technology have increased tremendously in recent decades. Label-free techniques have the unique advantage of investigating biological samples in vivo without introducing exogenous agents. This is especially beneficial for a rapid clinical translation as it reduces the need for toxicity studies and regulatory approval for exogenous labels. Emerging applications have utilized label-free optical technology for screening, diagnosis, and surgical guidance. Advancements in detection technology and rapid improvements in artificial intelligence have expedited the clinical implementation of some optical technologies. Among numerous biomedical application areas, middle-ear disease is a unique space where label-free technology has great potential. The middle ear has a unique anatomical location that can be accessed through a dark channel, the external auditory canal; it can be sampled through a tympanic membrane of approximately 100 microns in thickness. The tympanic membrane is the only membrane in the body that is surrounded by air on both sides, under normal conditions. Despite these favorable characteristics, current examination modalities for middle-ear space utilize century-old technology such as white-light otoscopy. This paper reviews existing label-free imaging technologies and their current progress in visualizing middle-ear diseases. We discuss potential opportunities, barriers, and practical considerations when transitioning label-free technology to clinical applications.
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Affiliation(s)
- Zeyi Zhou
- School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Rishikesh Pandey
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Tulio A Valdez
- Department of Otolaryngology, Stanford University, Palo Alto, CA 94304, USA
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5
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Shang L, Liang P, Xu L, Xue Y, Liu K, Wang Y, Bao X, Chen F, Peng H, Wang Y, Ju J, Li B. Stable SERS Detection of Lactobacillus fermentum Using Optical Tweezers in a Microfluidic Environment. Anal Chem 2024; 96:248-255. [PMID: 38113377 DOI: 10.1021/acs.analchem.3c03852] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Rapid identification of fermented lactic acid bacteria has long been a challenge in the brewing industry. This study combined label-free surface-enhanced Raman scattering (SERS) and optical tweezer technology to construct a test platform within a microfluidic environment. Six kinds of lactic acid bacteria common in industry were tested to prove the stability of the SERS spectra. The results demonstrated that the utilization of optical tweezers to securely hold the bacteria significantly enhanced the stability of the SERS spectra. Furthermore, SVM and XGBoost machine learning algorithms were utilized to analyze the obtained Raman spectra for identification, and the identification accuracies exceeded 95% for all tested lactic acid bacteria. The findings of this study highlight the crucial role of optical tweezers in improving the stability of SERS spectra by capturing bacteria in a microfluidic environment, prove that this technology could be used in the rapid identification of lactic acid bacteria, and show great significance in expanding the applicability of the SERS technique for other bacterial testing purposes.
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Affiliation(s)
- Lindong Shang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Peng Liang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lei Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, P. R. China
| | - Ying Xue
- HOOKE Instruments Ltd, Changchun 130031, P. R. China
| | - Kunxiang Liu
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yuntong Wang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiaodong Bao
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Fuyuan Chen
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hao Peng
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yu Wang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian Ju
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, P. R. China
| | - Bei Li
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun 130033, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- HOOKE Instruments Ltd, Changchun 130031, P. R. China
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6
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Yadav S, Bhardwaj R, Mishra P, Singh JP. A magnetic field augmented ultra-thin layer chromatography coupled surface enhanced Raman spectroscopy separation of hemozoin from bacterial mixture. J Chromatogr A 2023; 1708:464318. [PMID: 37660559 DOI: 10.1016/j.chroma.2023.464318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Malaria is considered as one the most widespread disease with highest possibility of co-infection at all levels of the disease prognosis. Rapid detection and discrimination of malaria from other co-infections remains a challenge. Hemozoin is a metabolic biproduct of malaraia possessing paramagnetic property due to presence of iron at its centre. Here, we report a label free, rapid and highly sensitive magnetic field based ultra-thin layer chromatography (UTLC) coupled with surface enhanced Raman spectroscopy (SERS) technique for detection and separation of hemozoin from a bacterial mixture. Highly optimized silver nanorods chip fabricated using glancing angle deposition (GLAD) is explored for the UTLC-SERS separation. These chips possessing channel like characteristic and high surface to the volume ratio serve as excellent UTLC plates. The magnetic nature of hemozoin has been exploited for its separation from the mixture of P. aeruginosa (Gram-negative) and S. aureus (Gram-positive) by allocating a 0.6 T magnet over the UTLC flow setup. The solvent front migrated approximately to a distance of 13 mm from the sample point due to the magnetic environment. Spatially resolved SERS data was collected along the mobile phase and separation of mixture was confirmed. Further, staining of hemozoin, P. aeruginosa and S. aureus was done using methylene blue, acridine orange and rhodamine 6 G respectively. The separation was confirmed for the stained analytes. The present developed method provides plate height as low as 18 µm and hemozoin detection limit as <10 parasites/mL. Therefore, we establish a highly specific and sensitive technique capable of separating small amounts of bioanalytes, aiding in the removal of co-infections from the disease at a very early stage of infection.
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Affiliation(s)
- Sarjana Yadav
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Ritu Bhardwaj
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Prashant Mishra
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - J P Singh
- Department of Physics, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India.
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7
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Perumal AB, Nambiar RB, Luo X, Su Z, Li X, He Y. Exploring dynamic changes of fungal cellular components during nanoemulsion treatment by multivariate microRaman imaging. Talanta 2023; 261:124666. [PMID: 37210918 DOI: 10.1016/j.talanta.2023.124666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
Recently, essential oils (EO) have gained a lot of interest for use as antifungal agent in food and agricultural industry and extensive research is ongoing to understand their mode of action. However, the exact mechanism is not yet elucidated. Here, we integrated spectral unmixing and Raman microspectroscopy imaging to unveil the antifungal mechanism of green tea EO based nanoemulsion (NE) against Magnaporthe oryzae. The dramatic change in protein, lipid, adenine, and guanine bands indicate that NE has a significant impact on the protein, lipid and metabolic processes of purine. The results also demonstrated that the NE treatment caused damage to fungal hyphae by inducing a physical injury leading to cell wall damage and loss of integrity. Our study shows that MCR-ALS (Multivariate Curve Resolution-Alternating Least Squares) and N-FINDR (N-finder algorithm) Raman imaging could serve as a suitable complementary package to the traditional methods, for revealing the antifungal mechanism of action of EO/NE.
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Affiliation(s)
- Anand Babu Perumal
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China.
| | - Reshma B Nambiar
- College of Animal Science, Zhejiang University, Hangzhou, 310058, China.
| | - Xuelun Luo
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Zhenzhu Su
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Xiaoli Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China.
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China.
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Haq AU, Majeed MI, Nawaz H, Rashid N, Javed MR, Raza A, Shakeel M, Zahra ST, Meraj L, Perveen A, Murtaza S, Khaliq S. Surface-enhanced Raman spectroscopy for monitoring antibacterial activity of imidazole derivative (1-benzyl-3-(sec‑butyl)-1H-imidazole-3-ium bromide) against Bacillus subtilis and Escherichia coli. Photodiagnosis Photodyn Ther 2023; 42:103533. [DOI: 10.1016/j.pdpdt.2023.103533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 02/17/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023]
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9
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Accelerating the Detection of Bacteria in Food Using Artificial Intelligence and Optical Imaging. Appl Environ Microbiol 2023; 89:e0182822. [PMID: 36533914 PMCID: PMC9888199 DOI: 10.1128/aem.01828-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In assessing food microbial safety, the presence of Escherichia coli is a critical indicator of fecal contamination. However, conventional detection methods require the isolation of bacterial macrocolonies for biochemical or genetic characterization, which takes a few days and is labor-intensive. In this study, we show that the real-time object detection and classification algorithm You Only Look Once version 4 (YOLOv4) can accurately identify the presence of E. coli at the microcolony stage after a 3-h cultivation. Integrating with phase-contrast microscopic imaging, YOLOv4 discriminated E. coli from seven other common foodborne bacterial species with an average precision of 94%. This approach also enabled the rapid quantification of E. coli concentrations over 3 orders of magnitude with an R2 of 0.995. For romaine lettuce spiked with E. coli (10 to 103 CFU/g), the trained YOLOv4 detector had a false-negative rate of less than 10%. This approach accelerates analysis and avoids manual result determination, which has the potential to be applied as a rapid and user-friendly bacterial sensing approach in food industries. IMPORTANCE A simple, cost-effective, and rapid method is desired to identify potential pathogen contamination in food products and thus prevent foodborne illnesses and outbreaks. This study combined artificial intelligence (AI) and optical imaging to detect bacteria at the microcolony stage within 3 h of inoculation. This approach eliminates the need for time-consuming culture-based colony isolation and resource-intensive molecular approaches for bacterial identification. The approach developed in this study is broadly applicable for the identification of diverse bacterial species. In addition, this approach can be implemented in resource-limited areas, as it does not require expensive instruments and significantly trained human resources. This AI-assisted detection not only achieves high accuracy in bacterial classification but also provides the potential for automated bacterial detection, reducing labor workloads in food industries, environmental monitoring, and clinical settings.
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Bhunia AK, Singh AK, Parker K, Applegate BM. Petri-plate, bacteria, and laser optical scattering sensor. Front Cell Infect Microbiol 2022; 12:1087074. [PMID: 36619754 PMCID: PMC9813400 DOI: 10.3389/fcimb.2022.1087074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Classical microbiology has paved the path forward for the development of modern biotechnology and microbial biosensing platforms. Microbial culturing and isolation using the Petri plate revolutionized the field of microbiology. In 1887, Julius Richard Petri invented possibly the most important tool in microbiology, the Petri plate, which continues to have a profound impact not only on reliably isolating, identifying, and studying microorganisms but also manipulating a microbe to study gene expression, virulence properties, antibiotic resistance, and production of drugs, enzymes, and foods. Before the recent advances in gene sequencing, microbial identification for diagnosis relied upon the hierarchal testing of a pure culture isolate. Direct detection and identification of isolated bacterial colonies on a Petri plate with a sensing device has the potential for revolutionizing further development in microbiology including gene sequencing, pathogenicity study, antibiotic susceptibility testing , and for characterizing industrially beneficial traits. An optical scattering sensor designated BARDOT (bacterial rapid detection using optical scattering technology) that uses a red-diode laser, developed at the beginning of the 21st century at Purdue University, some 220 years after the Petri-plate discovery can identify and study bacteria directly on the plate as a diagnostic tool akin to Raman scattering and hyperspectral imaging systems for application in clinical and food microbiology laboratories.
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Affiliation(s)
- Arun K. Bhunia
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States,Purdue University, Purdue University Interdisciplinary Life Science Program (PULSe), West Lafayette, IN, United States,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, United States,Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States,*Correspondence: Arun K. Bhunia,
| | - Atul K. Singh
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States,Clear Labs, San Carlos, CA, United States
| | - Kyle Parker
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Bruce M. Applegate
- Molecular Food Microbiology Laboratory, Department of Food Science, Purdue University, West Lafayette, IN, United States,Purdue University, Purdue University Interdisciplinary Life Science Program (PULSe), West Lafayette, IN, United States,Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN, United States,Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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Hu H, Wang J, Yi X, Lin K, Meng S, Zhang X, Jiang C, Tang Y, Wang M, He J, Xu X, Song Y. Stain-free Gram staining classification of pathogens via single-cell Raman spectroscopy combined with machine learning. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:4014-4020. [PMID: 36196964 DOI: 10.1039/d2ay01056a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Gram staining (GS) is one of the routine microbiological operations to classify bacteria based on the cell wall structure. Accurate GS classification of pathogens is of great significance since it helps correct administration of antimicrobial treatment. The laborious procedure and low sensitivity results related to conventional GS have resulted in reluctance among clinicians. In this study, we integrate confocal Raman spectroscopy and machine learning techniques to distinguish Gram-negative (GN) or Gram-positive (GP) bacteria. A single-cell Raman database including seven most common clinical pathogens (three GP strains and four GN strains) was constructed. Machine learning algorithms including the support-vector machine (SVM), k-nearest neighbors' algorithm (k-NN), gradient boosting machine (GBM), linear discriminant analysis (LDA), and t-distributed stochastic neighbor embedding (t-SNE) were trained to achieve the binary classification for GS. With such a relatively small database, the SVM model achieved the highest accuracy of 98.1%. The molecular signatures of GN and GP embedded in their Raman fingerprints were identified with hierarchical cluster analysis (HCA). The results indicated that Raman peaks for peptidoglycan and teichoic acid were the most significant factors that contributed to accurate classification. The Raman machine learning approach could greatly enhance the diagnosis of pathogenic infections.
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Affiliation(s)
- Huijie Hu
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, PR China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Xiaofei Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, PR China.
| | - Kaicheng Lin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Xin Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
- Chongqing Guoke Medical Technology Development Co., Ltd, Chongqing 400799, PR China
| | - Chenyu Jiang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
- Jinan Guoke Medical Technology Development Co., Ltd, Jinan 250102, PR China
| | - Yuguo Tang
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, PR China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, PR China.
| | - 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, PR China.
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, PR China.
| | - Yizhi Song
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, PR China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
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12
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Locke AK, Zaki FR, Fitzgerald ST, Sudhir K, Monroy GL, Choi H, Won J, Mahadevan-Jansen A, Boppart SA. Differentiation of otitis media-causing bacteria and biofilms via Raman spectroscopy and optical coherence tomography. Front Cell Infect Microbiol 2022; 12:869761. [PMID: 36034696 PMCID: PMC9400059 DOI: 10.3389/fcimb.2022.869761] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/30/2022] [Indexed: 11/25/2022] Open
Abstract
In the management of otitis media (OM), identification of causative bacterial pathogens and knowledge of their biofilm formation can provide more targeted treatment approaches. Current clinical diagnostic methods rely on the visualization of the tympanic membrane and lack real-time assessment of the causative pathogen(s) and the nature of any biofilm that may reside behind the membrane and within the middle ear cavity. In recent years, optical coherence tomography (OCT) has been demonstrated as an improved in vivo diagnostic tool for visualization and morphological characterization of OM biofilms and middle ear effusions; but lacks specificity about the causative bacterial species. This study proposes the combination of OCT and Raman spectroscopy (RS) to examine differences in the refractive index, optical attenuation, and biochemical composition of Haemophilus influenzae, Streptococcus pneumoniae, Moraxella catarrhalis, and Pseudomonas aeruginosa; four of the leading otopathogens in OM. This combination provides a dual optical approach for identifying and differentiating OM-causing bacterial species under three different in vitro growth environments (i.e., agar-grown colonies, planktonic cells from liquid cultures, and biofilms). This study showed that RS was able to identify key biochemical variations to differentiate all four OM-causing bacteria. Additionally, biochemical spectral changes (RS) and differences in the mean attenuation coefficient (OCT) were able to distinguish the growth environment for each bacterial species.
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Affiliation(s)
- Andrea K. Locke
- Vanderbilt Biophotonics Center, School of Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Chemistry, College of Arts and Science, Vanderbilt University, Nashville, TN, United States
| | - Farzana R. Zaki
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Sean T. Fitzgerald
- Vanderbilt Biophotonics Center, School of Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, United States
| | - Kavya Sudhir
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Bioengineering, The Grainger College of Engineering, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Guillermo L. Monroy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Honggu Choi
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Jungeun Won
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Bioengineering, The Grainger College of Engineering, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Anita Mahadevan-Jansen
- Vanderbilt Biophotonics Center, School of Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Otolaryngology - Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Stephen A. Boppart
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Bioengineering, The Grainger College of Engineering, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Carle Illinois College of Medicine, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, United States
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13
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Cui D, Kong L, Wang Y, Zhu Y, Zhang C. In situ identification of environmental microorganisms with Raman spectroscopy. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 11:100187. [PMID: 36158754 PMCID: PMC9488013 DOI: 10.1016/j.ese.2022.100187] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/13/2022] [Accepted: 05/15/2022] [Indexed: 05/28/2023]
Abstract
Microorganisms in natural environments are crucial in maintaining the material and energy cycle and the ecological balance of the environment. However, it is challenging to delineate environmental microbes' actual metabolic pathways and intraspecific heterogeneity because most microorganisms cannot be cultivated. Raman spectroscopy is a culture-independent technique that can collect molecular vibration profiles from cells. It can reveal the physiological and biochemical information at the single-cell level rapidly and non-destructively in situ. The first part of this review introduces the principles, advantages, progress, and analytical methods of Raman spectroscopy applied in environmental microbiology. The second part summarizes the applications of Raman spectroscopy combined with stable isotope probing (SIP), fluorescence in situ hybridization (FISH), Raman-activated cell sorting and genomic sequencing, and machine learning in microbiological studies. Finally, this review discusses expectations of Raman spectroscopy and future advances to be made in identifying microorganisms, especially for uncultured microorganisms.
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Affiliation(s)
- Dongyu Cui
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lingchao Kong
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yi Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuanqing Zhu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, University of Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
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14
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New Insights into the Multivariate Analysis of SER Spectra Collected on Blood Samples for Prostate Cancer Detection: Towards a Better Understanding of the Role Played by Different Biomolecules on Cancer Screening: A Preliminary Study. Cancers (Basel) 2022; 14:cancers14133227. [PMID: 35804993 PMCID: PMC9264810 DOI: 10.3390/cancers14133227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary In recent years, research on biofluids using Raman and SERS has expanded dramatically, indicating the enormous promise of this technology as a high-throughput tool for identifying cancer and other disorders. In the investigations thus far, researchers have concentrated on a specific illness or condition, but the techniques employed to acquire experimental spectra prevent direct comparison of the data. This necessitates comparative research of a variety of diseases and an increase in scientific cooperation to standardize experimental conditions. In our study, positive results were reached by applying a combined SERS multivariate analysis (MVA) to the urgent problem of prostate cancer diagnosis that was directly linked to real-world settings in healthcare. Moreover, in comparison to the prostate-specific antigen (PSA) test, which has a high sensitivity but limited specificity, our combined SERS-MVA method has greater specificity, which may assist in preventing the overtreatment of patients. Abstract It is possible to obtain diagnostically relevant data on the changes in biochemical elements brought on by cancer via the use of multivariate analysis of vibrational spectra recorded on biological fluids. Prostate cancer and control groups included in this research generated almost similar SERS spectra, which means that the values of peak intensities present in SERS spectra can only give unspecific and limited information for distinguishing between the two groups. Our diagnostic algorithm for prostate cancer (PCa) differentiation was built using principal component analysis and linear discriminant analysis (PCA-LDA) analysis of spectral data, which has been widely used in spectral data management in many studies and has shown promising results so far. In order to fully utilize the entire SERS spectrum and automatically determine the most meaningful spectral features that can be used to differentiate PCa from healthy patients, we perform a multivariate analysis on both the entire and specific spectral intervals. Using the PCA-LDA model, the prostate cancer and control groups are clearly distinguished in our investigation. The separability of the following two data sets is also evaluated using two alternative discrimination techniques: principal least squares discriminant analysis (PLS-DA) and principal component analysis—support vector machine (PCA-SVM).
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15
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Discrimination of Stressed and Non-Stressed Food-Related Bacteria Using Raman-Microspectroscopy. Foods 2022; 11:foods11101506. [PMID: 35627076 PMCID: PMC9141442 DOI: 10.3390/foods11101506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 01/27/2023] Open
Abstract
As the identification of microorganisms becomes more significant in industry, so does the utilization of microspectroscopy and the development of effective chemometric models for data analysis and classification. Since only microorganisms cultivated under laboratory conditions can be identified, but they are exposed to a variety of stress factors, such as temperature differences, there is a demand for a method that can take these stress factors and the associated reactions of the bacteria into account. Therefore, bacterial stress reactions to lifetime conditions (regular treatment, 25 °C, HCl, 2-propanol, NaOH) and sampling conditions (cold sampling, desiccation, heat drying) were induced to explore the effects on Raman spectra in order to improve the chemometric models. As a result, in this study nine food-relevant bacteria were exposed to seven stress conditions in addition to routine cultivation as a control. Spectral alterations in lipids, polysaccharides, nucleic acids, and proteins were observed when compared to normal growth circumstances without stresses. Regardless of the involvement of several stress factors and storage times, a model for differentiating the analyzed microorganisms from genus down to strain level was developed. Classification of the independent training dataset at genus and species level for Escherichia coli and at strain level for the other food relevant microorganisms showed a classification rate of 97.6%.
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16
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Shen H, Rösch P, Popp J. Fiber Probe-Based Raman Spectroscopic Identification of Pathogenic Infection Microorganisms on Agar Plates. Anal Chem 2022; 94:4635-4642. [PMID: 35254815 DOI: 10.1021/acs.analchem.1c04507] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rapid identification of microorganisms is clinically meaningful, and it helps to decelerate the spread of drug resistance and improve patient treatment. In this study, we present a rapid fiber probe-based Raman technique with an excitation wavelength of 785 nm, which is applied to classify and identify nine different species of microorganisms. The cost-effective fiber probe compresses the dimension of the system and provides a more reliable and stable database. All microorganisms were simply cultivated on Luria-Bertani (LB) agar, and Raman spectra were obtained directly from the microbial colonies with the fiber probe within 30 s. The classification model consists of principal component analysis (PCA) in combination with linear discriminant analysis (LDA) and was examined by applying leave-one-batch-out cross-validation (LOBOCV). This model achieved an accuracy of 98.9%. In addition, the validation and identification processes based on independent replicates achieved accuracies of 99.8% and 100%, respectively. The results demonstrated that fiber probe Raman spectroscopy in combination with chemometric analysis allowed a rapid classification and identification of microorganisms only with a normal culture. Therefore, it is promising especially for medical applications and could moreover be helpful to investigate and identify microorganisms rapidly in further studies.
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Affiliation(s)
- Haodong Shen
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany.,Leibniz Institute of Photonic Technology Jena - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Str. 9, D-07745 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Helmholtzweg 4, D-07743 Jena, Germany.,InfectoGnostics Research Campus Jena, Philosophenweg 7, D-07743 Jena, Germany.,Leibniz Institute of Photonic Technology Jena - Member of the Research Alliance "Leibniz Health Technologies", Albert-Einstein-Str. 9, D-07745 Jena, Germany
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17
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A Review of Raman-Based Technologies for Bacterial Identification and Antimicrobial Susceptibility Testing. PHOTONICS 2022. [DOI: 10.3390/photonics9030133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Antimicrobial resistance (AMR) is a global medical threat that seriously endangers human health. Rapid bacterial identification and antimicrobial susceptibility testing (AST) are key interventions to combat the spread and emergence of AMR. Although current clinical bacterial identification and AST provide comprehensive information, they are labor-intensive, complex, inaccurate, and slow (requiring several days, depending on the growth of pathogenic bacteria). Recently, Raman-based identification and AST technologies have played an increasingly important role in fighting AMR. This review summarizes major Raman-based techniques for bacterial identification and AST, including spontaneous Raman scattering, surface-enhanced Raman scattering (SERS), and coherent Raman scattering (CRS) imaging. Then, we discuss recent developments in rapid identification and AST methods based on Raman technology. Finally, we highlight the major challenges and potential future efforts to improve clinical outcomes through rapid bacterial identification and AST.
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18
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Shlosberg Y, Farber Y, Hasson S, Bulatov V, Schechter I. Identification of bacteria by poly-aromatic hydrocarbon biosensors. Anal Bioanal Chem 2022; 414:3153-3160. [PMID: 35129639 DOI: 10.1007/s00216-022-03947-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/19/2022] [Accepted: 01/31/2022] [Indexed: 12/01/2022]
Abstract
Human health is consistently threatened by different species of pathogenic bacteria. To fight the spread of diseases, it is important to develop rapid methods for bacterial identification. Over the years, different kinds of biosensors were developed for this cause. Another environmental risk is poly-aromatic hydrocarbons (PAHs) that may be emitted from industrial facilities and pollute environmental water and soil. One of the methods for their purification is conducted by the addition of bacteria that can degrade the PAHs, while the bacteria can be filtrated at the end of the process. Although many studies reported monitoring of the PAHs degradation by fluorescence, not much attention was dedicated to studying the influence of the PAHs on the intrinsic fluorescence of the degrading bacteria. In this work, we apply synchronous fluorescence (SF) measurements to study the ability of the 5 PAHs: 9-Antracene carboxylic acid (9ACA), Pyrene, Perylene, Pentacene, and Chrysene to interact with bacteria and change its fluorescence spectra. We show that upon incubation of each PAH with the bacterium E. coli, only the 2 PAHs 9ACA and Perylene cause an intensity decrease in the emission at λ = 300-375 nm, which derives from the emission of tyrosine and tryptophan (TT). Also, we show that upon incubation of 9ACA and Perylene with 5 different pathogenic bacteria, the intensity increase or decrease in the TT emission is unique to each bacterial species. Based on this observation, we suggest that the PAHs 9ACA and Perylene can be utilized as biosensors for bacterial identification.
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Affiliation(s)
- Yaniv Shlosberg
- Schulich Faculty of Chemistry, 3200003, Technion, Haifa, Israel.
| | - Yair Farber
- Quality and Reliability Engineering Department, Kinneret Academic College, 1513200, Zemach, Israel.,Grand Water Research Institute, 3200003, Technion, Haifa, Israel
| | - Salah Hasson
- Schulich Faculty of Chemistry, 3200003, Technion, Haifa, Israel
| | - Valery Bulatov
- Schulich Faculty of Chemistry, 3200003, Technion, Haifa, Israel
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19
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Cui L, Li HZ, Yang K, Zhu LJ, Xu F, Zhu YG. Raman biosensor and molecular tools for integrated monitoring of pathogens and antimicrobial resistance in wastewater. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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20
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Fast label-free identification of bacteria by synchronous fluorescence of amino acids. Anal Bioanal Chem 2021; 413:6857-6866. [PMID: 34491394 DOI: 10.1007/s00216-021-03642-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Fast identification of pathogenic bacteria is an essential need for patient's diagnostic in hospitals and environmental monitoring of water and air quality. Bacterial cells consist of a very high amount of biological molecules whose content changes in response to different environmental conditions. The similarity between the molecular compositions of different bacterial cells limits the possibility to find unique markers to enable differentiation among species. Although many biological molecules in the cells absorb at the UV-Vis region, only a few of them can be detected in whole cells by their intrinsic fluorescence. Among these molecules are the amino acids phenylalanine, tyrosine, and tryptophan. In this work, we develop a rapid method for bacterial identification by synchronous fluorescence. We show that we can quantify the concentration for the 3 amino acids without any significant interference from other fluorophores in the cells and that we can differentiate among 6 pathogenic bacterial species by using the concentrations of their amino acids as a bacterial fingerprint. Fluorescent amino acids exist in all living cells. Therefore, this method has the potential to be applicative for the rapid identification of cells from all kinds of organisms.
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21
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Perumal AB, Li X, Su Z, He Y. Preparation and characterization of a novel green tea essential oil nanoemulsion and its antifungal mechanism of action against Magnaporthae oryzae. ULTRASONICS SONOCHEMISTRY 2021; 76:105649. [PMID: 34186493 PMCID: PMC8250457 DOI: 10.1016/j.ultsonch.2021.105649] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 05/21/2023]
Abstract
Blast is one of the most devastating fungal diseases of rice caused by Magnaporthe oryzae. Plant essential oil (EO) can function as antifungal agents and are regarded as a safe and acceptable method for plant disease control. However, EOs are unstable and hydrophobic, which limits its use. In the present study, we aimed for the preparation and characterization of a nanoemulsion (NE) from green tea essential oil (GTO) by ultrasonication method and determined the antifungal activity of NE onM. oryzae. The particle size and zeta potential of the NE were 86.98 nm and -15.1 mV, respectively. The chemical composition and functional groups of GTO and NE were studied by using GC-MS analysis, portable Raman spectroscopy, and FTIR coupled with chemometric analysis. GC-MS analysis showed the major components in GTO and NE were n-Hexyl cinnamaldehyde and L-α-Terpineol. Both GTO and NE showed good antioxidant activity and total phenol content. Moreover, the NE showed good antifungal activity againstM. oryzae which was further confirmed by scanning electron microscopy (SEM) examination. Also, confocal Raman micro-spectroscopy (CRM) revealed the antifungal mechanism of GTO and NE on M. oryzae which proves the cell damage. To the best of our knowledge, this is the first study on the antifungal activity of GTO and NE against M. oryzae and also the use of CRM for the evaluation of the chemical changes in single fungal hyphae in a holistic approach. This study suggests that the prepared NE could be a potential candidate for use as a substitute for synthetic fungicides.
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Affiliation(s)
- Anand Babu Perumal
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Xiaoli Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Zhenzhu Su
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Yong He
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
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22
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Saif FA, Yaseen SA, Alameen AS, Mane SB, Undre PB. Identification and characterization of Aspergillus species of fruit rot fungi using microscopy, FT-IR, Raman and UV-Vis spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 246:119010. [PMID: 33035886 DOI: 10.1016/j.saa.2020.119010] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/19/2020] [Accepted: 09/23/2020] [Indexed: 05/11/2023]
Abstract
During the investigation of fungal isolation from fruit, the major genera were Aspergillus, Penicillium, cladosporium, Alternaria, fusarium, Colletotrichum were found. Among them Aspergillus (15 species) was found major dominant on different fruits. Fifteen different Aspergillus species viz. Aspergillus brasiliensis, Aspergillus phoenicis, Aspergillus carbonarius, four Aspergillus flavus, Aspergillus acidus, two Aspergillus awamori, Aspergillus aculeatus, Aspergillus eucalypticola, Aspergillus oryzae and two Aspergillus Spp. have been differentiate and identify using morphology (microscopic technique), Fourier Transforms Infrared spectroscopy (FTIR), Raman Spectroscopy (RS) and UV-visible spectrophotometry (UV-vis). The fungal mass in powder form was used in present study. In FTIR the finger print region is important for the characterization of Aspergillus because this region is unique and contains peaks indicating the presence of DNA. From the results were found Fourier transform infrared (FTIR) technique and Raman spectroscopy a useful tool, sensitive, fast, economical, accurate, not require sample preparation and successfully used to identify fungi.
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Affiliation(s)
- F A Saif
- Microwave Research Laboratory, Department of Physics, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra 431004, India
| | - S A Yaseen
- Microwave Research Laboratory, Department of Physics, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra 431004, India
| | - A S Alameen
- Microwave Research Laboratory, Department of Physics, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra 431004, India
| | - S B Mane
- Microbical Cultural Laboratory, Department of Botany, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra 431004, India
| | - P B Undre
- Microwave Research Laboratory, Department of Physics, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Maharashtra 431004, India.
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23
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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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24
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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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25
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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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Prasad A, Hasan SMA, Gartia MR. Optical Identification of Middle Ear Infection. Molecules 2020; 25:molecules25092239. [PMID: 32397569 PMCID: PMC7248855 DOI: 10.3390/molecules25092239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 11/16/2022] Open
Abstract
Ear infection is one of the most commonly occurring inflammation diseases in the world, especially for children. Almost every child encounters at least one episode of ear infection before he/she reaches the age of seven. The typical treatment currently followed by physicians is visual inspection and antibiotic prescription. In most cases, a lack of improper treatment results in severe bacterial infection. Therefore, it is necessary to design and explore advanced practices for effective diagnosis. In this review paper, we present the various types of ear infection and the related pathogens responsible for middle ear infection. We outline the conventional techniques along with clinical trials using those techniques to detect ear infections. Further, we highlight the need for emerging techniques to reduce ear infection complications. Finally, we emphasize the utility of Raman spectroscopy as a prospective non-invasive technique for the identification of middle ear infection.
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Evaluation of the impact of buffered peptone water composition on the discrimination between Salmonella enterica and Escherichia coli by Raman spectroscopy. Anal Bioanal Chem 2020; 412:3595-3604. [PMID: 32248395 DOI: 10.1007/s00216-020-02596-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/19/2020] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
The detection of Salmonella spp. in food samples is regulated by the ISO 6579:2002 standard, which requires that precise procedures are followed to ensure the reliability of the detection process. This standard requires buffered peptone water as a rich medium for the enrichment of bacteria. However, the effects of different brands of buffered peptone water on the identification of microorganisms by Raman spectroscopy are unknown. In this regard, our study evaluated the discrimination between two bacterial species, Salmonella enterica and Escherichia coli, inoculated and analyzed with six of the most commonly used buffered peptone water brands. The results showed that bacterial cells behaved differently according to the brand used in terms of biomass production and the spectral fingerprint. The identification accuracy of the analyzed strains was between 85% and 100% depending on the given brand. Several batches of two brands were studied to evaluate the classification rates between the analyzed bacterial species. The chemical analysis performed on these brands showed that the nutrient content was slightly different and probably explained the observed effects. On the basis of these results, Raman spectroscopy operators are encouraged to select an adequate culture medium and continue its use throughout the identification process to guarantee optimal recognition of the microorganism of interest.
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Rangan S, Schulze HG, Vardaki MZ, Blades MW, Piret JM, Turner RFB. Applications of Raman spectroscopy in the development of cell therapies: state of the art and future perspectives. Analyst 2020; 145:2070-2105. [DOI: 10.1039/c9an01811e] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
This comprehensive review article discusses current and future perspectives of Raman spectroscopy-based analyses of cell therapy processes and products.
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Affiliation(s)
- Shreyas Rangan
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
- School of Biomedical Engineering
| | - H. Georg Schulze
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
| | - Martha Z. Vardaki
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
| | - Michael W. Blades
- Department of Chemistry
- The University of British Columbia
- Vancouver
- Canada
| | - James M. Piret
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
- School of Biomedical Engineering
| | - Robin F. B. Turner
- Michael Smith Laboratories
- The University of British Columbia
- Vancouver
- Canada
- Department of Chemistry
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Li H, Martin FL, Jones KC, Zhang D. Interrogating the Transient Selectivity of Bacterial Chemotaxis-Driven Affinity and Accumulation of Carbonaceous Substances via Raman Microspectroscopy. Front Microbiol 2019; 10:2215. [PMID: 31636611 PMCID: PMC6787638 DOI: 10.3389/fmicb.2019.02215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/10/2019] [Indexed: 12/28/2022] Open
Abstract
Carbonaceous substances are fundamental organic nutrients for microbial metabolism and catabolism in natural habitats. Microbial abilities to sense, accumulate, and utilize organic carbonaceous substances in the complex nutrient environment are important for their growth and ecological functions. Bacterial chemotaxis is an effective mechanism for microbial utilization of carbonaceous substances under nutrient depletion conditions. Although bacterial accumulation and utilization to individual carbonaceous substance in long-term cultivation has been well studied, their selective affinity of mixed carbonaceous substances remains to be investigated, primarily because of technical limitations of conventional methods. Herein, we applied Raman microspectroscopy to identify chemotaxis-driven affinity and accumulation of four organic carbonaceous substances (glucose, succinate, acetate, and salicylate) by three bacterial strains (Acinetobacter baylyi, Pseudomonas fluorescence, and Escherichia coli). A. baylyi exhibited strong binding affinity toward glucose and succinate, whereas P. fluorescence and E. coli were preferentially responsive to glucose and acetate. For the first time, bacterial transient selectivity of carbonaceous substances was studied via interrogating Raman spectral alterations. Post-exposure to carbonaceous-substance mixtures, the three bacterial strains showed distinct selective behaviors. Stronger selective affinity enhanced the chemotaxis-related signal transduction in A. baylyi cells, whereas the carbonaceous substance signal transduction in E. coli was decreased by higher selective affinity. In P. fluorescence, there was no specific effect of selective affinity on signal transduction. Our study suggests that Raman microspectroscopy can successfully investigate and distinguish different scenarios of bacterial competitive and transient unitization of organic carbonaceous substances.
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Affiliation(s)
- Hanbing Li
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, China.,Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, United Kingdom
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Lancaster, United Kingdom
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing, China
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31
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Lin Z, Zhao X, Huang J, Liu W, Zheng Y, Yang X, Zhang Y, Lamy de la Chapelle M, Fu W. Rapid screening of colistin-resistant Escherichia coli, Acinetobacter baumannii and Pseudomonas aeruginosa by the use of Raman spectroscopy and hierarchical cluster analysis. Analyst 2019; 144:2803-2810. [PMID: 30882113 DOI: 10.1039/c8an02220h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Colistin is recognized as the last therapeutic option for multidrug-resistant Gram-negative bacteria infection. In addition, bacterial resistance to colistin could be transmitted between different species through plasmid-mediated mcr-1 gene transfer. Therefore, rapid screening of colistin-resistant isolates will play a key role in controlling the spread of resistance and improving patient outcomes. We developed a rapid method for the detection of colistin-resistance in Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa bacteria based on Raman spectroscopy and hierarchical cluster analysis. Bacteria were incubated with and without colistin using CAMHB as the liquid culture medium. They were then centrifuged and dried on a glass slide. Five Raman spectra of each of the samples were recorded and analyzed by the hierarchical cluster analysis method to determine whether the bacteria were resistant. To evaluate this method, 123 clinical bacterial isolates (42 isolates of E. coli, 41 isolates of A. baumannii and 40 isolates of P. aeruginosa) were tested. The detection sensitivity and specificity were 90.9% and 91.1%, respectively, compared with the reference broth microdilution method. The screening is easy to perform and can be completed in 1.5 h, suggesting that it holds great potential to be an initial screening method in countries and areas where colistin becomes the last resort antibiotic.
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Affiliation(s)
- Zhongquan Lin
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.
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M Y, Chawla K, Bankapur A, Acharya M, D’Souza JS, Chidangil S. A micro-Raman and chemometric study of urinary tract infection-causing bacterial pathogens in mixed cultures. Anal Bioanal Chem 2019; 411:3165-3177. [DOI: 10.1007/s00216-019-01784-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/07/2019] [Accepted: 03/15/2019] [Indexed: 01/30/2023]
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Kumamoto Y, Mochizuki K, Hashimoto K, Harada Y, Tanaka H, Fujita K. High-Throughput Cell Imaging and Classification by Narrowband and Low-Spectral-Resolution Raman Microscopy. J Phys Chem B 2019; 123:2654-2661. [PMID: 30830787 DOI: 10.1021/acs.jpcb.8b11295] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigated the use of narrowband Raman spectra for rapid label-free molecular imaging aimed at cell classification using principal component regression and linear discriminant analysis. In the classification of breast nontumorigenic epithelial and cancer cell lines, the classification accuracies using a spectral range of 100 cm-1 were equivalent to or better than that with using the fingerprint and high-wavenumber regions. Narrowing the Raman spectral range for analysis allows reduction of the charge-coupled device (CCD) pixels required for spectrum detection, resulting in the improvement of image acquisition speed with adequate classification accuracy. Our measurements revealed that the wavenumber region at 1397-1501 cm-1 can provide molecular information sufficient for cell classification without causing notable errors in the baseline-correction. A spectral resolution of ∼9 cm-1 was found to be sufficient to provide high accuracy in cell classification, which allowed us to apply pixel binning at the CCD readout for further acceleration of the imaging speed. As a result, the acquisition time for a 1200 × 1500 pixels Raman hyperspectral image at 1397-1501 cm-1 was reduced to 21 min. Under this condition, different cell lines were classified at accuracies higher than 90%. The presented approach will improve throughput of cell and tissue analysis and classification using Raman spectroscopy and extend practical uses of Raman imaging in biology and medicine.
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Affiliation(s)
- Yasuaki Kumamoto
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences , Kyoto Prefectural University of Medicine , 465 Kajiicho, Kawaramachi-Hirokoji , Kamigyo, Kyoto , Kyoto 6028566 , Japan
| | | | - Kosuke Hashimoto
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences , Kyoto Prefectural University of Medicine , 465 Kajiicho, Kawaramachi-Hirokoji , Kamigyo, Kyoto , Kyoto 6028566 , Japan
| | - Yoshinori Harada
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences , Kyoto Prefectural University of Medicine , 465 Kajiicho, Kawaramachi-Hirokoji , Kamigyo, Kyoto , Kyoto 6028566 , Japan
| | - Hideo Tanaka
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences , Kyoto Prefectural University of Medicine , 465 Kajiicho, Kawaramachi-Hirokoji , Kamigyo, Kyoto , Kyoto 6028566 , Japan
| | - Katsumasa Fujita
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences , Kyoto Prefectural University of Medicine , 465 Kajiicho, Kawaramachi-Hirokoji , Kamigyo, Kyoto , Kyoto 6028566 , Japan
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34
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Wei C, Li M, Zhao X. Surface-Enhanced Raman Scattering (SERS) With Silver Nano Substrates Synthesized by Microwave for Rapid Detection of Foodborne Pathogens. Front Microbiol 2018; 9:2857. [PMID: 30619101 PMCID: PMC6300495 DOI: 10.3389/fmicb.2018.02857] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 11/06/2018] [Indexed: 12/30/2022] Open
Abstract
Rapid and sensitive methods have been developed to detect foodborne pathogens, a development that is important for food safety. The aim of this study is to explore Surface-enhanced Raman scattering (SERS) with silver nano substrates to detect and identify the following three foodborne pathogens: Escherichia coli O157: H7, Staphylococcus aureus and Salmonella. All the cells were resuspended with 10 mL silver colloidal nanoparticles, making a concentration of 107 CFU/mL, and were then exposed to 785 nm laser excitation. In this study, the results showed that all the bacteria can be sensitively and reproducibly detected directly by SERS. The distinctive differences can be observed in the SERS spectral data of the three food-borne pathogens, and the silver colloidal nanoparticles can be used as highly sensitive SERS-active substrates. In addition, the assay time required only a few minutes, which indicated that SERS coupled with the silver colloidal nanoparticles is a promising method for the detection and characterization of food-borne pathogens. At the same time, principle component analysis (PCA) and hierarchical cluster analysis (HCA) made the different bacterial strains clearly differentiated based on the barcode spectral data reduction. Therefore, the SERS methods hold great promise for the detection and identification of food-borne pathogens and even for applications in food safety.
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Affiliation(s)
| | | | - Xihong Zhao
- Research Center for Environmental Ecology and Engineering, Key Laboratory for Green Chemical Process of Ministry of Education, Key Laboratory for Hubei Novel Reactor & Green Chemical Technology, School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
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35
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P Santos I, van Doorn R, Caspers PJ, Bakker Schut TC, Barroso EM, Nijsten TEC, Noordhoek Hegt V, Koljenović S, Puppels GJ. Improving clinical diagnosis of early-stage cutaneous melanoma based on Raman spectroscopy. Br J Cancer 2018; 119:1339-1346. [PMID: 30410059 PMCID: PMC6265324 DOI: 10.1038/s41416-018-0257-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/06/2018] [Accepted: 08/17/2018] [Indexed: 12/31/2022] Open
Abstract
Background Clinical diagnosis of early melanoma (Breslow thickness less than 0.8 mm) is crucial to disease-free survival. However, it is subjective and can be exceedingly difficult, leading to missed melanomas, or unnecessary excision of benign pigmented skin lesions. An objective technique is needed to improve the diagnosis of early melanoma. Methods We have developed a method to improve diagnosis of (thin) melanoma, based on Raman spectroscopy. In an ex vivo study in a tertiary referral (pigmented lesions) centre, high-wavenumber Raman spectra were collected from 174 freshly excised melanocytic lesions suspicious for melanoma. Measurements were performed on multiple locations within the lesions. A diagnostic model was developed and validated on an independent data set of 96 lesions. Results Approximately 60% of the melanomas included in this study were melanomas in situ. The invasive melanomas had an average Breslow thickness of 0.89 mm. The diagnostic model correctly classified all melanomas (including in situ) with a specificity of 43.8%, and showed a potential improvement of the number needed to treat from 6.0 to 2.7, at a sensitivity of 100%. Conclusion This work signifies an important step towards accurate and objective clinical diagnosis of melanoma and in particular melanoma with Breslow thickness <0.8 mm.
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Affiliation(s)
- Inês P Santos
- Department of Dermatology, Erasmus MC, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, Netherlands
| | - Peter J Caspers
- Department of Dermatology, Erasmus MC, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Tom C Bakker Schut
- Department of Dermatology, Erasmus MC, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Elisa M Barroso
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and Orthodontics, Erasmus MC, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Tamar E C Nijsten
- Department of Dermatology, Erasmus MC, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Vincent Noordhoek Hegt
- Department of Pathology, Erasmus MC, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Senada Koljenović
- Department of Pathology, Erasmus MC, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Gerwin J Puppels
- Department of Dermatology, Erasmus MC, Erasmus University Medical Center Rotterdam, Rotterdam, Netherlands.
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36
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Muhamadali H, Subaihi A, Mohammadtaheri M, Xu Y, Ellis DI, Ramanathan R, Bansal V, Goodacre R. Rapid, accurate, and comparative differentiation of clinically and industrially relevant microorganisms via multiple vibrational spectroscopic fingerprinting. Analyst 2018; 141:5127-36. [PMID: 27414261 DOI: 10.1039/c6an00883f] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Despite the fact that various microorganisms (e.g., bacteria, fungi, viruses, etc.) have been linked with infectious diseases, their crucial role towards sustaining life on Earth is undeniable. The huge biodiversity, combined with the wide range of biochemical capabilities of these organisms, have always been the driving force behind their large number of current, and, as of yet, undiscovered future applications. The presence of such diversity could be said to expedite the need for the development of rapid, accurate and sensitive techniques which allow for the detection, differentiation, identification and classification of such organisms. In this study, we employed Fourier transform infrared (FT-IR), Raman, and surface enhanced Raman scattering (SERS) spectroscopies, as molecular whole-organism fingerprinting techniques, combined with multivariate statistical analysis approaches for the classification of a range of industrial, environmental or clinically relevant bacteria (P. aeruginosa, P. putida, E. coli, E. faecium, S. lividans, B. subtilis, B. cereus) and yeast (S. cerevisiae). Principal components-discriminant function analysis (PC-DFA) scores plots of the spectral data collected from all three techniques allowed for the clear differentiation of all the samples down to sub-species level. The partial least squares-discriminant analysis (PLS-DA) models generated using the SERS spectral data displayed lower accuracy (74.9%) when compared to those obtained from conventional Raman (97.8%) and FT-IR (96.2%) analyses. In addition, whilst background fluorescence was detected in Raman spectra for S. cerevisiae, this fluorescence was quenched when applying SERS to the same species, and conversely SERS appeared to introduce strong fluorescence when analysing P. putida. It is also worth noting that FT-IR analysis provided spectral data of high quality and reproducibility for the whole sample set, suggesting its applicability to a wider range of samples, and perhaps the most suitable for the analysis of mixed cultures in future studies. Furthermore, our results suggest that while each of these spectroscopic approaches may favour different organisms (sample types), when combined, they would provide complementary and more in-depth knowledge (structural and/or metabolic state) of biological systems. To the best of our knowledge, this is the first time that such a comparative and combined spectroscopic study (using FT-IR, Raman and SERS) has been carried out on microbial samples.
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Affiliation(s)
- Howbeer Muhamadali
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Abdu Subaihi
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Mahsa Mohammadtaheri
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, Australia
| | - Yun Xu
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - David I Ellis
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
| | - Rajesh Ramanathan
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, Australia
| | - Vipul Bansal
- Ian Potter NanoBioSensing Facility, NanoBiotechnology Research Laboratory, School of Science, RMIT University, Melbourne, Australia
| | - Royston Goodacre
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK.
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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: 31] [Impact Index Per Article: 5.2] [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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Li Y, Cope HA, Rahman SM, Li G, Nielsen PH, Elfick A, Gu AZ. Toward Better Understanding of EBPR Systems via Linking Raman-Based Phenotypic Profiling with Phylogenetic Diversity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:8596-8606. [PMID: 29943965 DOI: 10.1021/acs.est.8b01388] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This study reports a proof-of concept study to demonstrate the novel approach of phenotyping microbial communities in enhanced biological phosphorus removal (EBPR) systems using single cell Raman microspectroscopy and link it with phylogentic structures. We use hierarchical clustering analysis (HCA) of single-cell Raman spectral fingerprints and intracellular polymer signatures to separate and classify the functionally relevant populations in EBPR systems, namely polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs), as well as other microbial populations. We then investigated the link between Raman-based community phenotyping and 16S rRNA gene-based phylogenetic characterization of four lab-scale EBPR systems with varying solid retention time (SRT) to gain insights into possible genotype-function relationships. Combined and simultaneous phylogenetic and phenotypic evaluation of EBPR ecosystems revealed SRT-dependent phylogenetic and phenotypic characteristics of the PAOs and GAOs, and their association with EBPR performance. The phenotypic diversity and plasticity of PAO populations, which otherwise could not be obtained with phylogenetic analysis alone, showed complex but potentially crucial association with EBPR process stability.
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Affiliation(s)
- Yueyun Li
- Civil and Environmental Engineering Department , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Helen A Cope
- School of Engineering, Institute for Bioengineering , The University of Edinburgh , Edinburgh , U.K
| | - Sheikh M Rahman
- Civil and Environmental Engineering Department , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Guangyu Li
- Civil and Environmental Engineering Department , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience , Aalborg University , Aalborg , Denmark
| | - Alistair Elfick
- School of Engineering, Institute for Bioengineering , The University of Edinburgh , Edinburgh , U.K
| | - April Z Gu
- Civil and Environmental Engineering Department , Northeastern University , Boston , Massachusetts 02115 , United States
- School of Civil and Environmental Engineering , Cornell University , Ithaca , New York 14853 , United States
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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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40
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The application of UV resonance Raman spectroscopy for the differentiation of clinically relevant Candida species. Anal Bioanal Chem 2018; 410:5839-5847. [DOI: 10.1007/s00216-018-1196-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/30/2018] [Accepted: 06/13/2018] [Indexed: 01/21/2023]
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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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Kumamoto Y, Harada Y, Takamatsu T, Tanaka H. Label-free Molecular Imaging and Analysis by Raman Spectroscopy. Acta Histochem Cytochem 2018; 51:101-110. [PMID: 30083018 PMCID: PMC6066646 DOI: 10.1267/ahc.18019] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 05/25/2018] [Indexed: 01/06/2023] Open
Abstract
Raman scattering of a cell conveys the intrinsic information inherent to chemical structures of biomolecules. The spectroscopy of Raman scattering, or Raman spectroscopy, allows label-free and quantitative molecular sensing of a biological sample in situ without disruption. For the last five decades Raman spectroscopy has been widely utilized in biological research fields. However, it is just within the latest decade that molecular imaging and discrimination of living cells and tissues have become practically available. Here we overview recent progress in Raman spectroscopy and its application to life sciences. We discuss imaging of functional molecules in living cells and tissues; e.g., cancer cells and ischemic or infarcted hearts, together with a number of studies in the biomedical fields. We further explore comprehensive understandings of a complex spectrum by multivariate analysis for, e.g., accurate peripheral nerve detection, and characterization of the histological differences in the healing process of myocardial infarct. Although limitations still remain, e.g., weakness of the scattering intensity and practical difficulty in comprehensive molecular analysis, continuous progress in related technologies will allow wider use of Raman spectroscopy for biomedical applications.
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Affiliation(s)
- Yasuaki Kumamoto
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine
| | - Yoshinori Harada
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine
| | - Tetsuro Takamatsu
- Department of Medical Photonics, Kyoto Prefectural University of Medicine
| | - Hideo Tanaka
- Department of Pathology and Cell Regulation, Graduate School of Medical Sciences, Kyoto Prefectural University of Medicine
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43
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Pavlicek RL, Crane NJ, Ghebremedhin M, Cilwa KE, Elster EA. Diagnostic Bacteriology: Raman Spectroscopy. Methods Mol Biol 2018; 1616:249-261. [PMID: 28600775 DOI: 10.1007/978-1-4939-7037-7_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Current clinical methodology for identification of bacterial infections relies predominantly on culturing microbes from patient material and performing biochemical tests. This can often be an inefficient and lengthy process, which has a significant detrimental effect upon patient care. Techniques used in other aspects of molecular research have the potential to revolutionize the way in which diagnostic tests are used and delivered in the clinical setting. The need for rapid, accurate, and cost-effective molecular techniques in the diagnostic laboratory is imperative to improving patient care, preventing the spread of drug resistance and decreasing the overall burden associated with nosocomial infections. Raman spectroscopy and surface-enhanced Raman spectroscopy (SERS) are powerful vibrational spectroscopy techniques that are being developed for highly sensitive pathogen identification in complex clinical samples. Raman spectroscopy is a molecular technique that is capable of probing samples noninvasively and nondestructively. It has been used with high specificity to assess tissue and bacterial samples at the molecular level with diverse clinical and diagnostic applications. SERS has recently developed out of the advances in the Raman spectroscopy arena. This technique is designed to amplify Raman scattering and allows for better differentiation of bacterial isolates. Although the current parameters for the use of SERS require a pure culture and are relatively monoparametric, current breakthroughs and testing are pushing the technology to new levels and thus changing the face of modern bacterial diagnostics.
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Affiliation(s)
| | - Nicole J Crane
- The Department of Surgery at Uniformed Services University of the Health Sciences & The Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Meron Ghebremedhin
- Department of Regenerative Medicine, Naval Medical Research Center, Silver Spring, MD, USA
| | - Katherine E Cilwa
- Department of Regenerative Medicine, Naval Medical Research Center, Silver Spring, MD, USA
| | - Eric A Elster
- The Department of Surgery at Uniformed Services University of the Health Sciences & The Walter Reed National Military Medical Center, Bethesda, MD, USA.
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44
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Wieland K, Kuligowski J, Ehgartner D, Ramer G, Koch C, Ofner J, Herwig C, Lendl B. Toward a Noninvasive, Label-Free Screening Method for Determining Spore Inoculum Quality of Penicillium chrysogenum Using Raman Spectroscopy. APPLIED SPECTROSCOPY 2017; 71:2661-2669. [PMID: 28776414 DOI: 10.1177/0003702817727728] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report on a label-free, noninvasive method for determination of spore inoculum quality of Penicillium chrysogenum prior to cultivation/germination. Raman microspectroscopy providing direct, molecule-specific information was used to extract information on the viability state of spores sampled directly from the spore inoculum. Based on the recorded Raman spectra, a supervised classification method was established for classification between living and dead spores and thus determining spore inoculum quality for optimized process control. A fast and simple sample preparation method consisting of one single dilution step was employed to eliminate interfering signals from the matrix and to achieve isolation of single spores on the sample carrier (CaF2). Aiming to avoid any influence of the killing procedure in the Raman spectrum of the spore, spores were considered naturally dead after more than one year of storage time. Fluorescence staining was used as reference method. A partial least squares discriminant analysis classifier was trained with Raman spectra of 258 living and dead spores (178 spectra for calibration, 80 spectra for validation). The classifier showed good performance when being applied to a 1 µL droplet taken from a 1:1 mixture of living and dead spores. Of 135 recorded spectra, 51% were assigned to living spores while 49% were identified as dead spores by the classifier. The results obtained in this work are a fundamental step towards developing an automated, label-free, and noninvasive screening method for assessing spore inoculum quality.
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Affiliation(s)
- Karin Wieland
- 1 Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Julia Kuligowski
- 1 Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
- 2 Neonatal Research Unit, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Daniela Ehgartner
- 3 Christian Doppler Laboratory on Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Georg Ramer
- 1 Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Cosima Koch
- 1 Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Johannes Ofner
- 1 Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
| | - Christoph Herwig
- 3 Christian Doppler Laboratory on Mechanistic and Physiological Methods for Improved Bioprocesses, Institute of Chemical Engineering, TU Wien, Vienna, Austria
| | - Bernhard Lendl
- 1 Institute of Chemical Technologies and Analytics, TU Wien, Vienna, Austria
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45
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Gan Q, Wang X, Wang Y, Xie Z, Tian Y, Lu Y. Culture-Free Detection of Crop Pathogens at the Single-Cell Level by Micro-Raman Spectroscopy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1700127. [PMID: 29201605 PMCID: PMC5700641 DOI: 10.1002/advs.201700127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/10/2017] [Indexed: 05/10/2023]
Abstract
The rapid and sensitive identification of invasive plant pathogens has important applications in biotechnology, plant quarantine, and food security. Current methods are far too time-consuming and need a pre-enrichment period ranging from hours to days. Here, a micro-Raman spectroscopy-based bioassay for culture-free pathogen quarantine inspection at the single cell level within 40 min is presented. The application of this approach can readily and specifically detect plant pathogens Burkholderia gladioli pv. alliicola and Erwinia chrysanthemi that are closely related pathogenically. Furthermore, the single-bacterium detection was able to discriminate them from a reference Raman spectral library including multiple quarantine-relevant pathogens with broad host ranges and an array of pathogenic variants. To show the usefulness of this assay, Burkholderia gladioli pv. alliicola and Erwinia chrysanthemi are detected at single-bacterium level in plant tissue lesions without pre-enrichment. The results are confirmed by the plate-counting method and a genetic molecular approach, which display comparable recognition ratios to the Raman spectroscopy-based bioassay. The results represent a critical step toward the use of micro-Raman spectroscopy in rapid and culture-free discrimination of quarantine relevant plant pathogens.
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Affiliation(s)
- Qinhua Gan
- State Key Laboratory of Marine Resource Utilization in South China SeaCollege of OceanologyHainan UniversityHaikouHainan Province570228China
- Inspection and Quarantine Technology CenterShandong Entry‐Exit Inspection and Quarantine BureauQingdaoShandong Province266002China
| | - Xuetao Wang
- Hisense CompanyQingdaoShandong Province266555China
| | - Yun Wang
- Shanghai Hesen Biotech Co LTDShanghai201802China
| | - Zhenyu Xie
- State Key Laboratory of Marine Resource Utilization in South China SeaCollege of OceanologyHainan UniversityHaikouHainan Province570228China
| | - Yang Tian
- Institute of Deep‐sea Science and EngineeringChinese Academy of SciencesSanya572000China
| | - Yandu Lu
- State Key Laboratory of Marine Resource Utilization in South China SeaCollege of OceanologyHainan UniversityHaikouHainan Province570228China
- Laboratory of Tropical Biological Resources of Ministry of EducationHainan UniversityHaikou570228China
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46
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Ayala OD, Wakeman CA, Pence IJ, O'Brien CM, Werkhaven JA, Skaar EP, Mahadevan-Jansen A. Characterization of bacteria causing acute otitis media using Raman microspectroscopy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2017; 9:1864-1871. [PMID: 34858522 PMCID: PMC8635270 DOI: 10.1039/c7ay00128b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Otitis media (OM) is a prevalent disease that is the most frequent cause of physician visits and prescription of antibiotics for children. Current methods to diagnose OM and differentiate between the two main types of OM, acute otitis media (AOM) and otitis media with effusion (OME), rely on interpreting symptoms that may overlap between them. Since AOM requires antibiotic treatment and OME does not, there is a clinical need to distinguish between AOM and OME to determine whether antibiotic treatment is necessary and guide future prescriptions. We used an optical spectroscopy technique, Raman spectroscopy (RS), to identify and characterize the biochemical features of the three main pathogens that cause AOM in vitro. A Renishaw inVia confocal Raman microscope at 785 nm was used to spectrally investigate the Raman signatures of Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae. Biochemical features or biomarkers important for classification of each bacterial species were identified and yielded a 97% accuracy of discrimination. To test the effectiveness of Raman-based bacterial classification in a clinical sample, human middle ear effusion (MEE) from patients affected by recurrent AOM was collected, cultured, and measured using RS. The probability of bacterial involvement from each of the three main bacteria that cause AOM was determined from the clinical MEE samples. These results suggest the potential of utilizing RS to aid in accurately diagnosing AOM and providing physicians with bacterial identification to guide treatment.
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Affiliation(s)
- O D Ayala
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - C A Wakeman
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - I J Pence
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - C M O'Brien
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - J A Werkhaven
- Department of Otolaryngology and Head and Neck Surgery, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - E P Skaar
- Department of Pathology, Microbiology, & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - A Mahadevan-Jansen
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
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47
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Polisetti S, Baig NF, Morales-Soto N, Shrout JD, Bohn PW. Spatial Mapping of Pyocyanin in Pseudomonas Aeruginosa Bacterial Communities Using Surface Enhanced Raman Scattering. APPLIED SPECTROSCOPY 2017; 71:215-223. [PMID: 27354400 PMCID: PMC5475280 DOI: 10.1177/0003702816654167] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Surface enhanced Raman spectroscopy (SERS) imaging was used in conjunction with principal component analysis (PCA) for the in situ spatiotemporal mapping of the virulence factor pyocyanin in communities of the pathogenic bacterium Pseudomonas aeruginosa. The combination of SERS imaging and PCA analysis provides a robust method for the characterization of heterogeneous biological systems while circumventing issues associated with interference from sample autofluorescence and low reproducibility of SERS signals. The production of pyocyanin is found to depend both on the growth carbon source and on the specific strain of P. aeruginosa studied. A cystic fibrosis lung isolate strain of P. aeruginosa synthesizes and secretes pyocyanin when grown with glucose and glutamate, while the laboratory strain exhibits detectable production of pyocyanin only when grown with glutamate as the source of carbon. Pyocyanin production in the laboratory strain grown with glucose was below the limit of detection of SERS. In addition, the combination of SERS imaging and PCA can elucidate subtle differences in the molecular composition of biofilms. PCA loading plots from the clinical isolate exhibit features corresponding to vibrational bands of carbohydrates, which represent the mucoid biofilm matrix specific to that isolate, features that are not seen in the PCA loading plots of the laboratory strain.
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Affiliation(s)
- Sneha Polisetti
- 1 Department of Chemical and Biomolecular Engineering, University of Notre Dame, USA
| | - Nameera F Baig
- 2 Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, USA
| | - Nydia Morales-Soto
- 3 Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, USA
- 4 Eck Institute for Global Health, University of Notre Dame, USA
| | - Joshua D Shrout
- 3 Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, USA
- 4 Eck Institute for Global Health, University of Notre Dame, USA
- 5 Department of Biological Sciences, University of Notre Dame, USA
| | - Paul W Bohn
- 1 Department of Chemical and Biomolecular Engineering, University of Notre Dame, USA
- 2 Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, USA
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48
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Samek O, Obruča S, Šiler M, Sedláček P, Benešová P, Kučera D, Márova I, Ježek J, Bernatová S, Zemánek P. Quantitative Raman Spectroscopy Analysis of Polyhydroxyalkanoates Produced by Cupriavidus necator H16. SENSORS 2016; 16:s16111808. [PMID: 27801828 PMCID: PMC5134467 DOI: 10.3390/s16111808] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 02/04/2023]
Abstract
We report herein on the application of Raman spectroscopy to the rapid quantitative analysis of polyhydroxyalkanoates (PHAs), biodegradable polyesters accumulated by various bacteria. This theme was exemplified for quantitative detection of the most common member of PHAs, poly(3-hydroxybutyrate) (PHB) in Cupriavidus necator H16. We have identified the relevant spectral region (800–1800 cm−1) incorporating the Raman emission lines exploited for the calibration of PHB (PHB line at 1736 cm−1) and for the selection of the two internal standards (DNA at 786 cm−1 and Amide I at 1662 cm−1). In order to obtain quantitative data for calibration of intracellular content of PHB in bacterial cells reference samples containing PHB amounts—determined by gas chromatography—from 12% to 90% (w/w) were used. Consequently, analytical results based on this calibration can be used for fast and reliable determination of intracellular PHB content during biotechnological production of PHB since the whole procedure—from bacteria sampling, centrifugation, and sample preparation to Raman analysis—can take about 12 min. In contrast, gas chromatography analysis takes approximately 8 h.
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Affiliation(s)
- Ota Samek
- Institute of Scientific Instruments of the CAS, Brno 61264, Czech Republic.
| | - Stanislav Obruča
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Brno 61200, Czech Republic.
| | - Martin Šiler
- Institute of Scientific Instruments of the CAS, Brno 61264, Czech Republic.
| | - Petr Sedláček
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Brno 61200, Czech Republic.
| | - Pavla Benešová
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Brno 61200, Czech Republic.
| | - Dan Kučera
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Brno 61200, Czech Republic.
| | - Ivana Márova
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Brno 61200, Czech Republic.
| | - Jan Ježek
- Institute of Scientific Instruments of the CAS, Brno 61264, Czech Republic.
| | - Silva Bernatová
- Institute of Scientific Instruments of the CAS, Brno 61264, Czech Republic.
| | - Pavel Zemánek
- Institute of Scientific Instruments of the CAS, Brno 61264, Czech Republic.
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49
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Zhao Y, Monroy GL, You S, Shelton RL, Nolan RM, Tu H, Chaney EJ, Boppart SA. Rapid diagnosis and differentiation of microbial pathogens in otitis media with a combined Raman spectroscopy and low-coherence interferometry probe: toward in vivo implementation. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:107005. [PMID: 27802456 PMCID: PMC5997004 DOI: 10.1117/1.jbo.21.10.107005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/07/2016] [Indexed: 05/03/2023]
Abstract
We investigate and demonstrate the feasibility of using a combined Raman scattering (RS) spectroscopy and low-coherence interferometry (LCI) probe to differentiate microbial pathogens and improve our diagnostic ability of ear infections [otitis media (OM)]. While the RS probe provides noninvasive molecular information to identify and differentiate infectious microorganisms, the LCI probe helps to identify depth-resolved structural information as well as to guide and monitor positioning of the Raman spectroscopy beam for relatively longer signal acquisition times. A series of phantom studies, including the use of human middle ear effusion samples, were performed to mimic the conditions of in vivo investigations. These were also conducted to validate the feasibility of using this combined RS/LCI probe for point-of-care diagnosis of the infectious pathogen(s) in OM patients. This work establishes important parameters for future in vivo investigations of fast and accurate determination and diagnosis of infectious microorganisms in OM patients, potentially improving the efficacy and outcome of OM treatments, and importantly reducing the misuse of antibiotics in the presence of viral infections.
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Affiliation(s)
- Youbo Zhao
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Guillermo L. Monroy
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Bioengineering, 1304 West Springfield Avenue, Urbana, Illinois 61801, United States
| | - Sixian You
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Bioengineering, 1304 West Springfield Avenue, Urbana, Illinois 61801, United States
| | - Ryan L. Shelton
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ryan M. Nolan
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Haohua Tu
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Eric J. Chaney
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
| | - Stephen A. Boppart
- Beckman Institute for Advanced Science and Technology, 405 North Mathews Avenue, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Bioengineering, 1304 West Springfield Avenue, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Electrical and Computer Engineering, 306 North Wright Street, Urbana, Illinois 61801, United States
- University of Illinois at Urbana–Champaign, Department of Internal Medicine, 506 South Mathews Avenue, Urbana, Illinois 61801, United States
- Address all correspondence to: Stephen A. Boppart, E-mail:
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50
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Dekter HE, Orelio CC, Morsink MC, Tektas S, Vis B, Te Witt R, van Leeuwen WB. Antimicrobial susceptibility testing of Gram-positive and -negative bacterial isolates directly from spiked blood culture media with Raman spectroscopy. Eur J Clin Microbiol Infect Dis 2016; 36:81-89. [PMID: 27638006 DOI: 10.1007/s10096-016-2773-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/30/2016] [Indexed: 11/24/2022]
Abstract
Patients suffering from bacterial bloodstream infections have an increased risk of developing systematic inflammatory response syndrome (SIRS), which can result in rapid deterioration of the patients' health. Diagnostic methods for bacterial identification and antimicrobial susceptibility tests are time-consuming. The aim of this study was to investigate whether Raman spectroscopy would be able to rapidly provide an antimicrobial susceptibility profile from bacteria isolated directly from positive blood cultures. First, bacterial strains (n = 133) were inoculated in tryptic soy broth and incubated in the presence or absence of antibiotics for 5 h. Antimicrobial susceptibility profiles were analyzed by Raman spectroscopy. Subsequently, a selection of strains was isolated from blood cultures and analyzed similarly. VITEK®2 technology and broth dilution were used as the reference methods. Raman spectra from 67 antibiotic-susceptible strains showed discriminatory spectra in the absence or at low concentrations of antibiotics as compared to high antibiotic concentrations. For 66 antibiotic-resistant strains, no antimicrobial effect was observed on the bacterial Raman spectra. Full concordance with VITEK®2 data and broth dilution was obtained for the antibiotic-susceptible strains, 68 % and 98 %, respectively, for the resistant strains. Discriminative antimicrobial susceptibility testing (AST) profiles were obtained for all bacterial strains isolated from blood cultures, resulting in full concordance with the VITEK®2 data. It can be concluded that Raman spectroscopy is able to detect the antimicrobial susceptibility of bacterial species isolated from a positive blood culture bottle within 5 h. Although Raman spectroscopy is cheap and rapid, further optimization is required, to fulfill a great promise for future AST profiling technology development.
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Affiliation(s)
- H E Dekter
- Research Department of Innovative Molecular Diagnostics, University of Applied Sciences Leiden, J. H. Oortweg 21, 2333 CH, Leiden, The Netherlands
| | - C C Orelio
- Research Department of Innovative Molecular Diagnostics, University of Applied Sciences Leiden, J. H. Oortweg 21, 2333 CH, Leiden, The Netherlands
| | - M C Morsink
- Research Department of Innovative Molecular Diagnostics, University of Applied Sciences Leiden, J. H. Oortweg 21, 2333 CH, Leiden, The Netherlands
| | - S Tektas
- Research Department of Innovative Molecular Diagnostics, University of Applied Sciences Leiden, J. H. Oortweg 21, 2333 CH, Leiden, The Netherlands
| | - B Vis
- Research Department of Innovative Molecular Diagnostics, University of Applied Sciences Leiden, J. H. Oortweg 21, 2333 CH, Leiden, The Netherlands
| | - R Te Witt
- Netherlands Molecular Diagnostic Laboratory B.V. (NMDL), Visseringlaan 25, 2288 ER, Rijswijk, The Netherlands
| | - W B van Leeuwen
- Research Department of Innovative Molecular Diagnostics, University of Applied Sciences Leiden, J. H. Oortweg 21, 2333 CH, Leiden, The Netherlands.
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