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Dunnington EL, Wong BS, Fu D. Innovative Approaches for Drug Discovery: Quantifying Drug Distribution and Response with Raman Imaging. Anal Chem 2024; 96:7926-7944. [PMID: 38625100 PMCID: PMC11108735 DOI: 10.1021/acs.analchem.4c01413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Affiliation(s)
| | | | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
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2
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Patil N, Howe O, Cahill P, Byrne HJ. Monitoring and modelling the dynamics of the cellular glycolysis pathway: A review and future perspectives. Mol Metab 2022; 66:101635. [PMID: 36379354 PMCID: PMC9703637 DOI: 10.1016/j.molmet.2022.101635] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The dynamics of the cellular glycolysis pathway underpin cellular function and dysfunction, and therefore ultimately health, disease, diagnostic and therapeutic strategies. Evolving our understanding of this fundamental process and its dynamics remains critical. SCOPE OF REVIEW This paper reviews the medical relevance of glycolytic pathway in depth and explores the current state of the art for monitoring and modelling the dynamics of the process. The future perspectives of label free, vibrational microspectroscopic techniques to overcome the limitations of the current approaches are considered. MAJOR CONCLUSIONS Vibrational microspectroscopic techniques can potentially operate in the niche area of limitations of other omics technologies for non-destructive, real-time, in vivo label-free monitoring of glycolysis dynamics at a cellular and subcellular level.
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Affiliation(s)
- Nitin Patil
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland; School of Physics and Optometric & Clinical Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland.
| | - Orla Howe
- School of Biological and Health Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland
| | - Paul Cahill
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Hugh J Byrne
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland
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3
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Clark MG, Gonzalez GA, Zhang C. Pulse-Picking Multimodal Nonlinear Optical Microscopy. Anal Chem 2022; 94:15405-15414. [DOI: 10.1021/acs.analchem.2c03284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew G. Clark
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana47907, United States
| | - Gil A. Gonzalez
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana47907, United States
| | - Chi Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana47907, United States
- Purdue Center for Cancer Research, 201 S University Street, West Lafayette, Indiana47907, United States
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, 207 S Martin Jischke Drive, West Lafayette, Indiana47907, United States
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4
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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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5
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Sun B, Wang Z, Lin J, Chen C, Zheng G, Yue S, Wang H, Kang X, Chen X, Hong W, Wang P. Automatic quantitative analysis of metabolism inactivation concentration in single bacterium using stimulated Raman scattering microscopy with deep learning image segmentation. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2022. [DOI: 10.1016/j.medntd.2022.100114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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6
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Sun B, Kang X, Yue S, Lan L, Li R, Chen C, Zhang W, He S, Zhang C, Fan Y, Wang P, Zheng G, Hong W. A rapid procedure for bacterial identification and antimicrobial susceptibility testing directly from positive blood cultures. Analyst 2021; 147:147-154. [PMID: 34860216 DOI: 10.1039/d1an01210j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is an urgent need to develop a rapid procedure that can rapidly identify and obtain antimicrobial susceptibility testing (AST) results directly from positive blood cultures. Here, we report a semi-automatic bacterial diagnosis procedure, which includes (1) a bacterial concentration process to isolate bacteria from a positive blood culture bottle (PBCB), (2) an identification process using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), and (3) a rapid AST process based on stimulated Raman scattering imaging of deuterium oxide (D2O) incorporation in bacteria. A total of 105 samples were tested for bacterial identification, and a bacterial identification accuracy of 92.3% was achieved. AST takes about 2.5 h after identification. This semi-automatic procedure only takes 3.5 h, which is demonstrated to be the fastest process to obtain identification and AST results starting from PBCBs.
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Affiliation(s)
- Bo Sun
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China. .,Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Xixiong Kang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Shuhua Yue
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Lu Lan
- Vibronix Inc., West Lafayette, IN, USA
| | - Rui Li
- Vibronix Inc., West Lafayette, IN, USA
| | - Chen Chen
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Weifeng Zhang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Shipei He
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Chenxi Zhang
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Yubo Fan
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China. .,School of Medical Science and Engineering, Beihang University, Beijing, China
| | - Pu Wang
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
| | - Guanghui Zheng
- Laboratory Diagnosis Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Weili Hong
- Institute of Medical Photonics, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, China.
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7
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Zhang C, Aldana-Mendoza JA. Coherent Raman scattering microscopy for chemical imaging of biological systems. JPHYS PHOTONICS 2021. [DOI: 10.1088/2515-7647/abfd09] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Abstract
Coherent Raman scattering (CRS) processes, including both the coherent anti-Stokes Raman scattering and stimulated Raman scattering, have been utilized in state-of-the-art microscopy platforms for chemical imaging of biological samples. The key advantage of CRS microscopy over fluorescence microscopy is label-free, which is an attractive characteristic for modern biological and medical sciences. Besides, CRS has other advantages such as higher selectivity to metabolites, no photobleaching, and narrow peak width. These features have brought fast-growing attention to CRS microscopy in biological research. In this review article, we will first briefly introduce the history of CRS microscopy, and then explain the theoretical background of the CRS processes in detail using the classical approach. Next, we will cover major instrumentation techniques of CRS microscopy. Finally, we will enumerate examples of recent applications of CRS imaging in biological and medical sciences.
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8
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Label-free metabolic imaging by mid-infrared optoacoustic microscopy in living cells. Nat Biotechnol 2019; 38:293-296. [PMID: 31873214 DOI: 10.1038/s41587-019-0359-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/12/2019] [Indexed: 12/20/2022]
Abstract
We develop mid-infrared optoacoustic microscopy (MiROM) for label-free, bond-selective, live-cell metabolic imaging, enabling spatiotemporal monitoring of carbohydrates, lipids and proteins in cells and tissues. Using acoustic detection of optical absorption, MiROM converts mid-infrared sensing into a positive-contrast imaging modality with negligible photodamage and high sensitivity. We use MiROM to observe changes in intrinsic carbohydrate distribution from a diffusive spatial pattern to tight co-localization with lipid droplets during adipogenesis.
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Li X, Zhang D, Bai Y, Wang W, Liang J, Cheng JX. Fingerprinting a Living Cell by Raman Integrated Mid-Infrared Photothermal Microscopy. Anal Chem 2019; 91:10750-10756. [DOI: 10.1021/acs.analchem.9b02286] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Xiaojie Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Yeran Bai
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weibiao Wang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, China
| | - Jingqiu Liang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, Jilin 130033, China
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Hong W, Karanja CW, Abutaleb NS, Younis W, Zhang X, Seleem MN, Cheng JX. Antibiotic Susceptibility Determination within One Cell Cycle at Single-Bacterium Level by Stimulated Raman Metabolic Imaging. Anal Chem 2018; 90:3737-3743. [PMID: 29461044 DOI: 10.1021/acs.analchem.7b03382] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The widespread use of antibiotics has significantly increased the number of resistant bacteria, which has also increased the urgency of rapid bacterial detection and profiling their antibiotic response. Current clinical methods for antibiotic susceptibility testing (AST) rely on culture and require at least 16 to 24 h to conduct. Therefore, there is an urgent need for a rapid method that can test the susceptibility of bacteria in a culture-free manner. Here we demonstrate a rapid AST method by monitoring the glucose metabolic activity of live bacteria at the single-cell level with hyperspectral stimulated Raman scattering (SRS) imaging. Using vancomycin-susceptible and -resistant enterococci E. faecalis as models, we demonstrate that the metabolic uptake of deuterated glucose in a single living bacterium can be quantitatively monitored via hyperspectral SRS imaging. Remarkably, the metabolic activity of susceptible bacteria responds differently to antibiotics from the resistant strain within only 0.5 h from the addition of antibiotics. Therefore, bacterial susceptibility and the minimum inhibitory concentration (MIC) of antibiotics can be determined within one cell cycle. Our metabolic imaging method is applicable to other bacteria species including E. coli, K. Pneumoniae, and S. aureus as well as different antibiotics, regardless of their mechanisms of inhibiting or killing bacteria.
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Affiliation(s)
| | | | | | | | | | | | - Ji-Xin Cheng
- Department of Biomedical Engineering and Department of Electrical and Chemical Engineering , Boston University , Boston , Massachusetts 02215 , United States
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11
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Adamiak J, Bonifay V, Otlewska A, Sunner JA, Beech IB, Stryszewska T, Kańka S, Oracz J, Żyżelewicz D, Gutarowska B. Untargeted Metabolomics Approach in Halophiles: Understanding the Biodeterioration Process of Building Materials. Front Microbiol 2017; 8:2448. [PMID: 29321766 PMCID: PMC5732225 DOI: 10.3389/fmicb.2017.02448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/24/2017] [Indexed: 11/13/2022] Open
Abstract
The aim of the study was to explore the halophile metabolome in building materials using untargeted metabolomics which allows for broad metabolome coverage. For this reason, we used high-performance liquid chromatography interfaced to high-resolution mass spectrometry (HPLC/HRMS). As an alternative to standard microscopy techniques, we introduced pioneering Coherent Anti-stokes Raman Scattering Microscopy (CARS) to non-invasively visualize microbial cells. Brick samples saturated with salt solution (KCl, NaCl (two salinity levels), MgSO4, Mg(NO3)2), were inoculated with the mixture of preselected halophilic microorganisms, i.e., bacteria: Halobacillus styriensis, Halobacillus naozhouensis, Halobacillus hunanensis, Staphylococcus succinus, Marinococcus halophilus, Virgibacillus halodenitryficans, and yeast: Sterigmatomyces halophilus and stored at 28°C and 80% relative humidity for a year. Metabolites were extracted directly from the brick samples and measured via HPLC/HRMS in both positive and negative ion modes. Overall, untargeted metabolomics allowed for discovering the interactions of halophilic microorganisms with buildings materials which together with CARS microscopy enabled us to elucidate the biodeterioration process caused by halophiles. We observed that halophile metabolome was differently affected by different salt solutions. Furthermore, we found indications for haloadaptive strategies and degradation of brick samples due to microbial pigment production as a salt stress response. Finally, we detected changes in lipid content related to changes in the structure of phospholipid bilayers and membrane fluidity.
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Affiliation(s)
- Justyna Adamiak
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Vincent Bonifay
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Anna Otlewska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Jan A. Sunner
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Iwona B. Beech
- Center of Biofilm Engineering, Department of Chemical and Biochemical Engineering, Montana State University, Bozeman, MT, United States
| | - Teresa Stryszewska
- Institute of Building Materials and Structures, Faculty of Civil Engineering, Cracow University of Technology, Cracow, Poland
| | - Stanisław Kańka
- Institute of Building Materials and Structures, Faculty of Civil Engineering, Cracow University of Technology, Cracow, Poland
| | - Joanna Oracz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Dorota Żyżelewicz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Beata Gutarowska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
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Harrison JP, Berry D. Vibrational Spectroscopy for Imaging Single Microbial Cells in Complex Biological Samples. Front Microbiol 2017; 8:675. [PMID: 28450860 PMCID: PMC5390015 DOI: 10.3389/fmicb.2017.00675] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/31/2017] [Indexed: 01/08/2023] Open
Abstract
Vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of the samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of single-cell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.
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Affiliation(s)
- Jesse P Harrison
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry Meets Microbiology", University of ViennaVienna, Austria
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network "Chemistry Meets Microbiology", University of ViennaVienna, Austria
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Raman microspectroscopy, surface-enhanced Raman scattering microspectroscopy, and stable-isotope Raman microspectroscopy for biofilm characterization. Anal Bioanal Chem 2017; 409:4353-4375. [DOI: 10.1007/s00216-017-0303-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/31/2017] [Accepted: 03/08/2017] [Indexed: 12/27/2022]
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Abstract
Bacterial sensing is important for understanding the numerous roles bacteria play in nature and in technology, understanding and managing bacterial populations, detecting pathogenic bacterial infections, and preventing the outbreak of illness. Current analytical challenges in bacterial sensing center on the dilemma of rapidly acquiring quantitative information about bacteria with high detection efficiency, sensitivity, and specificity, while operating within a reasonable budget and optimizing the use of ancillary tools, such as multivariate statistics. This review starts from a general description of bacterial sensing methods and challenges, and then focuses on bacterial characterization using optical methods including Raman spectroscopy and imaging, infrared spectroscopy, fluorescence spectroscopy and imaging, and plasmonics, including both extended and localized surface plasmon resonance spectroscopy. The advantages and drawbacks of each method in relation to the others are discussed, as are their applications. A particularly promising direction in bacterial sensing lies in combining multiple approaches to achieve multiplex analysis, and examples where this has been achieved are highlighted.
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Affiliation(s)
- Jiayun Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA
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